Determine fixture path using the current working directory (#422)

Signed-off-by: guoguangwu <guoguangwug@gmail.com>
Co-authored-by: tjex <tjex@tjex.net>

.gitattributes

@@ -1,2 +0,0 @@
-*.db filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text

.github/DISCUSSION_TEMPLATE/help.yml

@@ -0,0 +1,19 @@
+title: "[Help] "
+body:
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Verify
+      options:
+        - label: I searched the existing discussions for help
+          required: true
+  - type: textarea
+    id: help
+    attributes:
+      label: How can we help you?
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        :warning: Unfortunately, my time is limited and I can't offer reliable user support. I might answer if you catch me on a slow day, or hopefully someone else will.

.github/DISCUSSION_TEMPLATE/ideas.yml

@@ -0,0 +1,14 @@
+body:
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Verify
+      options:
+        - label: I searched the existing discussions for similar ideas
+          required: true
+  - type: textarea
+    id: help
+    attributes:
+      label: Share your idea or feature request
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,65 @@
+name: Bug report
+description: File a bug report to help improve zk.
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for filing a bug report!
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Check if applicable
+      description: |
+        :warning: My time is limited and if I don't plan on fixing the reported bug myself, I might close this issue. No hard feelings.
+        :heart: But if you would like to contribute a fix yourself, **I'll be happy to guide you through the codebase and review a pull request**.
+      options:
+        - label: I have searched the existing issues (**required**)
+          required: true
+        - label: I'm willing to help fix the problem and contribute a pull request
+  - type: textarea
+    id: bug-description
+    attributes:
+      label: Describe the bug
+      description: Also tell me, what did you expect to happen?
+      placeholder: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: bug-steps
+    attributes:
+      label: How to reproduce?
+      description: |
+        Step by step explanation to reproduce the issue.
+
+        If you can, drag and drop:
+        - a zipped sample notebook
+        - screenshots or a screencast showing the issue
+      placeholder: |
+        1. Add a note with the content "..."
+        2. Run `zk edit --interactive`
+        3. See error
+        ...
+    validations:
+      required: true
+  - type: textarea
+    id: vim-config
+    attributes:
+      label: zk configuration
+      description: |
+        Paste the minimal `zk` configuration file (`.zk/config.toml`) reproducing the issue.
+      render: toml
+    validations:
+      required: true
+  - type: textarea
+    id: bug-environment
+    attributes:
+      label: Environment
+      description: |
+        Run the following shell commands and paste the result here:
+        ```
+        zk --version && echo "system: `uname -srmo`"
+        ```
+      placeholder: |
+        zk 0.13.0
+        system: Darwin 22.5.0 arm64
+      render: bash

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,10 @@
+name: Feature request
+description: Suggest an idea for this project.
+body:
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: If you have an idea, open a discussion
+      options:
+        - label: I will [create a new discussion](https://github.com/zk-org/zk/discussions/new?category=ideas) instead of an issue.
+

.github/ISSUE_TEMPLATE/support.yml

@@ -0,0 +1,13 @@
+name: User support
+description: You need help?
+body:
+  - type: markdown
+    attributes:
+      value: |
+        :warning: Unfortunately, my time is limited and I can't offer reliable user support. I might answer if you catch me on a slow day, or hopefully someone else will.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: If you need help, open a discussion
+      options:
+        - label: I will [create a new discussion](https://github.com/zk-org/zk/discussions/new?category=help) instead of an issue.

.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+
+  # Maintain dependencies for gomod
+  - package-ecosystem: "gomod"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    # Disable version updates for gomod dependencies
+    open-pull-requests-limit: 0

.github/workflows/build.yml

@@ -0,0 +1,37 @@
+name: Build
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        lfs: 'true'
+
+    - name: Set up Go
+      uses: actions/setup-go@v5
+      with:
+        go-version-file: 'go.mod'
+
+    - name: Install dependencies
+      run: |
+        go install github.com/mickael-menu/tesh@latest
+
+    - name: Build
+      run: make build
+
+    - name: Test
+      run: make test
+
+    - name: Tesh
+      # See https://github.com/actions/runner/issues/241#issuecomment-924327172
+      shell: script --return --quiet --command "bash {0}"
+      run: make tesh
+

.github/workflows/codeql.yml

@@ -0,0 +1,40 @@
+name: "CodeQL code scanning"
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main ]
+  schedule:
+    # Wed 23:33 UTC
+    - cron: '33 23 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'go' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3

.github/workflows/gh-pages.yml

@@ -0,0 +1,43 @@
+name: Deploy to GitHub Pages
+
+on:
+  release:
+    types:
+      - "published"
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Fix anchor tag in README
+        run: ex -s -c '%s/docs\/getting-started\.md/docs\/getting-started/|x' README.md
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./
+          destination: ./_site
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/release.yml

@@ -0,0 +1,19 @@
+name: Release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  homebrew:
+    runs-on: macos-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Update Homebrew formula
+        uses: dawidd6/action-homebrew-bump-formula@v3
+        with:
+          token: ${{secrets.HOMEBREW_GITHUB_TOKEN}}
+          formula: zk

.github/workflows/triage.yml

@@ -0,0 +1,31 @@
+name: Triage
+
+on:
+  push:
+    paths:
+      - .github/workflows/triage.yml
+  schedule:
+    # Once every day at midnight UTC
+    - cron: "0 0 * * *"
+      
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9
+        with:
+          days-before-stale: 30
+
+          days-before-issue-close: 5
+          stale-issue-label: 'stale'
+          stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs in the next 5 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 5 days with no activity.'
+          exempt-issue-labels: 'help wanted,feature request,enhancement,bug'
+
+          days-before-pr-close: -1
+          stale-pr-label: 'stale'
+          stale-pr-message: 'This pull request has been automatically marked as stale because it has not had recent activity.'

.gitignore

@@ -11,7 +11,14 @@
 # Output of the go coverage tool, specifically when used with LiteIDE
 *.out
 
+# Delve debug files
+*__debug_bin*
+
 # Dependency directories (remove the comment below to include it)
 # vendor/
 
-.zk
+# IDEs/Editors
+.vscode/
+
+notebook.db
+zk

CHANGELOG.md

@@ -2,7 +2,275 @@
 
 All notable changes to this project will be documented in this file.
 
-<!--## Unreleased-->
+## Unreleased
+
+## 0.14.1
+
+### Fixed
+
+* Fixed parsing large notes @khimaros in https://github.com/zk-org/zk/pull/339
+* fix day range parsing (zk-org/zk#382) by @tjex in https://github.com/zk-org/zk/pull/384
+* accept tripple dash file URIs as valid links by @tjex in https://github.com/zk-org/zk/pull/391
+* fix(lsp): fix trigger completion of zk LSP by @Rahlir in https://github.com/zk-org/zk/pull/397
+* fix(lsp): ignore diagnostic check within code blocks by @Rahlir in https://github.com/zk-org/zk/pull/399
+* allow notebook as hidden dir by @tjex in https://github.com/zk-org/zk/pull/402
+
+## 0.14.0
+
+### Added
+
+* New [`tool.shell`](docs/tool-shell.md) configuration key to set a custom shell (contributed by [@lsvmello](https://github.com/zk-org/zk/pull/302)).
+* New [`notebook.dir`](docs/config-notebook.md) configuration key to set the default notebook (contributed by [@lsvmello](https://github.com/zk-org/zk/pull/304)).
+
+### Changed
+
+* The `note.ignore` configuration property was renamed to `note.exclude`, to be more consistent with the CLI flags.
+
+### Fixed
+
+* Fixed LSP positions using UTF-16 offsets (contributed by [@wrvsrx](https://github.com/zk-org/zk/pull/317)).
+
+## 0.13.0
+
+### Added
+
+* LSP:
+    * `zk.new` now returns the created note's content in its output (`content`), and has two new options:
+        * `dryRun` will prevent `zk.new` from creating the note on the file system.
+        * `insertContentAtLocation` can be used to insert the created note's content into an arbitrary location.
+    * A new `zk.link` command to insert a link to a given note (contributed by [@psanker](https://github.com/zk-org/zk/pull/284)).
+
+## 0.12.0
+
+### Added
+
+* LSP: Support for external URLs with `documentLink`.
+* New `{{date}}` template helper to obtain a date object from natural language (contributed by [@zalegrala](https://github.com/zk-org/zk/pull/262)).
+    ```
+    Get a relative date using natural language:
+    {{date "next week"}}
+
+    Format a date returned by `get-date`:
+    {{format-date (date "monday") "timestamp"}}
+    ```
+* `zk list` now support multiple `--match`/`-m` flags, which allows to search for several tokens appearing in any order in the notes (contributed by [@rktjmp](https://github.com/zk-org/zk/pull/268)).
+
+### Changed
+
+* **Breaking change:** The `{{date}}` template helper was renamed to `{{format-date}}`. You might need to update your configuration and templates.
+
+### Fixed
+
+* [#243](https://github.com/zk-org/zk/issues/243) LSP: Fixed finding backlink references for notes in a folder.
+* [#254](https://github.com/zk-org/zk/issues/254) Fixed SQL error when pairing `--link-to` and `--linked-by`.
+
+
+## 0.11.1
+
+### Changed
+
+* `zk new` now requires the `--interactive`/`-i` flag to read the note body from a pipe or standard input. [See rational](https://github.com/zk-org/zk/pull/242#issuecomment-1182602001).
+
+### Fixed
+
+* [#244](https://github.com/zk-org/zk/issues/244) Fixed `zk new` waiting for `Ctrl-D` to proceed (contributed by [@pkazmier](https://github.com/zk-org/zk/pull/242)).
+
+
+## 0.11.0
+
+### Added
+
+* Use regular expressions when searching for notes with `--match`.
+    ```sh
+    # Find notes containing emails.
+    $ zk list --match-strategy re --match ".+@.+"
+    $ zk list -Mr -m ".+@.+"
+    ```
+
+### Changed
+
+* The flags `--exact-match`/`-e` are deprecated in favor of `--match-strategy exact`/`-Me`.
+
+### Deprecated
+
+* The LSP server does not support resolving a wiki link to a note title anymore.
+    * For example, `[[Planet]]` can match a note with filename `i4w0 Planet.md` but not `i4w0.md` with a Markdown title `Planet` anymore.
+    * This "smart" fallback resolution based on note titles was too fragile and not supported by the `zk` CLI.
+
+### Fixed
+
+* [#233](https://github.com/zk-org/zk/issues/233) Hide index progress in non-interactive shells.
+* [#235](https://github.com/zk-org/zk/issues/235) Fix LSP link recognition with unicode (contributed by [@zkbpkp](https://github.com/zk-org/zk/issues/235)).
+* [#236](https://github.com/zk-org/zk/issues/236) Fix updating links after creating a new note.
+* [#239](https://github.com/zk-org/zk/discussions/239) Support standard input via shell redirection with `zk new`.
+
+
+## 0.10.1
+
+### Changed
+
+* Removed the dependency on `libicu`.
+
+### Fixed
+
+* Indexed links are now automatically updated when adding a new note, if it is a better match than the previous link target.
+
+
+## 0.10.0
+
+### Added
+
+* New `--date` flag for `zk new` to set the current date manually.
+* New `--id` flag for `zk new` to skip ID generation and use a provided value (contributed by [@skbolton](https://github.com/zk-org/zk/pull/183)).
+* [#144](https://github.com/zk-org/zk/issues/144) LSP auto-completion of YAML frontmatter tags.
+* [zk-nvim#26](https://github.com/zk-org/zk-nvim/issues/26) The LSP server doesn't use `additionalTextEdits` anymore to remove the trigger characters when completing links.
+    * You can customize the default behavior with the [`use-additional-text-edits` configuration key](docs/config-lsp.md).
+* [#163](https://github.com/zk-org/zk/issues/163) Use the `ZK_SHELL` environment variable to override the shell for `zk` only.
+* [#173](https://github.com/zk-org/zk/issues/173) Support for double star globbing in `note.ignore` config option.
+* [#137](https://github.com/zk-org/zk/issues/137) Customize the `fzf` options used by `zk`'s interactive modes with the [`fzf-options`](docs/tool-fzf.md) config option (contributed by [@Nelyah](https://github.com/zk-org/zk/pull/154)).
+
+* [#168](https://github.com/zk-org/zk/discussions/168) Customize the `fzf` key binding to create new notes with the [`fzf-bind-new`](docs/tool-fzf.md) config option.
+
+### Changed
+
+* The default `fzf` key binding to create a new note with `zk edit --interactive` was changed to `Ctrl-E`, to avoid conflict with the default `Ctrl-N` binding.
+
+### Fixed
+
+* [#126](https://github.com/zk-org/zk/issues/126) Embedded image links shown as not found.
+* [#152](https://github.com/zk-org/zk/issues/152) Incorrect timezone for natural dates.
+* [#170](https://github.com/zk-org/zk/issues/170) Broken wiki links in subdirectories.
+* [#185](https://github.com/zk-org/zk/issues/185) Don't parse a Markdown table header as a colon tag.
+
+
+## 0.9.0
+
+### Added
+
+* New LSP commands:
+    * [`zk.list`](docs/editors-integration.md#zklist) to search for notes.
+    * [`zk.tag.list`](docs/editors-integration.md#zktaglist) to retrieve the list of tags.
+* `--debug` mode which prints a stacktrace on `SIGINT`.
+
+### Fixed
+
+* [#111](https://github.com/zk-org/zk/issues/111) Filenames take precedence over folders when matching a sub-path with wiki links.
+* [#118](https://github.com/zk-org/zk/issues/118) Fix infinite loop when parsing a single-character hashtag.
+* [#121](https://github.com/zk-org/zk/issues/121) Take into account the `--no-input` flag with `zk init`.
+* [#120](https://github.com/zk-org/zk/discussions/120) Support RFC 3339 dates with the time flags (e.g. `--created-before`).
+
+
+## 0.8.0
+
+### Added
+
+* New `zk graph --format json` command which produces a JSON graph of the notes matching the given criteria.
+* New template variables `filename` and `filename-stem` when formatting notes (e.g. with `zk list --format`) and for the [`fzf-line`](docs/tool-fzf.md) config key.
+* Customize how LSP completion items appear in your editor when auto-completing links with the [`[lsp.completion]` configuration section](docs/config-lsp.md).
+    ```toml
+    [lsp.completion]
+    # Show the note title in the completion pop-up, or fallback on its path if empty.
+    note-label = "{{title-or-path}}"
+    # Filter out the completion pop-up using the note title or its path.
+    note-filter-text = "{{title}} {{path}}"
+    # Show the note filename without extension as detail.
+    note-detail = "{{filename-stem}}"
+    ```
+* New `--dry-run` flag for `zk new` which prints out the path and content of the generated note instead of saving it to the file system.
+* New `--verbose` flag for `zk index` which prints detailed information about the indexing process.
+* You can now filter through the [YAML frontmatter](docs/note-frontmatter.md) with `zk list --interactive`.
+
+### Fixed
+
+* [#89](https://github.com/zk-org/zk/issues/89) Calling `zk index` from outside the notebook (contributed by [@adamreese](https://github.com/zk-org/zk/pull/90)).
+* [#98](https://github.com/zk-org/zk/issues/98) Index wiki links using partial paths for `--linked-by` and `--link-to`.
+* [#98](https://github.com/zk-org/zk/issues/98) Ignore spaces around the pipe in wiki links for LSP diagnostics.
+
+
+## 0.7.0
+
+### Added
+
+* List the tags found in your notebook with `zk tag list`.
+    * Many options are available to customize the output, including JSON serialization. See `zk tag list --help`.
+* Support for LSP references to browse the backlinks of the current note, if the caret is not over a link.
+* New template variables are available when [generating custom Markdown links with `link-format`](docs/note-format.md).
+    * `filename`, `path`, `abs-path` and `rel-path` for many path flavors.
+    * `metadata` to use information (e.g. `id`) from the YAML frontmatter.
+* The LSP server is now matching wiki links to any part of a note's path or its title.
+    * Given the note `book/z5mj Information Graphics.md` with the title "Book Review of Information Graphics", the following wiki links would work from a note located under `journal/2020-09-25.md`:
+        ```markdown
+        [[../book/z5mj]]
+        [[book/z5mj]]
+        [[z5mj]]
+        [[book review information]]
+        [[Information Graphics]]
+        ```
+* Use the `{{abs-path}}` template variable when [formatting notes](docs/template-format.md) to print the absolute path to the note (contributed by [@pstuifzand](https://github.com/zk-org/zk/pull/60)).
+* A new `{{substring s index length}}` template helper extracts a portion of a given string, e.g.:
+    * `{{substring 'A full quote' 2 4}}` outputs `full`
+    * `{{substring 'A full quote' -5 5}` outputs `quote`
+
+### Fixed
+
+* UTF-8 handling in the LSP server.
+* [#78](https://github.com/zk-org/zk/issues/78) Do not exclude notes containing broken links from the index.
+* Allow setting the `--working-dir` and `--notebook-dir` flags before the `zk` subcommand when using aliases, e.g. `zk -W ~/notes my-alias`.
+* [#86](https://github.com/zk-org/zk/issues/86) Index encoded Markdown links.
+
+
+## 0.6.0
+
+### Added
+
+* Use JSON formats with `zk list` for easy post-processing:
+    * `--format json` prints a plain JSON array.
+    * `--format jsonl` prints one JSON note object per line, according to [JSON Lines](https://jsonlines.org/).
+* The new `{{json}}` template helper serializes any template context variable into a valid JSON value, e.g.:
+    * `{{json title}}` prints with quotes `"An interesting note"`
+    * `{{json .}}` serializes the full template context as a JSON object.
+* Use `--header` and `--footer` options with `zk list` to print arbitrary text at the start or end of the list.
+* Support for LSP references to browse the backlinks of the link under the caret (contributed by [@pstuifzand](https://github.com/zk-org/zk/pull/58)).
+* New [`note.ignore`](docs/config-note.md) configuration option to ignore files matching the given path globs when indexing notes.
+    ```yaml
+    [note]
+    ignore = [
+        "log-*.md"
+        "drafts/*"
+    ]
+    ```
+
+### Fixed
+
+* [#16](https://github.com/zk-org/zk/issues/16) Links with section anchors, e.g. `[[filename#section]]`.
+* Unicode support in wiki links. If you use accents or ideograms, please run `zk index --force` after upgrading to fix your index.
+
+
+## 0.5.0
+
+### Added
+
+* [Editor integration through LSP](https://github.com/zk-org/zk/issues/22):
+    * New code actions to create a note using the current selection as title.
+    * Custom commands to [run `new` and `index` from your editor](docs/editors-integration.md#custom-commands).
+    * Diagnostics to [report dead links or wiki link titles](docs/config-lsp.md).
+    * Auto-complete only the path of a Markdown link by typing `[custom title]((`.
+* Customize the format of `fzf`'s lines [with your own template](docs/tool-fzf.md).
+    ```toml
+    [tool]
+    fzf-line = "{{style 'green' path}}{{#each tags}} #{{this}}{{/each}} {{style 'black' body}}"
+    ```
+
+### Changed
+
+* Automatically index the notebook when saving a note with an LSP-enabled editor.
+    * This ensures that tags and notes auto-completion lists are up-to-date.
+
+### Fixed
+
+* Creating a new note from `fzf` in a directory containing spaces.
+* Fix completion with Neovim's built-in LSP client (contributed by [@cormacrelf](https://github.com/zk-org/zk/pull/39)).
+
 
 ## 0.4.0
 
@@ -10,18 +278,18 @@ All notable changes to this project will be documented in this file.
 
 * Interactive wizard for the `zk init` command.
 * An experimental Language Server for LSP-compatible editors:
-    * Auto-complete Markdown links with `[[` (setup wiki-links in the [note formats configuration](docs/note-format.md))
+    * Auto-complete Markdown links with `[[` (setup wiki links in the [note formats configuration](docs/note-format.md))
     * Auto-complete [hashtags and colon-separated tags](docs/tags.md).
     * Preview the content of a note when hovering a link.
     * Navigate in your notes by following internal links.
-    * [And more to come...](https://github.com/mickael-menu/zk/issues/22)
+    * [And more to come...](https://github.com/zk-org/zk/issues/22)
     * See [the documentation](docs/editors-integration.md) for configuration samples.
 * Pair `--match` with `--exact-match` / `-e` to search for (case insensitive) exact occurrences in your notes.
     * This can be useful when looking for terms including special characters, such as `[[name]]`.
 * Generating links to notes.
     * Use the `{{link}}` template variable when [formatting notes](docs/template-format.md) to print a link to the note, relative to the working directory.
     * Use the `{{format-link path title}}` template helper to render a custom link.
-    * Customize the link format from the [note formats settings](docs/note-format.md). You can for example choose regular Markdown links, Wiki-links or a custom format.
+    * Customize the link format from the [note formats settings](docs/note-format.md). You can for example choose regular Markdown links, wiki links or a custom format.
 
 ### Changed
 
@@ -59,7 +327,7 @@ All notable changes to this project will be documented in this file.
 
 ### Fixed
 
-* [#4](https://github.com/mickael-menu/zk/issues/4) Terminal borked when piping content with Vim
+* [#4](https://github.com/zk-org/zk/issues/4) Terminal borked when piping content with Vim
 
 
 ## 0.2.1
@@ -92,3 +360,4 @@ All notable changes to this project will be documented in this file.
 
 * Renamed `--linking-to` filtering option to `--link-to`.
 * Multiple `--extra` variables are now separated by `,` instead of `;`.
+

CONTRIBUTING.md

@@ -0,0 +1,62 @@
+# Contributing to `zk`
+
+## Understanding the codebase
+
+### Building the project
+
+It is recommended to use the `Makefile` for compiling the project, as the `go` command requires a few parameters.
+
+```shell
+make build
+```
+
+This will be expanded to the following command:
+
+```shell
+CGO_ENABLED=1 GOARCH=arm64 go build -tags "fts5" -ldflags "-X=main.Version=`git describe --tags --match v[0-9]* 2> /dev/null` -X=main.Build=`git rev-parse --short HEAD`"
+```
+
+- `CGO_ENABLED=1` enables CGO, which is required by the `mattn/go-sqlite3` dependency.
+- `GOARCH=arm64` is only required for Apple Silicon chips.
+- `-tags "fts5"` enables the FTS option with `mattn/go-sqlite3`, which handles much of the magic behind `zk`'s `--match` filtering option.
+- ``-ldflags "-X=main.Version=`git describe --tags --match v[0-9]* 2> /dev/null` -X=main.Build=`git rev-parse --short HEAD`"`` will automatically set `zk`'s build and version numbers using the latest Git tag and commit SHA.
+
+### Automated tests
+
+The project is vetted with two different kind of automated tests: unit tests and end-to-end tests.
+
+#### Unit tests
+
+Unit tests are using the standard [Go testing library](https://pkg.go.dev/testing). To execute them, use the command `make test`.
+
+They are ideal for testing parsing output or individual API edge cases and minutiae.
+
+#### End-to-end tests
+
+Most of `zk`'s functionality is tested with functional tests ran with [`tesh`](https://github.com/mickael-menu/tesh), which you can execute with `make tesh` (or `make teshb`, to debug whitespaces changes).
+
+When addressing a GitHub issue, it's a good idea to begin by creating a `tesh` file in `tests/issue-XXX.tesh`. If a starting notebook state is required, it can be added under `tests/fixtures`.
+
+If you modify the output of `zk`, you may disrupt some `tesh` files. You can use `make tesh-update` to automatically update them with the correct output.
+
+### CI workflows
+
+Several GitHub action workflows are executed when pull requests are merged or releases are created.
+
+- `.github/workflows/build.yml` checks that the project can be built and the tests still pass.
+- `.github/workflows/codeql.yml` runs static analysis to vet code quality.
+- `.github/workflows/gh-pages.yml` deploy the documentation files to GitHub Pages.
+- `.github/workflows/release.yml` submits a new version to Homebrew when a Git version tag is created.
+- `.github/workflows/triage.yml` automatically tags old issues and PRs as staled.
+
+## Releasing a new version
+
+When `zk` is ready to be released, you can update the `CHANGELOG.md` ([for example](https://github.com/zk-org/zk/commit/ea4457ad671aa85a6b15747460c6f2c9ad61bf73)) and create a new Git version tag (for example `v0.13.0`). Make sure you follow the [Semantic Versioning](https://semver.org) scheme.
+
+Then, create [a new GitHub release](https://github.com/zk-org/zk/releases) with a copy of the latest `CHANGELOG.md` entries and the binaries for all supported platforms.
+
+Binaries can be created automatically using `make dist-linux` and `make dist-macos`.
+
+Unfortunately, `make dist-macos` must be run manually on both an Apple Silicon and Intel chips. The Linux builds are created using Docker and [these custom images](https://github.com/zk-org/zk-xcompile), which are hosted via [ghcr.io within zk-org](https://github.com/orgs/zk-org/packages/container/package/zk-xcompile).
+
+This process is convoluted because `zk` requires CGO with `mattn/go-sqlite3`, which prevents using Go's native cross-compilation. Transitioning to a CGO-free SQLite driver such as [cznic/sqlite](https://gitlab.com/cznic/sqlite) could simplify the distribution process significantly.

Makefile

@@ -1,15 +1,86 @@
-VERSION := `git describe --tags --match v[0-9]* 2> /dev/null`
+# Build zk in the current folder.
+build:
+	$(call go,build)
+
+# Build and install `zk` using go's default bin directory.
+install:
+	$(call go,install)
+
+# Run unit tests.
+test:
+	$(call go,test,./...)
+
+# Run end-to-end tests.
+tesh: build
+	@PATH=".:$(shell pwd):$(PATH)" tesh tests tests/fixtures
+
+# Run end-to-end tests and prints difference as raw bytes.
+teshb: build
+	@PATH=".:$(shell pwd):$(PATH)" tesh -b tests tests/fixtures
+
+# Update end-to-end tests.
+tesh-update: build
+	PATH=".:$(shell pwd):$(PATH)" tesh -u tests tests/fixtures
+
+alpine:
+	$(call alpine,build)
 
-all: macos linux
+# Produce a release bundle for all platforms.
+dist: dist-macos dist-linux
 	rm -f zk
 
-macos:
-	rm -f zk && ./go build && zip -r "zk-${VERSION}-macos-`uname -m`.zip" zk
+# Produce a release bundle for macOS.
+dist-macos:
+	rm -f zk && make && zip -r "zk-${VERSION}-macos-`uname -m`.zip" zk
 
-linux:
-	rm -f zk && docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk mickaelmenu/zk-xcompile:linux-i386 /bin/bash -c './go build' && tar -zcvf "zk-${VERSION}-linux-i386.tar.gz" zk
-	rm -f zk && docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk mickaelmenu/zk-xcompile:linux-amd64 /bin/bash -c './go build' && tar -zcvf "zk-${VERSION}-linux-amd64.tar.gz" zk
-	rm -f zk && docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk mickaelmenu/zk-xcompile:linux-arm64 /bin/bash -c './go build' && tar -zcvf "zk-${VERSION}-linux-arm64.tar.gz" zk
+# Produce a release bundle for Linux.
+dist-linux: dist-linux-amd64 dist-linux-arm64 dist-linux-i386 dist-alpine-amd64 dist-alpine-arm64 dist-alpine-i386
+dist-linux-amd64:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:linux-amd64 /bin/bash -c 'make' \
+		&& tar -zcvf "zk-${VERSION}-linux-amd64.tar.gz" zk
+dist-linux-arm64:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:linux-arm64 /bin/bash -c 'make' \
+		&& tar -zcvf "zk-${VERSION}-linux-arm64.tar.gz" zk
+dist-linux-i386:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:linux-i386 /bin/bash -c 'make' \
+		&& tar -zcvf "zk-${VERSION}-linux-i386.tar.gz" zk
+dist-alpine-amd64:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:alpine-amd64 /bin/bash -c 'make alpine' \
+		&& tar -zcvf "zk-${VERSION}-alpine-amd64.tar.gz" zk
+dist-alpine-arm64:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:alpine-arm64 /bin/bash -c 'make alpine' \
+		&& tar -zcvf "zk-${VERSION}-alpine-arm64.tar.gz" zk
+dist-alpine-i386:
+	rm -f zk \
+		&& docker run --rm -v "${PWD}":/usr/src/zk -w /usr/src/zk ghcr.io/zk-org/zk-xcompile:alpine-i386 /bin/bash -c 'make alpine' \
+		&& tar -zcvf "zk-${VERSION}-alpine-i386.tar.gz" zk
 
+# Clean build products.
 clean:
 	rm -rf zk*
+
+
+VERSION := `git describe --tags --match v[0-9]* 2> /dev/null`
+BUILD := `git rev-parse --short HEAD`
+
+ENV_PREFIX := CGO_ENABLED=1
+# Add necessary env variables for Apple Silicon.
+ifeq ($(shell uname -sm),Darwin arm64)
+	ENV_PREFIX := $(ENV) GOARCH=arm64
+endif
+
+# Wrapper around the go binary, to set all the default parameters.
+define go
+	$(ENV_PREFIX) go $(1) -tags "fts5" -ldflags "-X=main.Version=$(VERSION) -X=main.Build=$(BUILD)" $(2)
+endef
+
+# Alpine (musl) requires statically linked libs. This should be compatible for
+# Void linux and other musl based distros aswell.
+define alpine
+	$(ENV_PREFIX) go $(1) -tags "fts5" -ldflags "-extldflags=-static -X=main.Version=$(VERSION) -X=main.Build=$(BUILD)" $(2)
+endef

README.md

@@ -1,10 +1,12 @@
 <div align="center">
-<h1>zk</h1>
+<img alt="zk logo" width="20%" src="./docs/assets/media/zk-black-modern.png" />
 <h4>A plain text note-taking assistant</h4>
 <img alt="Screencast" width="95%" src="docs/assets/media/screencast.svg"/>
-<p>Looking for a quick usage example? <a href="docs/getting-started.md">Let's get started</a>.</p>
 </div>
 
+Looking for a quick usage example? [Let's get started](docs/getting-started.md).
+
+
 ## Description
 
 `zk` is a command-line tool helping you to maintain a plain text [Zettelkasten](https://zettelkasten.de/introduction/) or [personal wiki](https://en.wikipedia.org/wiki/Personal_wiki).
@@ -14,9 +16,10 @@
 * [Creating notes from templates](docs/note-creation.md)
 * [Advanced search and filtering capabilities](docs/note-filtering.md) including [tags](docs/tags.md), links and mentions
 * [Integration with your favorite editors](docs/editors-integration.md):
-    * [`zk.nvim`](https://github.com/megalithic/zk.nvim) for Neovim 0.5+, maintained by [Seth Messer](https://github.com/megalithic)
-    * [`zk-vscode`](https://github.com/mickael-menu/zk-vscode) for Visual Studio Code
     * [Any LSP-compatible editor](docs/editors-integration.md)
+    * [`zk-nvim`](https://github.com/zk-org/zk-nvim) for Neovim 0.8+
+    * [`zk-vscode`](https://github.com/zk-org/zk-vscode) for Visual Studio Code
+    * (*unmaintained*) [`zk.nvim`](https://github.com/megalithic/zk.nvim) for Neovim 0.5+ by [Seth Messer](https://github.com/megalithic)
 * [Interactive browser](docs/tool-fzf.md), powered by `fzf`
 * [Git-style command aliases](docs/config-alias.md) and [named filters](docs/config-filter.md)
 * [Made with automation in mind](docs/automation.md)
@@ -36,47 +39,62 @@
 
 ## Install
 
-[Check out the latest release](https://github.com/mickael-menu/zk/releases) for pre-built binaries for macOS and Linux (`zk` was not tested on Windows).
-
-### Build from scratch
+[Check out the latest release](https://github.com/zk-org/zk/releases) for pre-built binaries for macOS and Linux (`zk` was not tested on Windows).
 
-Make sure you have a working [Go installation](https://golang.org/), then clone the repository:
+### Homebrew
 
 ```sh
-$ git clone https://github.com/mickael-menu/zk.git
-$ cd zk
-$ chmod a+x go
+brew install zk
 ```
 
-#### On macOS
-
-`icu4c` is required to build `zk`, which you can install with [Homebrew](https://brew.sh/).
+Or, if you want to the latest changes:
 
+```sh
+brew install --HEAD zk
 ```
-$ brew install icu4c
-$ ./go build
-$ ./zk -h
+
+### Nix
+
+```sh
+# Run zk from Nix store without installing it:
+nix run nixpkgs#zk
+# Or, to install it permanently:
+nix-env -iA zk
 ```
 
-##### Apple Silicon
+### Arch Linux
 
-The build command needs additional environment variables on Apple Silicon:
+You can install [the zk package](https://archlinux.org/packages/extra/x86_64/zk/) from the official repos.
 
-```
-$ GOARCH=arm64 CGO_CFLAGS="-I/opt/homebrew/opt/icu4c/include" CGO_LDFLAGS="-L/opt/homebrew/opt/icu4c/lib" ./go build
+```sh
+sudo pacman -S zk
 ```
 
-#### On Linux
+### Build from scratch
 
-`libicu-dev` is required to build `zk`, use your favorite package manager to install it.
+Make sure you have a working [Go 1.21+ installation](https://golang.org/), then clone the repository:
 
+```sh
+$ git clone https://github.com/zk-org/zk.git
+$ cd zk
 ```
-$ apt-install libicu-dev
-$ ./go build
+
+#### On macOS / Linux
+
+```
+$ make
 $ ./zk -h
 ```
 
+## Contributing
+
+We warmly welcome issues, PRs and [discussions](https://github.com/zk-org/zk/discussions).
+
+Here you can read [some useful info for contributing to `zk`](./CONTRIBUTING.md).
+
 ## Related projects
 
 * [Neuron](https://github.com/srid/neuron) – a great tool to publish a Zettelkasten on the web
+* [Emanote](https://emanote.srid.ca/) – an improved successor to Neuron
 * [sirupsen's zk](https://github.com/sirupsen/zk) – a collection of scripts with a similar purpose
+* [zk-spaced](https://github.com/matze/zk-spaced) – spaced repetition plugin for zk

_config.yml

@@ -0,0 +1,24 @@
+title: "zk"
+permalink: /:title
+defaults:
+  - scope:
+      path: "README.md"
+    values:
+      title: "zk"
+  - scope:
+      path: "" # all
+    values:
+      render_with_liquid: false
+exclude:
+  - ".github/"
+  - ".gitignore"
+  - "CHANGELOG.md"
+  - "CONTRIBUTING.md"
+  - "LICENSE"
+  - "Makefile"
+  - "go.mod"
+  - "go.sum"
+  - "internal/"
+  - "main.go"
+  - "tests/"
+

docs/_config.yml

@@ -1,2 +0,0 @@
-permalink: /:title
-theme: jekyll-theme-modernist

docs/_layouts/default.html

@@ -1,57 +0,0 @@
-<!doctype html>
-<html lang="{{ site.lang | default: "en-US" }}">
-  <head>
-    <meta charset="utf-8">
-    <meta http-equiv="X-UA-Compatible" content="IE=edge">
-
-{% seo %}
-
-    <link rel="stylesheet" href="{{ '/assets/css/style.css?v=' | append: site.github.build_revision | relative_url }}">
-    <script src="{{ '/assets/js/scale.fix.js' | relative_url }}"></script>
-    <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
-
-    <!--[if lt IE 9]>
-    <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
-    <![endif]-->
-  </head>
-  <body>
-    <div class="wrapper">
-      <header {% unless site.description or site.github.project_tagline %} class="without-description" {% endunless %}>
-        <h1><a href="https://mickael-menu.github.io/zk/">{{ site.title | default: site.github.repository_name }}</a></h1>
-        {% if site.description or site.github.project_tagline %}
-          <p>{{ site.description | default: site.github.project_tagline }}</p>
-        {% endif %}
-        <p class="view"><a href="{{ site.github.repository_url }}">View the Project on GitHub <small>{{ github_name }}</small></a></p>
-        <ul>
-        {% if site.show_downloads %}
-          <li><a href="{{ site.github.zip_url }}">Download <strong>ZIP File</strong></a></li>
-          <li><a href="{{ site.github.tar_url }}">Download <strong>TAR Ball</strong></a></li>
-        {% endif %}
-          <li><a href="{{ site.github.repository_url }}">View On <strong>GitHub</strong></a></li>
-        </ul>
-      </header>
-      <section>
-
-      {{ content }}
-
-      </section>
-    </div>
-    <footer>
-    {% if site.github.is_project_page %}
-      <p>Project maintained by <a href="{{ site.github.owner_url }}">{{ site.github.owner_name }}</a></p>
-    {% endif %}
-    </footer>
-    <!--[if !IE]><script>fixScale(document);</script><![endif]-->
-
-    {% if site.google_analytics %}
-      <script>
-        (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-        (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-        m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-        })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-        ga('create', '{{ site.google_analytics }}', 'auto');
-        ga('send', 'pageview');
-      </script>
-    {% endif %}
-  </body>
-</html>

docs/assets/css/style.scss

@@ -1,9 +0,0 @@
----
----
-
-@import "{{ site.theme }}";
-
-code, pre {
-    font-size: inherit;
-}
-

docs/automation.md

@@ -7,4 +7,4 @@
 * [send notes for processing by other programs](external-processing.md)
 * [create a note with initial content](note-creation.md) from a standard input pipe
 
-If you find out that `zk` does not behave as expected or could communicate better with other programs, [please post an issue](https://github.com/mickael-menu/zk/issues).
+If you find out that `zk` does not behave as expected or could communicate better with other programs, [please post an issue](https://github.com/zk-org/zk/issues).

docs/config-alias.md

@@ -6,9 +6,10 @@ Declaring your own aliases is a great way to make your experience with `zk` easi
 
 ## Configuring aliases
 
-Command aliases are declared in your [configuration file](config.md), under the `[alias]` section. They are executed with `$SHELL -c`, which allows you to:
+Command aliases are declared in your [configuration file](config.md), under the `[alias]` section. They are executed with [your default shell](tool-shell.md), which allows you to:
 
 * expand arguments with `$@` or `$*`
+    * [it is recommended to wrap `$@` in quotes](https://github.com/zk-org/zk/issues/316#issuecomment-1543564168)
 * expand environment variables
 * run several commands with `&&`
 * pipe several commands with `|`
@@ -17,7 +18,7 @@ An alias can call other aliases but cannot call itself. This enables you to over
 
 ```toml
 [alias]
-edit = "zk edit --interactive $@"
+edit = 'zk edit --interactive "$@"'
 ```
 
 When running an alias, the `ZK_NOTEBOOK_DIR` environment variable is set to the absolute path of the current notebook. You can use it to run commands working no matter the location of the working directory.

docs/config-group.md

@@ -34,7 +34,7 @@ You can override the global [note configuration](config-note.md) and [extra user
 
 ```toml
 [group.journal.note]
-filename = "{{date now}}"
+filename = "{{format-date now}}"
 template = "journal.md"
 
 [group.journal.extra]

docs/config-lsp.md

@@ -0,0 +1,62 @@
+# LSP configuration
+
+The `[lsp]` [configuration file](config.md) section provides settings to fine-tune the [LSP editors integration](editors-integration.md).
+
+## Completion
+
+Customize how completion items appear in your editor when auto-completing links with the `[lsp.completion]` sub-section.
+
+| Setting                     | Type       | Description                                                                           |
+|-----------------------------|------------|---------------------------------------------------------------------------------------|
+| `note-label`                | `template` | Label displayed in the completion pop-up for each note                                |
+| `note-filter-text`          | `template` | Text used as a source when filtering the completion pop-up with keystrokes            |
+| `note-detail`               | `template` | Additional information about a completion item                                        |
+| `use-additional-text-edits` | `boolean`  | Indicates whether `additionalTextEdits` will be used to remove the trigger characters |
+
+Each key accepts a [template](template.md) with the following context:
+
+| Variable        | Type     | Description                                                        |
+|-----------------|----------|--------------------------------------------------------------------|
+| `filename`      | string   | Filename of the note, including its extension                      |
+| `filename-stem` | string   | Filename of the note without the file extension                    |
+| `path`          | string   | File path to the note, relative to the notebook root               |
+| `abs-path`      | string   | Absolute file path to the note                                     |
+| `rel-path`      | string   | File path to the note, relative to the current directory           |
+| `title`         | string   | Note title                                                         |
+| `title-or-path` | string   | Note title or path if empty                                        |
+| `metadata`      | map      | YAML frontmatter metadata, e.g. `metadata.description`<sup>1</sup> |
+
+1. YAML keys are normalized to lower case.
+
+
+## Diagnostics
+
+Use the `[lsp.diagnostics]` sub-section to configure how LSP diagnostics are reported to your editors. Each diagnostic setting can be:
+
+* An empty string or `none` to ignore this diagnostic.
+* `hint`, `info`, `warning` or `error` to enable and set the severity of the diagnostic.
+
+| Setting      | Default   | Description                                                               |
+|--------------|-----------|---------------------------------------------------------------------------|
+| `wiki-title` | `"none"`  | Report titles of wiki-links, which is useful if you use IDs for filenames |
+| `dead-link`  | `"error"` | Warn for dead links between notes                                         |
+
+## Complete example
+
+```toml
+[lsp]
+
+[lsp.diagnostics]
+# Report titles of wiki-links as hints.
+wiki-title = "hint"
+# Warn for dead links between notes.
+dead-link = "error"
+
+[lsp.completion]
+# Show the note title in the completion pop-up, or fallback on its path if empty.
+note-label = "{{title-or-path}}"
+# Filter out the completion pop-up using the note title or its path.
+note-filter-text = "{{title}} {{path}}"
+# Show the note filename without extension as detail.
+note-detail = "{{filename-stem}}"
+```

docs/config-note.md

@@ -14,6 +14,8 @@ The `[note]` section from the [configuration file](config.md) is used to set the
 * `template` (string)
     * Path to the [template](template.md) used to generate the note content.
     * Either an absolute path, or relative to `.zk/templates/`.
+* `exclude` (list of strings)
+    * List of [path globs](https://en.wikipedia.org/wiki/Glob_\(programming\)) excluded during note indexing.
 * `id-charset` (string)
     * Characters set used to [generate random IDs](note-id.md).
     * You can use:
@@ -46,10 +48,10 @@ Here are some common filename patterns you may want to use:
     * Readable and practical for web servers, but fragile in case of renaming.
 * `{{id}}-{{slug title}}` – e.g. `i2hn8-an-interesting-concept.md`
     * The best of both worlds? Readable but if you link only with the prefix ID, you can rename without breaking links.
-* `{{date now 'timestamp'}}` – e.g. `200911172034.md`
+* `{{format-date now 'timestamp'}}` – e.g. `200911172034.md`
     * Verbose, but sortable by creation date and stable.
-* `{{date now 'timestamp'}} {{title}}` – e.g. `200911172034 An interesting concept.md`
+* `{{format-date now 'timestamp'}} {{title}}` – e.g. `200911172034 An interesting concept.md`
     * The format of [The Archive](https://zettelkasten.de/the-archive/) and [sirupsen's zk](https://github.com/sirupsen/zk).
-* `{{date now '%Y-%m-%d'}}` – e.g. `2009-11-17.md`
+* `{{format-date now '%Y-%m-%d'}}` – e.g. `2009-11-17.md`
     * Sortable, human-friendly format for a daily journal.
     * i.e. [Maintaining a daily journal](daily-journal.md).

docs/config-notebook.md

@@ -0,0 +1,15 @@
+# Notebook configuration
+
+The `[notebook]` section from the [configuration file](config.md) is used to set the default notebook directory.
+If the path starts with `~` it will be replaced with the user home directory (`$HOME`). This property also supports environment variables.
+
+```toml
+[notebook]
+dir = "~/notebook" # same as "$HOME/notebook"
+```
+
+ The following properties are customizable:
+
+* `dir` (string)
+    * Path of the default notebook.
+    * Only available in the global config file (`~/.config/zk/config.toml`).

docs/config.md

@@ -2,14 +2,17 @@
 
 Each [notebook](notebook.md) contains a configuration file used to customize your experience with `zk`. This file is located at `.zk/config.toml` and uses the [TOML format](https://github.com/toml-lang/toml). It is composed of several optional sections:
 
+* `[notebook]` configures the [default notebook](config-notebook.md)
 * `[note]` sets the [note creation rules](config-note.md)
 * `[extra]` contains free [user variables](config-extra.md) which can be expanded in templates
 * `[group]` defines [note groups](config-group.md) with custom rules
-* `[format]` configures the [note format settings](note-format.md), such as Markdown options.
+* `[format]` configures the [note format settings](note-format.md), such as Markdown options
 * `[tool]` customizes interaction with external programs such as:
     * [your default editor](tool-editor.md)
+    * [your default shell](tool-shell.md)
     * [your default pager](tool-pager.md)
     * [`fzf`](tool-fzf.md)
+* `[lsp]` setups the [Language Server Protocol settings](config-lsp.md) for [editors integration](editors-integration.md)
 * `[filter]` declares your [named filters](config-filter.md)
 * `[alias]` holds your [command aliases](config-alias.md)
 
@@ -24,6 +27,10 @@ Notebook configuration files will inherit the settings defined in the global con
 Here's an example of a complete configuration file:
 
 ```toml
+# NOTEBOOK SETTINGS
+[notebook]
+dir = "~/notebook"
+
 # NOTE SETTINGS
 [note]
 
@@ -62,11 +69,11 @@ author = "Mickaël"
 
 
 # GROUP OVERRIDES
-[dir.journal]
+[group.journal]
 paths = ["journal/weekly", "journal/daily"]
 
-[dir.journal.note]
-filename = "{{date now}}"
+[group.journal.note]
+filename = "{{format-date now}}"
 
 
 # MARKDOWN SETTINGS
@@ -83,6 +90,9 @@ colon-tags = true
 # Default editor used to open notes.
 editor = "nvim"
 
+# Default shell used by aliases and commands.
+shell = "/bin/bash"
+
 # Pager used to scroll through long output.
 pager = "less -FIRX"
 
@@ -104,5 +114,13 @@ recent = "zk edit --sort created- --created-after 'last two weeks' --interactive
 
 # Show a random note.
 lucky = "zk list --quiet --format full --sort random --limit 1"
-```
 
+# LSP (EDITOR INTEGRATION)
+[lsp]
+
+[lsp.diagnostics]
+# Report titles of wiki-links as hints.
+wiki-title = "hint"
+# Warn for dead links between notes.
+dead-link = "error"
+```

docs/daily-journal.md

@@ -2,7 +2,7 @@
 
 Let's assume you want to write daily notes named like `2021-02-16.md` in a `journal/daily` sub-directory. This common use case is a good fit for creating a [note group](config-group.md) overriding the default [note creation](note-creation.md) settings.
 
-First, create a `group` entry in the [configuration file](config.md) to set the note settings for this directory. Refer to the [template syntax reference](template.md) to understand how to use the `{{date}}` helper.
+First, create a `group` entry in the [configuration file](config.md) to set the note settings for this directory. Refer to the [template syntax reference](template.md) to understand how to use the `{{format-date}}` helper.
 
 ```toml
 [group.daily]
@@ -10,8 +10,8 @@ First, create a `group` entry in the [configuration file](config.md) to set the
 paths = ["journal/daily"]
 
 [group.daily.note]
-# %Y-%m-%d is actually the default format, so you could use {{date now}} instead.
-filename = "{{date now '%Y-%m-%d'}}"
+# %Y-%m-%d is actually the default format, so you could use {{format-date now}} instead.
+filename = "{{format-date now '%Y-%m-%d'}}"
 extension = "md"
 template = "daily.md"
 ```
@@ -19,7 +19,7 @@ template = "daily.md"
 Next, create a template file under `.zk/templates/daily.md` to render the note content. Here we used the date again to generate a title like "February 16, 2021".
 
 ```markdown
-# {{date now "long"}}
+# {{format-date now "long"}}
 
 What did I do today?
 ```
@@ -43,3 +43,7 @@ Let's unpack this alias:
 * `$ZK_NOTEBOOK_DIR` is set to the absolute path of the current [notebook](notebook.md) when running an alias. Using it allows you to run `zk daily` no matter where you are in the notebook folder hierarchy.
 * We need to use double quotes around `$ZK_NOTEBOOK_DIR`, otherwise it will not be expanded.
 
+If you want to edit today's note, simply use this alias:
+```sh
+$ zk daily
+```

docs/editors-integration.md

@@ -2,8 +2,8 @@
 
 There are several extensions available to integrate `zk` in your favorite editor:
 
-* [`zk.nvim`](https://github.com/megalithic/zk.nvim) for Neovim 0.5+, maintained by [Seth Messer](https://github.com/megalithic)
-* [`zk-vscode`](https://github.com/mickael-menu/zk-vscode) for Visual Studio Code
+* [`zk-nvim`](https://github.com/zk-org/zk-nvim) for Neovim 0.5+
+* [`zk-vscode`](https://github.com/zk-org/zk-vscode) for Visual Studio Code
 
 ## Language Server Protocol
 
@@ -13,16 +13,24 @@ There are several extensions available to integrate `zk` in your favorite editor
 * Auto-complete [hashtags and colon-separated tags](tags.md).
 * Preview the content of a note when hovering a link.
 * Navigate in your notes by following internal links.
-* [And more to come...](https://github.com/mickael-menu/zk/issues/22)
+* Create a new note using the current selection as title.
+* Diagnostics for dead links and wiki-links titles.
+* [And more to come...](https://github.com/zk-org/zk/issues/22)
+  
+You can configure some of these features in your notebook's [configuration file](config-lsp.md).
 
-To start the Language Server, use the `zk lsp` command. Refer to the following sections for editor-specific examples. [Feel free to share the configuration for your editor](https://github.com/mickael-menu/zk/issues/22).
+### Editor LSP configurations
 
-### Vim and Neovim
+To start the Language Server, use the `zk lsp` command. Refer to the following sections for editor-specific examples. [Feel free to share the configuration for your editor](https://github.com/zk-org/zk/issues/22).
 
-#### Vim and Neovim 0.4
+#### Vim and Neovim
+
+##### Vim and Neovim 0.4
 
 With [`coc.nvim`](https://github.com/neoclide/coc.nvim), run `:CocConfig` and add the following in the settings file:
 
+<details><summary><tt>coc-settings.json</tt></summary>
+
 ```jsonc
 {
   // Important, otherwise link completion containing spaces and other special characters won't work.
@@ -38,11 +46,39 @@ With [`coc.nvim`](https://github.com/neoclide/coc.nvim), run `:CocConfig` and ad
   }
 }
 ```
+</details>
+
+Here are some additional useful key bindings and custom commands:
+
+<details><summary><tt>~/.config/nvim/init.vim</tt></summary>
+
+```viml
+" User command to index the current notebook.
+"
+" zk.index expects a notebook path as first argument, so we provide the current
+" buffer path with expand("%:p").
+command! -nargs=0 ZkIndex :call CocAction("runCommand", "zk.index", expand("%:p"))
+nnoremap <leader>zi :ZkIndex<CR>
+
+" User command to create and open a new note, to be called like this:
+" :ZkNew {"title": "An interesting subject", "dir": "inbox", ...}
+"
+" Note the concatenation with the "edit" command to open the note right away.
+command! -nargs=? ZkNew :exec "edit ".CocAction("runCommand", "zk.new", expand("%:p"), <args>).path
+
+" Create a new note after prompting for its title.
+nnoremap <leader>zn :ZkNew {"title": input("Title: ")}<CR>
+" Create a new note in the directory journal/daily.
+nnoremap <leader>zj :ZkNew {"dir": "journal/daily"}<CR>
+```
+</details>
 
-#### Neovim 0.5 built-in LSP client
+##### Neovim 0.5 built-in LSP client
 
 Using [`nvim-lspconfig`](https://github.com/neovim/nvim-lspconfig):
 
+<details><summary><tt>~/.config/nvim/init.lua</tt></summary>
+
 ```lua
 local lspconfig = require('lspconfig')
 local configs = require('lspconfig/configs')
@@ -62,11 +98,14 @@ lspconfig.zk.setup({ on_attach = function(client, buffer)
   -- Add keybindings here, see https://github.com/neovim/nvim-lspconfig#keybindings-and-completion
 end })
 ```
+</details>
 
-### Sublime Text
+#### Sublime Text
 
 Install the [Sublime LSP](https://github.com/sublimelsp/LSP) package, then run the **Preferences: LSP Settings** command. Add the following to the settings file:
 
+<details><summary><tt>LSP.sublime-settings</tt></summary>
+
 ```jsonc
 {
   "clients": {
@@ -80,7 +119,133 @@ Install the [Sublime LSP](https://github.com/sublimelsp/LSP) package, then run t
   }
 }
 ```
+</details>
 
-### Visual Studio Code
+#### Visual Studio Code
 
 Install the [`zk-vscode`](https://marketplace.visualstudio.com/items?itemName=mickael-menu.zk-vscode) extension from the Marketplace.
+
+### Custom commands
+
+Using `zk`'s LSP custom commands, you can call `zk` commands right from your editor. Please refer to your editor's documentation on how to bind keyboard shortcuts to custom LSP commands.
+
+#### `zk.index`
+
+This LSP command calls `zk index` to refresh your notebook's index. It can be useful to make sure that the auto-completion is up-to-date. `zk.index` takes two arguments:
+
+1. A path to a file or directory in the notebook to index.
+2. <details><summary>(Optional) A dictionary of additional options (click to expand)</summary>
+    
+    | Key     | Type    | Description                       |
+    |---------|---------|-----------------------------------|
+    | `force` | boolean | Reindexes all the notes when true |
+    </details>
+
+`zk.index` returns a dictionary of indexing statistics.
+
+#### `zk.new`
+
+This LSP command calls `zk new` to create a new note. It can be useful to quickly create a new note with a key binding. `zk.new` takes two arguments:
+
+1. A path to any file or directory in the notebook, to locate it.
+2. <details><summary>(Optional) A dictionary of additional options (click to expand)</summary>
+    
+    | Key                       | Type                 | Description                                                                                                          |
+    |---------------------------|----------------------|----------------------------------------------------------------------------------------------------------------------|
+    | `title`                   | string               | Title of the new note                                                                                                |
+    | `content`                 | string               | Initial content of the note                                                                                          |
+    | `dir`                     | string               | Parent directory, relative to the root of the notebook                                                               |
+    | `group`                   | string               | [Note configuration group](config-group.md)                                                                          |
+    | `template`                | string               | [Custom template used to render the note](template-creation.md)                                                      |
+    | `extra`                   | dictionary           | A dictionary of extra variables to expand in the template                                                            |
+    | `date`                    | string               | A date of creation for the note in natural language, e.g. "tomorrow"                                                 |
+    | `edit`                    | boolean              | When true, the editor will open the newly created note (**not supported by all editors**)                            |
+    | `dryRun`                  | boolean              | When true, `zk` will not actually create the note on the file system, but will return its generated content and path |
+    | `insertLinkAtLocation`    | location<sup>1</sup> | A location in another note where a link to the new note will be inserted                                             |
+    | `insertContentAtLocation` | location<sup>1</sup> | A location in another note where the content of the new note will be inserted                                        |
+
+    1. The `location` type is an [LSP Location object](https://microsoft.github.io/language-server-protocol/specification#location), for example:
+
+    ```json
+    {
+        "uri":"file:///Users/mickael/notes/9se3.md",
+        "range": {
+            "end":{"line": 5, "character":149},
+            "start":{"line": 5, "character":137}
+        }
+    }
+    ```
+    </details>
+
+`zk.new` returns a dictionary with two properties:
+
+* `path` containing the absolute path to the created note.
+* `content` containing the raw content of the created note.
+
+#### `zk.link`
+
+This LSP command allows editors to tap into the note linking mechanism. It takes three arguments:
+
+1. A `path` to any file in the notebook that will be linked to
+2. An LSP `location` object that points to where the link will be inserted
+3. An optional title of the link. If `title` is not provided, the title of the note will be inserted instead
+
+`zk.link` returns a JSON object with the path to the linked note, if the linking was successful.
+
+**Note**: This command is _not_ exposed in the command line. This command is targeted at editor / plugin authors to extend zk functionality.
+
+#### `zk.list`
+
+This LSP command calls `zk list` to search a notebook. It takes two arguments:
+
+1. A path to any file or directory in the notebook, to locate it.
+2. <details><summary>A dictionary of additional options (click to expand)</summary>
+    
+  | Key                | Type           | Required?   | Description                                                                                               |
+  | ------------------ | -------------- | ----------- | -------------------------------------------------------------------------                                 |
+  | `select`           | string array   | Yes         | List of note fields to return<sup>1</sup>                                                                 |
+  | `hrefs`            | string array   | No          | Find notes matching the given path, including its descendants                                             |
+  | `limit`            | integer        | No          | Limit the number of notes found                                                                           |
+  | `match`            | string array   | No          | Terms to search for in the notes                                                                          |
+  | `exactMatch`       | boolean        | No          | (deprecated: use `matchStrategy`) Search for exact occurrences of the `match` argument (case insensitive) |
+  | `matchStrategy`    | string         | No          | Specify match strategy, which may be "fts" (default), "exact" or "re"                                     |
+  | `excludeHrefs`     | string array   | No          | Ignore notes matching the given path, including its descendants                                           |
+  | `tags`             | string array   | No          | Find notes tagged with the given tags                                                                     |
+  | `mention`          | string array   | No          | Find notes mentioning the title of the given ones                                                         |
+  | `mentionedBy`      | string array   | No          | Find notes whose title is mentioned in the given ones                                                     |
+  | `linkTo`           | string array   | No          | Find notes which are linking to the given ones                                                            |
+  | `linkedBy`         | string array   | No          | Find notes which are linked by the given ones                                                             |
+  | `orphan`           | boolean        | No          | Find notes which are not linked by any other note                                                         |
+  | `related`          | string array   | No          | Find notes which might be related to the given ones                                                       |
+  | `maxDistance`      | integer        | No          | Maximum distance between two linked notes                                                                 |
+  | `recursive`        | boolean        | No          | Follow links recursively                                                                                  |
+  | `created`          | string         | No          | Find notes created on the given date                                                                      |
+  | `createdBefore`    | string         | No          | Find notes created before the given date                                                                  |
+  | `createdAfter`     | string         | No          | Find notes created after the given date                                                                   |
+  | `modified`         | string         | No          | Find notes modified on the given date                                                                     |
+  | `modifiedBefore`   | string         | No          | Find notes modified before the given date                                                                 |
+  | `modifiedAfter`    | string         | No          | Find notes modified after the given date                                                                  |
+  | `sort`             | string array   | No          | Order the notes by the given criterion                                                                    |
+
+    1. As the output of this command might be very verbose and put a heavy load on the LSP client, you need to explicitly set which note fields you want to receive with the `select` option. The following fields are available: `filename`, `filenameStem`, `path`, `absPath`, `title`, `lead`, `body`, `snippets`, `rawContent`, `wordCount`, `tags`, `metadata`, `created`, `modified` and `checksum`.
+
+    </details>
+
+`zk.list` returns the found notes as a JSON array.
+
+#### `zk.tag.list`
+
+This LSP command calls `zk tag list` to return the list of tags in a notebook. It takes two arguments:
+
+1. A path to any file or directory in the notebook, to locate it.
+2. <details><summary>(Optional) A dictionary of additional options (click to expand)</summary>
+    
+    | Key    | Type         | Required? | Description                                      |
+    |--------|--------------|-----------|--------------------------------------------------|
+	| `sort` | string array | No        | Order the tags by the given criteria<sup>1</sup> |
+
+    1. The available sort criteria are `name` and `note-count`. You can change the order by appending `-` or `+` to the criterion.
+
+    </details>
+
+`zk.tag.list` returns the tags as a JSON array.

docs/getting-started.md

@@ -27,7 +27,7 @@ You can customize your experience using [custom templates](template.md) to gener
 
 If you are not sure whether a note already exists for a particular subject, the "search or create" mode might be more appropriate than `zk new`. It is inspired by [Notational Velocity](https://notational.net/) and enables searching for an existing note or creating a new one in a single action.
 
-From `zk`'s interactive edit screen, press `Ctrl-N` to create a new note using the current search query as title.
+From `zk`'s interactive edit screen, press `Ctrl-E` to create a new note using the current search query as title.
 
 <div align="center"><img alt="Create a note" width="85%" src="assets/media/new2.svg"/></div>
 

docs/neuron.md

@@ -27,3 +27,7 @@ But you can make your [notebook](notebook.md) even more tightly integrated with
     serve = "neuron gen -wS"
     gen = "neuron gen -o public"
     ```
+
+## Emanote
+
+Emanote is neuron's successor. For Emanote-specific configuration, see https://emanote.srid.ca/start/resources/zk.

docs/note-creation.md

@@ -10,15 +10,21 @@ By default, `zk new` will start [your editor](tool-editor.md) after creating the
 
 If you are not sure whether a note already exists for a particular subject, the "search or create" mode might be more appropriate than `zk new`. It is inspired by [Notational Velocity](https://notational.net/) and enables searching for an existing note or creating a new one in a single action.
 
-This option is available when running `zk edit --interactive`, which spawns [`fzf`](tool-fzf.md) to filter selected notes. From `fzf`, press `Ctrl-N` to create a new note using the current search query as title.
+This option is available when running `zk edit --interactive`, which spawns [`fzf`](tool-fzf.md) to filter selected notes. From `fzf`, press `Ctrl-E` to create a new note using the current search query as title.
 
 ## Create a note with initial content
 
-Initial content can be fed to the template through a standard input pipe, which will be expandable with the `{{content}}` [template variable](template-creation.md).
+Initial content can be fed to the template through standard input using `zk new --interactive`, which will be expandable with the `{{content}}` [template variable](template-creation.md).
 
 For example, to use the content of the macOS clipboard as the initial content you can run:
 
 ```sh
-$ pbpaste | zk new
+$ pbpaste | zk new --interactive
+```
+
+Alternatively, you can use the content of a file:
+
+```sh
+$ zk new --interactive < file.txt
 ```
 

docs/note-filtering.md

@@ -45,11 +45,50 @@ $ zk list --linked-by "`zk inline journal`"
 
 Use `--match <query>` (or `-m`) to search through the title and body of notes.
 
-The search is powered by a [full-text search](https://en.wikipedia.org/wiki/Full-text_search) database enabling near-instant results. Queries are not case-sensitive and terms are tokenized, which means that searching for `create` will also match `created` and `creating`.
+The search is powered by different strategies to answer various use cases:
+
+* `fts` (default) uses a [full-text search](https://en.wikipedia.org/wiki/Full-text_search) database to offer near-instant results and advanced search operators.
+* `exact` is useful if you need to find patterns containing special characters.
+* `re` enables regular expression for advanced use cases.
+
+Change the currently used strategy with `--match-strategy <strategy>` (or `-M`). To set the default strategy, you can declare a [custom alias](config-alias.md):
+
+```toml
+[alias]
+list = "zk list --match-strategy re $@"
+```
+
+The `--match` option may be given multiple times, where each argument will be combined with a boolean AND.
+
+For example,
+
+```sh
+$ zk list --tag "recipe" --match "pizza -pineapple" --match "mushrooms"
+```
+
+Is equivalent to,
+
+```sh
+$ zk list --tag "recipe" --match "(pizza -pineapple) AND (mushrooms)"
+```
+
+
+### Full-text search (`fts`)
+
+The default match strategy is powered by a [full-text search](https://en.wikipedia.org/wiki/Full-text_search) database enabling near-instant results. Queries are not case-sensitive and terms are tokenized, which means that searching for `create` will also match `created` and `creating`.
 
 A syntax similar to Google Search is available for advanced search queries.
 
-### Combining terms
+```sh
+# FTS is the default match strategy
+$ zk list --match "tesla OR edison"
+
+# ...but you can enable it explicitly.
+$ zk list --match-strategy fts --match "tesla OR edison"
+$ zk list -Mf -m "tesla OR edison"
+```
+
+#### Combining terms
 
 By default, the search engine will find the notes containing all the terms in the query, in any order.
 
@@ -83,7 +122,7 @@ Finally, you can filter out results by excluding a term with `NOT` (all caps) or
 "tesla -car"
 ```
 
-### Search in specific fields
+#### Search in specific fields
 
 If you want to search only in the title or body of notes, prefix a query with `title:` or `body:`.
 
@@ -92,7 +131,7 @@ If you want to search only in the title or body of notes, prefix a query with `t
 "body: (tesla OR edison)"
 ```
 
-### Prefix terms
+#### Prefix terms
 
 Match any term beginning with the given prefix with a wildcard `*`.
 
@@ -106,13 +145,25 @@ Prefixing a query with `^` will match notes whose title or body start with the f
 "title: ^journal"
 ```
 
-### Search for special characters
+### Exact matches (`exact`)
 
-If you need to find patterns containing special characters, such as an `email@addre.ss` or a `[[wiki-link]]`, use the `--exact-match` / `-e` option. The search will be case-insensitive.
+If you need to find patterns containing special characters, such as an `email@addre.ss` or a `[[wiki-link]]`, use the `exact` match strategy. The search will be case-insensitive.
 
+```sh
+$ zk list --match-strategy exact --match "[[link]]"
+$ zk list -Me -m "[[link]]"
 ```
-$ zk list --exact-match --match "[[link]]"
-$ zk list -em "[[link]]"
+
+### Regular expressions (`re`)
+
+For advanced use cases, you can use the `re` match strategy to search the notebook using regular expressions. The supported syntax is similar to the one used by Python or Perl. [See the full reference](https://golang.org/s/re2syntax).
+
+:warning: Make sure to use quotes to prevent your shell from expanding wildcards.
+
+```sh
+# Find notes containing emails.
+$ zk list --match-strategy re --match ".+@.+"
+$ zk list -Mr -m ".+@.+"
 ```
 
 ## Filter by tags

docs/note-format.md

@@ -21,9 +21,22 @@ You can set up some features of `zk`'s Markdown parser from your [configuration
 
 ### Customizing the Markdown links generated by `zk`
 
-By default, `zk` will generate regular Markdown links for internal links. If you prefer to use `[[Wiki Links]]` instead, set the `link-format` setting to `wiki`. If you want to override completely the link format, you can also set `link-format` to a [custom template](template.md). Two variables `path` and `title` are available in the template, for example to generate a wiki-link with a title:
+By default, `zk` will generate regular Markdown links for internal links. If you prefer to use `[[Wiki Links]]` instead, set the `link-format` setting to `wiki`. If you want to override completely the link format, you can also set `link-format` to a [custom template](template.md). For example, to generate a wiki link using an ID from the frontmatter and a title:
 
 ```toml
 [format.markdown]
-link-format = "[[{{path}}|{{title}}]]"
+link-format = "[[{{metadata.id}}|{{title}}]]"
 ```
+
+The following variables are available in the template:
+
+| Variable   | Type   | Description                                               |
+|------------|--------|-----------------------------------------------------------|
+| `filename` | string | Filename of the note                                      |
+| `path`     | string | File path to the note, relative to the notebook directory |
+| `abs-path` | string | Absolute file path to the note                            |
+| `rel-path` | string | File path to the note, relative to the current directory  |
+| `title`    | string | Note title                                                |
+| `metadata` | map    | YAML frontmatter metadata, e.g. `metadata.id`<sup>1</sup> |
+
+1. YAML keys are normalized to lower case.

docs/notebook.md

@@ -6,6 +6,8 @@ To create a new notebook, simply run `zk init [<directory>]`.
 
 Most `zk` commands are operating "Git-style" on the notebook containing the current working directory (or one of its parents). However, you can explicitly set which notebook to use with `--notebook-dir` or the `ZK_NOTEBOOK_DIR` environment variable. Setting `ZK_NOTEBOOK_DIR` in your shell configuration (e.g. `~/.profile`) can be used to define a default notebook which `zk` commands will use when the working directory is not in another notebook.
 
+If the [default notebook](config-notebook.md) is set it will be used as `ZK_NOTEBOOK_DIR`, unless this environment variable is not already set.
+
 ## Anatomy of a notebook
 
 Similarly to Git, a notebook is identified by the presence of a `.zk` directory at its root. This directory contains the only `zk`-specific files in your notebook:

docs/tags.md

@@ -12,3 +12,16 @@ You can filter your notes by their tags using the `--tags` option, as demonstrat
 ```sh
 $ zk list --tag "inbox OR todo, NOT done"
 ```
+
+## Listing tags
+
+You can list all the tags found in your notebook using `zk tag list`.
+
+The following variables are available in the templates used when formatting tags, for example with `zk tag list --format <template>`.
+
+| Variable     | Type   | Description                                    |
+|--------------|--------|------------------------------------------------|
+| `id`         | int    | Unique ID of this tag in the Notebook database |
+| `name`       | string | Name of the tag                                |
+| `note-count` | int    | Number of notes attached to this tag           |
+

docs/template-creation.md

@@ -9,7 +9,7 @@ The following variables are available in the templates used when [creating new n
 | `content`     | string | Any text piped through the standard input                                             |
 | `dir`         | string | Parent directory in the notebook                                                      |
 | `extra.<key>` | string | [Additional variables](config-extra.md) provided through the config file or `--extra` |
-| `now`         | date   | Current date and time, useful when paired with [`{{date now}}`](template.md)          |
+| `now`         | date   | Current date and time, useful when paired with [`{{format-date now}}`](template.md)   |
 | `env`         | map    | Dictionary of case-sensitive environment variables, e.g. `{{env.PATH}}`.              |
 
 These additional variables are available only to the note content template, once the filename is generated.

docs/template-format.md

@@ -2,21 +2,24 @@
 
 The following variables are available in the templates used when formatting notes, for example with `zk list --format <template>`.
 
-| Variable      | Type     | Description                                                              |
-|---------------|----------|--------------------------------------------------------------------------|
-| `path`        | string   | File path to the note, relative to the current directory                 |
-| `title`       | string   | Note title                                                               |
-| `link`        | string   | Markdown link to the note, relative to the current directory<sup>1</sup> |
-| `lead`        | string   | First paragraph extracted from the note content                          |
-| `body`        | string   | All of the note content, minus the heading                               |
-| `snippets`    | [string] | List of context-sensitive relevant excerpts from the note                |
-| `raw-content` | string   | The full raw content of the note file                                    |
-| `word-count`  | int      | Number of words in the note                                              |
-| `tags`        | [string] | List of tags found in the note                                           |
-| `metadata`    | map      | YAML frontmatter metadata, e.g. `metadata.description`<sup>2</sup>       |
-| `created`     | date     | Date of creation of the note                                             |
-| `modified`    | date     | Last date of modification of the note                                    |
-| `checksum`    | string   | SHA-256 checksum of the note file                                        |
+| Variable        | Type     | Description                                                              |
+|-----------------|----------|--------------------------------------------------------------------------|
+| `filename`      | string   | Filename of the note, including its extension                            |
+| `filename-stem` | string   | Filename of the note without the file extension                          |
+| `path`          | string   | File path to the note, relative to the current directory                 |
+| `abs-path`      | string   | File path to the note, absolute path including the notebook directory    |
+| `title`         | string   | Note title                                                               |
+| `link`          | string   | Markdown link to the note, relative to the current directory<sup>1</sup> |
+| `lead`          | string   | First paragraph extracted from the note content                          |
+| `body`          | string   | All of the note content, minus the heading                               |
+| `snippets`      | [string] | List of context-sensitive relevant excerpts from the note                |
+| `raw-content`   | string   | The full raw content of the note file                                    |
+| `word-count`    | int      | Number of words in the note                                              |
+| `tags`          | [string] | List of tags found in the note                                           |
+| `metadata`      | map      | YAML frontmatter metadata, e.g. `metadata.description`<sup>2</sup>       |
+| `created`       | date     | Date of creation of the note                                             |
+| `modified`      | date     | Last date of modification of the note                                    |
+| `checksum`      | string   | SHA-256 checksum of the note file                                        |
 
 1. The format of the generated Markdown links can be customized in the [note format configuration](note-format.md).
 2. YAML keys are normalized to lower case.

docs/template.md

@@ -24,13 +24,39 @@ can generate (depending on the user config):
 
 The second parameter `title` is optional.
 
-### Date helper
+### String helpers
 
-The `{{date}}` helper formats the given date for display.
+There are a couple of template helpers operating on strings.
+
+#### Concat helper
+
+The `{{concat s1 s2}}` helper concatenates two strings together. For example `{{concat '> ' 'A quote'}}` produces `> A quote`.
+
+#### Substring helper
+
+* The `{{substring s index length}}` helper extracts a portion of the given string. For example:
+    * `{{substring 'A full quote' 2 4}}` outputs `full`
+    * `{{substring 'A full quote' -5 5}}` outputs `quote`
+
+### Date helpers
+
+#### Date from natural string helper
+
+You can get a date object from a natural human date (e.g. `tomorrow`, `2 weeks ago`, `2022-03-24`) using the `{{date}}` helper. It is most useful when paired with the `{{format-date}}` helper.
+
+```
+{{date "tomorrow"}}
+
+{{format-date (date "last week") "timestamp"}}
+```
+
+#### Date formatting helper
+
+The `{{format-date}}` helper formats the given date for display.
 
 Template contexts usually provide a `now` variable which can be used to print the current date.
 
-The default format output by `{{date <variable>}}` looks like `2009-11-17`, but you can choose a different format by providing a second argument, e.g. `{{date now "medium"}}`.
+The default format output by `{{format-date <variable>}}` looks like `2009-11-17`, but you can choose a different format by providing a second argument, e.g. `{{format-date now "medium"}}`.
 
 | Format           | Output                     | Notes                                            |
 |------------------|----------------------------|--------------------------------------------------|
@@ -44,7 +70,7 @@ The default format output by `{{date <variable>}}` looks like `2009-11-17`, but
 | `timestamp-unix` | 1258490098                 | Number of seconds since January 1, 1970          |
 | `elapsed`        | 12 years ago               | Time elapsed since then in human-friendly format |
 
-If none of the provided formats suit you, you can use a custom format using `strftime`-style placeholders, e.g. `{{date now "%m-%d-%Y"}}`. See `man strftime` for a list of placeholders.
+If none of the provided formats suit you, you can use a custom format using `strftime`-style placeholders, e.g. `{{format-date now "%m-%d-%Y"}}`. See `man strftime` for a list of placeholders.
 
 ### Slug helper
 
@@ -99,3 +125,17 @@ The `{{style}}` helper is mostly useful when formatting content for the command-
 {{#style 'underline'}}Another text{{/style}}
 ```
 
+### JSON helper
+
+The `{{json}}` helper serializes its argument to a JSON value. This is useful to generate valid JSON objects, for example:
+
+```
+{ "title": {{json title}}, "tags": {{json tags}} }
+->
+{ "title": "A \"quoted\" title", "tags": ["example", "json"] }
+```
+
+**Warning**: The template parser trips on `}}}`, so make sure to add an extra space before the third `}`.
+
+You can serialize the whole template context as a JSON object with `{{json .}}`, which is how `zk list --format json` produces its output.
+

docs/tool-fzf.md

@@ -4,7 +4,7 @@
 
 Besides the standard [`fzf` configuration options](https://github.com/junegunn/fzf) documented on its website, `zk` offers additional options you can set in the `[tool]` [configuration section](config.md).
 
-If you wish to customize more of `fzf` behavior, [please post a feature request](https://github.com/mickael-menu/zk/issues).
+If you wish to customize more of `fzf` behavior, [please post a feature request](https://github.com/zk-org/zk/issues).
 
 ## Preview command
 
@@ -23,3 +23,70 @@ Or, if you prefer to preview more metadata, you can use a nested `zk` command.
 [tool]
 fzf-preview = "zk list --quiet --format full --limit 1 {-1}"
 ```
+
+## Line format
+
+With the `fzf-line` setting property, you can provide your own [template](template.md) to customize the format of each `fzf` line. The lines are used by `fzf` for the fuzzy matching, so if you want to search in the full note content, do not forget to add `{{body}}` in your custom template.
+
+The default line template is `{{style "title" title-or-path}} {{style "understate" body}} {{style "understate" (json metadata)}}`.
+
+Here's an example using different colors and showing the list of tags as #hashtags:
+
+```toml
+[tool]
+fzf-line = "{{style 'blue' rel-path}}{{#each tags}} #{{this}}{{/each}} {{style 'black' body}}"
+```
+
+### Template context
+
+The following variables are available in the line template.
+
+| Variable        | Type     | Description                                                        |
+|-----------------|----------|--------------------------------------------------------------------|
+| `filename`      | string   | Filename of the note, including its extension                      |
+| `filename-stem` | string   | Filename of the note without the file extension                    |
+| `path`          | string   | File path to the note, relative to the notebook root               |
+| `abs-path`      | string   | Absolute file path to the note                                     |
+| `rel-path`      | string   | File path to the note, relative to the current directory           |
+| `title`         | string   | Note title                                                         |
+| `title-or-path` | string   | Note title or path if empty                                        |
+| `body`          | string   | All of the note content, minus the heading                         |
+| `raw-content`   | string   | The full raw content of the note file                              |
+| `word-count`    | int      | Number of words in the note                                        |
+| `tags`          | [string] | List of tags found in the note                                     |
+| `metadata`      | map      | YAML frontmatter metadata, e.g. `metadata.description`<sup>1</sup> |
+| `created`       | date     | Date of creation of the note                                       |
+| `modified`      | date     | Last date of modification of the note                              |
+| `checksum`      | string   | SHA-256 checksum of the note file                                  |
+
+1. YAML keys are normalized to lower case.
+
+
+## `fzf` options
+
+You can override the default `fzf` options used by `zk` with `fzf-options`. Look at `man fzf` for the list of available options.
+
+```toml
+[tool]
+fzf-options = "--height 40% --border"
+```
+
+Note that this overrides all the default options used by `zk`, you might want to keep some of them:
+
+* `--tiebreak begin` Prefer matches located at the beginning of the line
+* `--exact` Look for exact matches instead of fuzzy ones by default
+* `--tabstop 4` Length of tab characters
+* `--height 100%` Height of the list relative to the terminal window
+* `--layout reverse` Display the input field at the top
+* `--no-hscroll` Make sure the path and titles are always visible
+* `--color hl:-1,hl+:-1` Don't highlight search terms
+* `--preview-window wrap` Enable line wrapping in the preview window
+
+## Key bindings
+
+When running `fzf` with `zk edit --interactive`, you can [create a new note with the `Ctrl-E` key binding](note-creation.md#search-or-create-with-a-single-command). This binding is customizable with `fzf-bind-new`. You can also disable it by setting it to an empty string (`""`).
+
+```toml
+[tool]
+fzf-bind-new = "Ctrl-C"
+```

docs/tool-shell.md

@@ -0,0 +1,14 @@
+# Setting your default shell
+
+This is *currently* not supported on Windows (that defaults always to `cmd`).
+
+You can customize which shell to use to run aliases and commands either from the [configuration file](config.md) or environment variables. In order of precedence, `zk` will use:
+
+1. `ZK_SHELL` environment variable
+2. `shell` configuration property
+    ```toml
+    [tool]
+    shell = "/bin/bash"
+    ```
+3. `SHELL` environment variable
+4. `sh` as fallback

go

@@ -1,6 +0,0 @@
-#!/bin/bash
-
-VERSION=`git describe --tags --match v[0-9]* 2> /dev/null`
-BUILD=`git rev-parse --short HEAD`
-
-CGO_ENABLED=1 go $1 -tags "fts5 icu" -ldflags "-X=main.Version=$VERSION -X=main.Build=$BUILD" ${@:2}

go.mod

@@ -1,37 +1,54 @@
-module github.com/mickael-menu/zk
+module github.com/zk-org/zk
 
-go 1.15
-
-replace github.com/tliron/glsp => github.com/mickael-menu/glsp v0.1.0
+go 1.21
 
 require (
-	github.com/AlecAivazis/survey/v2 v2.2.12
-	github.com/alecthomas/kong v0.2.16-0.20210209082517-405b2f4fd9a4
+	github.com/AlecAivazis/survey/v2 v2.3.4
+	github.com/alecthomas/kong v0.5.0
 	github.com/aymerick/raymond v2.0.2+incompatible
-	github.com/fatih/color v1.10.0
-	github.com/go-testfixtures/testfixtures/v3 v3.4.1
-	github.com/google/go-cmp v0.5.2
-	github.com/gosimple/slug v1.9.0
+	github.com/bmatcuk/doublestar/v4 v4.0.2
+	github.com/fatih/color v1.13.0
+	github.com/go-testfixtures/testfixtures/v3 v3.6.1
+	github.com/google/go-cmp v0.5.8
+	github.com/gosimple/slug v1.12.0
 	github.com/kballard/go-shellquote v0.0.0-20180428030007-95032a82bc51
-	github.com/lestrrat-go/strftime v1.0.4
-	github.com/mattn/go-isatty v0.0.12
-	github.com/mattn/go-sqlite3 v1.14.6
-	github.com/mgutz/ansi v0.0.0-20200706080929-d51e80ef957d // indirect
-	github.com/mickael-menu/pretty v0.2.3
+	github.com/lestrrat-go/strftime v1.0.6
+	github.com/mattn/go-isatty v0.0.14
+	github.com/mattn/go-sqlite3 v1.14.22
 	github.com/mvdan/xurls v1.1.0
-	github.com/pelletier/go-toml v1.8.1
+	github.com/pelletier/go-toml v1.9.5
+	github.com/pkg/errors v0.9.1
 	github.com/relvacode/iso8601 v1.1.0
-	github.com/rogpeppe/go-internal v1.6.2 // indirect
 	github.com/rvflash/elapsed v0.2.0
-	github.com/schollz/progressbar/v3 v3.7.4
+	github.com/schollz/progressbar/v3 v3.8.6
 	github.com/tj/go-naturaldate v1.3.0
-	github.com/tliron/glsp v0.0.0-20210308190902-c7ec7df19257
-	github.com/tliron/kutil v0.1.22
-	github.com/yuin/goldmark v1.3.2
-	github.com/yuin/goldmark-meta v1.0.0
-	golang.org/x/crypto v0.0.0-20210421170649-83a5a9bb288b // indirect
-	golang.org/x/sys v0.0.0-20210423185535-09eb48e85fd7 // indirect
-	golang.org/x/term v0.0.0-20210422114643-f5beecf764ed // indirect
-	golang.org/x/text v0.3.6 // indirect
-	gopkg.in/djherbis/times.v1 v1.2.0
+	github.com/tliron/glsp v0.1.1
+	github.com/tliron/kutil v0.1.59
+	github.com/yuin/goldmark v1.4.12
+	github.com/yuin/goldmark-meta v1.1.0
+	github.com/zk-org/pretty v0.2.4
+	gopkg.in/djherbis/times.v1 v1.3.0
+)
+
+require (
+	github.com/gorilla/websocket v1.5.0 // indirect
+	github.com/gosimple/unidecode v1.0.1 // indirect
+	github.com/kr/pretty v0.3.0 // indirect
+	github.com/kr/text v0.2.0 // indirect
+	github.com/mattn/go-colorable v0.1.12 // indirect
+	github.com/mattn/go-runewidth v0.0.13 // indirect
+	github.com/mgutz/ansi v0.0.0-20200706080929-d51e80ef957d // indirect
+	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
+	github.com/petermattis/goid v0.0.0-20220526132513-07eaf5d0b9f4 // indirect
+	github.com/rivo/uniseg v0.2.0 // indirect
+	github.com/rogpeppe/go-internal v1.9.0 // indirect
+	github.com/sasha-s/go-deadlock v0.3.1 // indirect
+	github.com/sourcegraph/jsonrpc2 v0.1.0 // indirect
+	github.com/zchee/color/v2 v2.0.6 // indirect
+	golang.org/x/crypto v0.17.0 // indirect
+	golang.org/x/sys v0.15.0 // indirect
+	golang.org/x/term v0.15.0 // indirect
+	golang.org/x/text v0.14.0 // indirect
+	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
 )

go.sum

@@ -1,263 +1,49 @@
-cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
-cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
-cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
-cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
-cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
-cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To=
-cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4=
-cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M=
-cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
-cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
-cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
-cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE=
-cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc=
-cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
-cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
-cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk=
-cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
-cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
-cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
-cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
-cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos=
-cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk=
-dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
-github.com/AlecAivazis/survey/v2 v2.2.7 h1:5NbxkF4RSKmpywYdcRgUmos1o+roJY8duCLZXbVjoig=
-github.com/AlecAivazis/survey/v2 v2.2.7/go.mod h1:9DYvHgXtiXm6nCn+jXnOXLKbH+Yo9u8fAS/SduGdoPk=
-github.com/AlecAivazis/survey/v2 v2.2.12 h1:5a07y93zA6SZ09gOa9wLVLznF5zTJMQ+pJ3cZK4IuO8=
-github.com/AlecAivazis/survey/v2 v2.2.12/go.mod h1:6d4saEvBsfSHXeN1a5OA5m2+HJ2LuVokllnC77pAIKI=
-github.com/Azure/go-ansiterm v0.0.0-20170929234023-d6e3b3328b78/go.mod h1:LmzpDX56iTiv29bbRTIsUNlaFfuhWRQBWjQdVyAevI8=
-github.com/Azure/go-autorest v14.2.0+incompatible/go.mod h1:r+4oMnoxhatjLLJ6zxSWATqVooLgysK6ZNox3g/xq24=
-github.com/Azure/go-autorest/autorest v0.11.1/go.mod h1:JFgpikqFJ/MleTTxwepExTKnFUKKszPS8UavbQYUMuw=
-github.com/Azure/go-autorest/autorest/adal v0.9.0/go.mod h1:/c022QCutn2P7uY+/oQWWNcK9YU+MH96NgK+jErpbcg=
-github.com/Azure/go-autorest/autorest/adal v0.9.5/go.mod h1:B7KF7jKIeC9Mct5spmyCB/A8CG/sEz1vwIRGv/bbw7A=
-github.com/Azure/go-autorest/autorest/date v0.3.0/go.mod h1:BI0uouVdmngYNUzGWeSYnokU+TrmwEsOqdt8Y6sso74=
-github.com/Azure/go-autorest/autorest/mocks v0.4.0/go.mod h1:LTp+uSrOhSkaKrUy935gNZuuIPPVsHlr9DSOxSayd+k=
-github.com/Azure/go-autorest/autorest/mocks v0.4.1/go.mod h1:LTp+uSrOhSkaKrUy935gNZuuIPPVsHlr9DSOxSayd+k=
-github.com/Azure/go-autorest/logger v0.2.0/go.mod h1:T9E3cAhj2VqvPOtCYAvby9aBXkZmbF5NWuPV8+WeEW8=
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+gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
+gopkg.in/djherbis/times.v1 v1.3.0 h1:uxMS4iMtH6Pwsxog094W0FYldiNnfY/xba00vq6C2+o=
+gopkg.in/djherbis/times.v1 v1.3.0/go.mod h1:AQlg6unIsrsCEdQYhTzERy542dz6SFdQFZFv6mUY0P8=
 gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
-gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys=
 gopkg.in/inconshreveable/log15.v2 v2.0.0-20180818164646-67afb5ed74ec/go.mod h1:aPpfJ7XW+gOuirDoZ8gHhLh3kZ1B08FtV2bbmy7Jv3s=
-gopkg.in/inf.v0 v0.9.1/go.mod h1:cWUDdTG/fYaXco+Dcufb5Vnc6Gp2YChqWtbxRZE0mXw=
-gopkg.in/ini.v1 v1.51.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=
-gopkg.in/natefinch/lumberjack.v2 v2.0.0/go.mod h1:l0ndWWf7gzL7RNwBG7wST/UCcT4T24xpD6X8LsfU/+k=
-gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo=
-gopkg.in/square/go-jose.v2 v2.2.2/go.mod h1:M9dMgbHiYLoDGQrXy7OpJDJWiKiU//h+vD76mk0e1AI=
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 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
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 gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
 gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
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internal/adapter/editor/editor.go

@@ -6,10 +6,10 @@ import (
 	"strings"
 
 	"github.com/kballard/go-shellquote"
-	"github.com/mickael-menu/zk/internal/util/errors"
-	executil "github.com/mickael-menu/zk/internal/util/exec"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	osutil "github.com/mickael-menu/zk/internal/util/os"
+	"github.com/zk-org/zk/internal/util/errors"
+	executil "github.com/zk-org/zk/internal/util/exec"
+	"github.com/zk-org/zk/internal/util/opt"
+	osutil "github.com/zk-org/zk/internal/util/os"
 )
 
 // Editor represents an external editor able to edit the notes.
@@ -37,7 +37,7 @@ func (e *Editor) Open(paths ...string) error {
 	// /dev/tty is restored as stdin, in case the user used a pipe to feed
 	// initial note content to `zk new`. Without this, Vim doesn't work
 	// properly in this case.
-	// See https://github.com/mickael-menu/zk/issues/4
+	// See https://github.com/zk-org/zk/issues/4
 	cmd := executil.CommandFromString(e.editor + " " + shellquote.Join(paths...) + " </dev/tty")
 	cmd.Stdin = os.Stdin
 	cmd.Stdout = os.Stdout

internal/adapter/editor/editor_test.go

@@ -4,8 +4,8 @@ import (
 	"os"
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/util/opt"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/util/opt"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestEditorUsesZkEditorFirst(t *testing.T) {

internal/adapter/fs/fs.go

@@ -1,12 +1,11 @@
 package fs
 
 import (
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"strings"
 
-	"github.com/mickael-menu/zk/internal/util"
+	"github.com/zk-org/zk/internal/util"
 )
 
 // FileStorage implements the port core.FileStorage.
@@ -79,11 +78,7 @@ func (fs *FileStorage) FileExists(path string) (bool, error) {
 
 func (fs *FileStorage) DirExists(path string) (bool, error) {
 	fi, err := fs.fileInfo(path)
-	if err != nil {
-		return false, err
-	} else {
-		return fi != nil && (*fi).Mode().IsDir(), nil
-	}
+	return !os.IsNotExist(err) && fi != nil && (*fi).Mode().IsDir(), nil
 }
 
 func (fs *FileStorage) fileInfo(path string) (*os.FileInfo, error) {
@@ -118,7 +113,7 @@ func (fs *FileStorage) IsDescendantOf(dir string, path string) (bool, error) {
 }
 
 func (fs *FileStorage) Read(path string) ([]byte, error) {
-	return ioutil.ReadFile(path)
+	return os.ReadFile(path)
 }
 
 func (fs *FileStorage) Write(path string, content []byte) error {

internal/adapter/fzf/fzf.go

@@ -8,9 +8,10 @@ import (
 	"strings"
 	"sync"
 
-	"github.com/mickael-menu/zk/internal/util/errors"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	stringsutil "github.com/mickael-menu/zk/internal/util/strings"
+	"github.com/kballard/go-shellquote"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/opt"
+	stringsutil "github.com/zk-org/zk/internal/util/strings"
 )
 
 // ErrCancelled is returned when the user cancelled fzf.
@@ -26,6 +27,8 @@ var (
 type Opts struct {
 	// Preview command executed by fzf when hovering a line.
 	PreviewCmd opt.String
+	// Optionally provide additional arguments, taken from the config `fzf-options` property.
+	Options opt.String
 	// Amount of space between two non-empty fields.
 	Padding int
 	// Delimiter used by fzf between fields.
@@ -72,21 +75,18 @@ func New(opts Opts) (*Fzf, error) {
 		opts.Delimiter = "\x01"
 	}
 
+	// Hard-coded fzf options that are required by zk.
 	args := []string{
-		"--delimiter", opts.Delimiter,
-		"--tiebreak", "begin",
 		"--ansi",
-		"--exact",
-		"--tabstop", "4",
-		"--height", "100%",
-		"--layout", "reverse",
-		//"--info", "inline",
-		// Make sure the path and titles are always visible
-		"--no-hscroll",
-		// Don't highlight search terms
-		"--color", "hl:-1,hl+:-1",
-		"--preview-window", "wrap",
+		"--delimiter", opts.Delimiter,
+	}
+
+	// Additional options.
+	additionalArgs, err := shellquote.Split(opts.Options.String())
+	if err != nil {
+		return nil, errors.Wrapf(err, "can't split the fzf-options: %s", opts.Options.String())
 	}
+	args = append(args, additionalArgs...)
 
 	header := ""
 	binds := []string{}

internal/adapter/fzf/note_filter.go

@@ -4,18 +4,21 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
+	"time"
 
-	"github.com/mickael-menu/zk/internal/adapter/term"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	stringsutil "github.com/mickael-menu/zk/internal/util/strings"
+	"github.com/zk-org/zk/internal/adapter/term"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util/opt"
+	stringsutil "github.com/zk-org/zk/internal/util/strings"
 )
 
 // NoteFilter uses fzf to filter interactively a set of notes.
 type NoteFilter struct {
-	opts     NoteFilterOpts
-	fs       core.FileStorage
-	terminal *term.Terminal
+	opts           NoteFilterOpts
+	fs             core.FileStorage
+	terminal       *term.Terminal
+	templateLoader core.TemplateLoader
 }
 
 // NoteFilterOpts holds the configuration for the fzf notes filtering.
@@ -28,6 +31,12 @@ type NoteFilterOpts struct {
 	Interactive bool
 	// Indicates whether fzf is opened for every query, even if empty.
 	AlwaysFilter bool
+	// Format for a single line, taken from the config `fzf-line` property.
+	LineTemplate opt.String
+	// Optionally provide additional arguments, taken from the config `fzf-options` property.
+	FzfOptions opt.String
+	// Key binding for the new action.
+	NewBinding opt.String
 	// Preview command to run when selecting a note.
 	PreviewCmd opt.String
 	// When non null, a "create new note from query" binding will be added to
@@ -37,11 +46,12 @@ type NoteFilterOpts struct {
 	NotebookDir string
 }
 
-func NewNoteFilter(opts NoteFilterOpts, fs core.FileStorage, terminal *term.Terminal) *NoteFilter {
+func NewNoteFilter(opts NoteFilterOpts, fs core.FileStorage, terminal *term.Terminal, templateLoader core.TemplateLoader) *NoteFilter {
 	return &NoteFilter{
-		opts:     opts,
-		fs:       fs,
-		terminal: terminal,
+		opts:           opts,
+		fs:             fs,
+		terminal:       terminal,
+		templateLoader: templateLoader,
 	}
 }
 
@@ -55,9 +65,19 @@ func (f *NoteFilter) Apply(notes []core.ContextualNote) ([]core.ContextualNote,
 		return notes, nil
 	}
 
+	lineTemplate, err := f.templateLoader.LoadTemplate(f.opts.LineTemplate.OrString(defaultLineTemplate).String())
+	if err != nil {
+		return selectedNotes, err
+	}
+
 	for _, note := range notes {
-		absPaths = append(absPaths, filepath.Join(f.opts.NotebookDir, note.Path))
-		relPaths = append(relPaths, note.Path)
+		absPath := filepath.Join(f.opts.NotebookDir, note.Path)
+		absPaths = append(absPaths, absPath)
+		if relPath, err := f.fs.Rel(absPath); err == nil {
+			relPaths = append(relPaths, relPath)
+		} else {
+			relPaths = append(relPaths, note.Path)
+		}
 	}
 
 	zkBin, err := os.Executable()
@@ -73,16 +93,20 @@ func (f *NoteFilter) Apply(notes []core.ContextualNote) ([]core.ContextualNote,
 			suffix = " in " + dir.Name + "/"
 		}
 
-		bindings = append(bindings, Binding{
-			Keys:        "Ctrl-N",
-			Description: "create a note with the query as title" + suffix,
-			Action:      fmt.Sprintf("abort+execute(%s new %s --title {q} < /dev/tty > /dev/tty)", zkBin, dir.Path),
-		})
+		newBinding := f.opts.NewBinding.OrString("Ctrl-E").String()
+		if newBinding != "" {
+			bindings = append(bindings, Binding{
+				Keys:        newBinding,
+				Description: "create a note with the query as title" + suffix,
+				Action:      fmt.Sprintf(`abort+execute("%s" new "%s" --title {q} < /dev/tty > /dev/tty)`, zkBin, dir.Path),
+			})
+		}
 	}
 
 	previewCmd := f.opts.PreviewCmd.OrString("cat {-1}").Unwrap()
 
 	fzf, err := New(Opts{
+		Options:    f.opts.FzfOptions.OrString(defaultOptions),
 		PreviewCmd: opt.NewNotEmptyString(previewCmd),
 		Padding:    2,
 		Bindings:   bindings,
@@ -92,15 +116,36 @@ func (f *NoteFilter) Apply(notes []core.ContextualNote) ([]core.ContextualNote,
 	}
 
 	for i, note := range notes {
-		title := note.Title
-		if title == "" {
-			title = relPaths[i]
+		context := lineRenderContext{
+			Filename:     note.Filename(),
+			FilenameStem: note.FilenameStem(),
+			Path:         note.Path,
+			AbsPath:      absPaths[i],
+			RelPath:      relPaths[i],
+			Title:        note.Title,
+			TitleOrPath:  note.Title,
+			Body:         stringsutil.JoinLines(note.Body),
+			RawContent:   stringsutil.JoinLines(note.RawContent),
+			WordCount:    note.WordCount,
+			Tags:         note.Tags,
+			Metadata:     note.Metadata,
+			Created:      note.Created,
+			Modified:     note.Modified,
+			Checksum:     note.Checksum,
 		}
-		fzf.Add([]string{
-			f.terminal.MustStyle(title, core.StyleYellow),
-			f.terminal.MustStyle(stringsutil.JoinLines(note.Body), core.StyleUnderstate),
-			f.terminal.MustStyle(absPaths[i], core.StyleUnderstate),
-		})
+		if context.TitleOrPath == "" {
+			context.TitleOrPath = note.Path
+		}
+
+		line, err := lineTemplate.Render(context)
+		if err != nil {
+			return selectedNotes, err
+		}
+
+		// The absolute path is appended at the end of the line to be used in
+		// the preview command.
+		absPathField := f.terminal.MustStyle(context.AbsPath, core.StyleUnderstate)
+		fzf.Add([]string{line, absPathField})
 	}
 
 	selection, err := fzf.Selection()
@@ -119,3 +164,35 @@ func (f *NoteFilter) Apply(notes []core.ContextualNote) ([]core.ContextualNote,
 
 	return selectedNotes, nil
 }
+
+var defaultLineTemplate = `{{style "title" title-or-path}} {{style "understate" body}} {{style "understate" (json metadata)}}`
+
+// defaultOptions are the default fzf options used when filtering notes.
+var defaultOptions = strings.Join([]string{
+	"--tiebreak begin",      // Prefer matches located at the beginning of the line
+	"--exact",               // Look for exact matches instead of fuzzy ones by default
+	"--tabstop 4",           // Length of tab characters
+	"--height 100%",         // Height of the list relative to the terminal window
+	"--layout reverse",      // Display the input field at the top
+	"--no-hscroll",          // Make sure the path and titles are always visible
+	"--color hl:-1,hl+:-1",  // Don't highlight search terms
+	"--preview-window wrap", // Enable line wrapping in the preview window
+}, " ")
+
+type lineRenderContext struct {
+	Filename     string
+	FilenameStem string `handlebars:"filename-stem"`
+	Path         string
+	AbsPath      string `handlebars:"abs-path"`
+	RelPath      string `handlebars:"rel-path"`
+	Title        string
+	TitleOrPath  string `handlebars:"title-or-path"`
+	Body         string
+	RawContent   string `handlebars:"raw-content"`
+	WordCount    int    `handlebars:"word-count"`
+	Tags         []string
+	Metadata     map[string]interface{}
+	Created      time.Time
+	Modified     time.Time
+	Checksum     string
+}

internal/adapter/handlebars/handlebars.go

@@ -6,20 +6,23 @@ import (
 	"path/filepath"
 
 	"github.com/aymerick/raymond"
-	"github.com/mickael-menu/zk/internal/adapter/handlebars/helpers"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/errors"
-	"github.com/mickael-menu/zk/internal/util/paths"
+	"github.com/zk-org/zk/internal/adapter/handlebars/helpers"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/paths"
 )
 
 func Init(supportsUTF8 bool, logger util.Logger) {
 	helpers.RegisterConcat()
 	helpers.RegisterDate(logger)
+	helpers.RegisterFormatDate(logger)
 	helpers.RegisterJoin()
+	helpers.RegisterJSON(logger)
 	helpers.RegisterList(supportsUTF8)
 	helpers.RegisterPrepend(logger)
 	helpers.RegisterShell(logger)
+	helpers.RegisterSubstring()
 }
 
 // Template renders a parsed handlebars template.

internal/adapter/handlebars/handlebars_test.go

@@ -7,12 +7,12 @@ import (
 	"testing"
 	"time"
 
-	"github.com/mickael-menu/zk/internal/adapter/handlebars/helpers"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/fixtures"
-	"github.com/mickael-menu/zk/internal/util/paths"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/adapter/handlebars/helpers"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/fixtures"
+	"github.com/zk-org/zk/internal/util/paths"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func init() {
@@ -137,6 +137,14 @@ func TestConcatHelper(t *testing.T) {
 	testString(t, "{{concat '> ' 'A quote'}}", nil, "> A quote")
 }
 
+func TestSubstringHelper(t *testing.T) {
+	testString(t, "{{substring '' 2 4}}", nil, "")
+	testString(t, "{{substring 'A full quote' 2 4}}", nil, "full")
+	testString(t, "{{substring 'A full quote' 40 4}}", nil, "")
+	testString(t, "{{substring 'A full quote' -5 5}}", nil, "quote")
+	testString(t, "{{substring 'A full quote' -5 6}}", nil, "quote")
+}
+
 func TestJoinHelper(t *testing.T) {
 	test := func(items []string, expected string) {
 		context := map[string]interface{}{"items": items}
@@ -149,6 +157,28 @@ func TestJoinHelper(t *testing.T) {
 	test([]string{"Item 1", "Item 2", "Item 3"}, "Item 1-Item 2-Item 3")
 }
 
+type testJSONObject struct {
+	Foo     string
+	Missing string   `json:"missing,omitempty"`
+	List    []string `json:"stringList"`
+}
+
+func TestJSONHelper(t *testing.T) {
+	test := func(value interface{}, expected string) {
+		context := map[string]interface{}{"value": value}
+		testString(t, "{{json value}}", context, expected)
+	}
+
+	test(`foo"bar"`, `"foo\"bar\""`)
+	test([]string{"foo", "bar"}, `["foo","bar"]`)
+	test(map[string]string{"foo": "bar"}, `{"foo":"bar"}`)
+	test(map[string]string{"foo": "bar"}, `{"foo":"bar"}`)
+	test(testJSONObject{
+		Foo:  "baz",
+		List: []string{"foo", "bar"},
+	}, `{"Foo":"baz","stringList":["foo","bar"]}`)
+}
+
 func TestPrependHelper(t *testing.T) {
 	// inline
 	testString(t, "{{prepend '> ' 'A quote'}}", nil, "> A quote")
@@ -196,19 +226,131 @@ func TestSlugHelper(t *testing.T) {
 	)
 }
 
+func TestFormatDateHelper(t *testing.T) {
+	context := map[string]interface{}{"now": time.Date(2009, 11, 17, 20, 34, 58, 651387237, time.UTC)}
+	testString(t, "{{format-date now}}", context, "2009-11-17")
+	testString(t, "{{format-date now 'short'}}", context, "11/17/2009")
+	testString(t, "{{format-date now 'medium'}}", context, "Nov 17, 2009")
+	testString(t, "{{format-date now 'long'}}", context, "November 17, 2009")
+	testString(t, "{{format-date now 'full'}}", context, "Tuesday, November 17, 2009")
+	testString(t, "{{format-date now 'year'}}", context, "2009")
+	testString(t, "{{format-date now 'time'}}", context, "20:34")
+	testString(t, "{{format-date now 'timestamp'}}", context, "200911172034")
+	testString(t, "{{format-date now 'timestamp-unix'}}", context, "1258490098")
+	testString(t, "{{format-date now 'cust: %Y-%m'}}", context, "cust: 2009-11")
+}
+
+func TestFormatDateHelperElapsedYear(t *testing.T) {
+	year := time.Now().UTC().Year() - 14
+	context := map[string]interface{}{"now": time.Date(year, 11, 17, 20, 34, 58, 651387237, time.UTC)}
+	testString(t, "{{format-date now 'elapsed'}}", context, "14 years ago")
+}
+
+func TestFormatDateHelperElapsedViaTimeMultiplication(t *testing.T) {
+	// test for time being provided in via multiplications on seconds, minutes
+	// and hours, as expected by github.com/rvflash/elapsed
+	cases := []struct {
+		elapsed time.Duration
+		want    string
+	}{
+		{
+			elapsed: -12 * time.Second,
+			want:    "not yet",
+		},
+		{
+			elapsed: time.Second,
+			want:    "just now",
+		},
+		{
+			elapsed: 59 * time.Second,
+			want:    "just now",
+		},
+		{
+			elapsed: 60 * time.Second,
+			want:    "1 minute ago",
+		},
+		{
+			elapsed: 1 * time.Minute,
+			want:    "1 minute ago",
+		},
+		{
+			elapsed: 2 * time.Minute,
+			want:    "2 minutes ago",
+		},
+		{
+			elapsed: 62 * time.Minute,
+			want:    "1 hour ago",
+		},
+		{
+			elapsed: time.Hour,
+			want:    "1 hour ago",
+		},
+		{
+			elapsed: 2 * time.Hour,
+			want:    "2 hours ago",
+		},
+		{
+			elapsed: 24 * time.Hour,
+			want:    "yesterday",
+		},
+		{
+			elapsed: 4 * 24 * time.Hour,
+			want:    "4 days ago",
+		},
+		{
+			elapsed: 7 * 24 * time.Hour,
+			want:    "1 week ago",
+		},
+		{
+			elapsed: 8 * 24 * time.Hour,
+			want:    "2 weeks ago",
+		},
+		{
+			elapsed: 18 * 24 * time.Hour,
+			want:    "3 weeks ago",
+		},
+		{
+			elapsed: 30 * 24 * time.Hour,
+			want:    "1 month ago",
+		},
+		{
+			elapsed: 31 * 24 * time.Hour,
+			want:    "2 months ago",
+		},
+		{
+			elapsed: 60 * 24 * time.Hour,
+			want:    "2 months ago",
+		},
+		{
+			elapsed: 61 * 24 * time.Hour,
+			want:    "3 months ago",
+		},
+		{
+			elapsed: 330 * 24 * time.Hour,
+			want:    "11 months ago",
+		},
+		{
+			elapsed: 331 * 24 * time.Hour,
+			want:    "1 year ago",
+		},
+		{
+			elapsed: 366 * 24 * time.Hour,
+			want:    "2 years ago",
+		},
+	}
+
+	for i, tc := range cases {
+		t.Run(fmt.Sprintf("%d_%s", i, tc.want), func(t *testing.T) {
+			templateContext := map[string]interface{}{"now": time.Now().Add(-tc.elapsed)}
+
+			testString(t, "{{format-date now 'elapsed'}}", templateContext, tc.want)
+		})
+	}
+}
+
 func TestDateHelper(t *testing.T) {
 	context := map[string]interface{}{"now": time.Date(2009, 11, 17, 20, 34, 58, 651387237, time.UTC)}
-	testString(t, "{{date now}}", context, "2009-11-17")
-	testString(t, "{{date now 'short'}}", context, "11/17/2009")
-	testString(t, "{{date now 'medium'}}", context, "Nov 17, 2009")
-	testString(t, "{{date now 'long'}}", context, "November 17, 2009")
-	testString(t, "{{date now 'full'}}", context, "Tuesday, November 17, 2009")
-	testString(t, "{{date now 'year'}}", context, "2009")
-	testString(t, "{{date now 'time'}}", context, "20:34")
-	testString(t, "{{date now 'timestamp'}}", context, "200911172034")
-	testString(t, "{{date now 'timestamp-unix'}}", context, "1258490098")
-	testString(t, "{{date now 'cust: %Y-%m'}}", context, "cust: 2009-11")
-	testString(t, "{{date now 'elapsed'}}", context, "12 years ago")
+	testString(t, "{{format-date (date \"2009-11-17T20:34:58\") 'timestamp'}}", context, "200911172034")
 }
 
 func TestShellHelper(t *testing.T) {
@@ -251,8 +393,8 @@ func testLoader(opts LoaderOpts) *Loader {
 	loader.RegisterHelper("style", helpers.NewStyleHelper(opts.Styler, &util.NullLogger))
 	loader.RegisterHelper("slug", helpers.NewSlugHelper("en", &util.NullLogger))
 
-	formatter := func(path, title string) (string, error) {
-		return path + " - " + title, nil
+	formatter := func(context core.LinkFormatterContext) (string, error) {
+		return context.Path + " - " + context.Title, nil
 	}
 	loader.RegisterHelper("format-link", helpers.NewLinkHelper(formatter, &util.NullLogger))
 

internal/adapter/handlebars/helpers/date.go

@@ -1,24 +1,51 @@
 package helpers
 
 import (
+	"os"
 	"time"
 
 	"github.com/aymerick/raymond"
 	"github.com/lestrrat-go/strftime"
-	"github.com/mickael-menu/zk/internal/util"
+	"github.com/zk-org/zk/internal/util"
+	dateutil "github.com/zk-org/zk/internal/util/date"
+	"github.com/pkg/errors"
 	"github.com/rvflash/elapsed"
 )
 
-// RegisterDate registers the {{date}} template helpers which format a given date.
+// RegisterDate registers the {{date}} template helper to use the `naturaldate` package to generate time.Time based on language strings.
+// This can be used in combination with the `format-date` helper to generate dates in the user's language.
+// {{format-date (date "last week") "timestamp"}}
+func RegisterDate(logger util.Logger) {
+	raymond.RegisterHelper("date", func(arg1 interface{}, arg2 interface{}) time.Time {
+		var t time.Time
+		switch date := arg1.(type) {
+		case string:
+			t, err := dateutil.TimeFromNatural(date)
+			if err != nil {
+				logger.Err(errors.Wrap(err, "the {{date}} template helper failed to parse the date"))
+			}
+			return t
+		case time.Time:
+			logger.Println("the {{date}} template helper was renamed to {{format-date}}, please update your configuration")
+			os.Exit(1)
+			return t
+		default:
+			logger.Println("the {{date}} template helper expects a natural human date as a string for its only argument")
+			return t
+		}
+	})
+}
+
+// RegisterFormatDate registers the {{format-date}} template helpers which format a given date.
 //
 // It supports various styles: short, medium, long, full, year, time,
 // timestamp, timestamp-unix or a custom strftime format.
 //
-// {{date now}} -> 2009-11-17
-// {{date now "medium"}} -> Nov 17, 2009
-// {{date now "%Y-%m"}} -> 2009-11
-func RegisterDate(logger util.Logger) {
-	raymond.RegisterHelper("date", func(date time.Time, arg interface{}) string {
+// {{format-date now}} -> 2009-11-17
+// {{format-date now "medium"}} -> Nov 17, 2009
+// {{format-date now "%Y-%m"}} -> 2009-11
+func RegisterFormatDate(logger util.Logger) {
+	raymond.RegisterHelper("format-date", func(date time.Time, arg interface{}) string {
 		format := "%Y-%m-%d"
 
 		if arg, ok := arg.(string); ok {
@@ -31,7 +58,7 @@ func RegisterDate(logger util.Logger) {
 		} else {
 			res, err := strftime.Format(format, date, strftime.WithUnixSeconds('s'))
 			if err != nil {
-				logger.Printf("the {{date}} template helper failed to format the date: %v", err)
+				logger.Printf("the {{format-date}} template helper failed to format the date: %v", err)
 				return ""
 			}
 			return res

internal/adapter/handlebars/helpers/json.go

@@ -0,0 +1,22 @@
+package helpers
+
+import (
+	"encoding/json"
+
+	"github.com/aymerick/raymond"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+)
+
+// RegisterJSON registers a {{json}} template helper which serializes its
+// parameter to a JSON value.
+func RegisterJSON(logger util.Logger) {
+	raymond.RegisterHelper("json", func(arg interface{}) string {
+		jsonBytes, err := json.Marshal(arg)
+		if err != nil {
+			logger.Err(errors.Wrapf(err, "%v: not a serializable argument for {{json}}", arg))
+			return ""
+		}
+		return string(jsonBytes)
+	})
+}

internal/adapter/handlebars/helpers/link.go

@@ -1,20 +1,26 @@
 package helpers
 
 import (
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
 )
 
 // NewLinkHelper creates a new template helper to generate an internal link
 // using a LinkFormatter.
 //
-// {{link "path/to/note.md" "An interesting subject"}} -> (depends on the LinkFormatter)
+// {{format-link "path/to/note.md" "An interesting subject"}} -> (depends on the LinkFormatter)
 //   [[path/to/note]]
 //   [An interesting subject](path/to/note)
 func NewLinkHelper(formatter core.LinkFormatter, logger util.Logger) interface{} {
 	return func(path string, opt interface{}) string {
 		title, _ := opt.(string)
-		link, err := formatter(path, title)
+		link, err := formatter(core.LinkFormatterContext{
+			Path:     path,
+			RelPath:  path,
+			AbsPath:  path,
+			Title:    title,
+			Metadata: map[string]interface{}{},
+		})
 		if err != nil {
 			logger.Err(err)
 			return ""

internal/adapter/handlebars/helpers/prepend.go

@@ -2,8 +2,8 @@ package helpers
 
 import (
 	"github.com/aymerick/raymond"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/strings"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/strings"
 )
 
 // RegisterPrepend registers a {{prepend}} template helper which prepend a

internal/adapter/handlebars/helpers/shell.go

@@ -4,8 +4,8 @@ import (
 	"strings"
 
 	"github.com/aymerick/raymond"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/exec"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/exec"
 )
 
 // RegisterShell registers the {{sh}} template helper, which runs shell commands.

internal/adapter/handlebars/helpers/slug.go

@@ -3,7 +3,7 @@ package helpers
 import (
 	"github.com/aymerick/raymond"
 	"github.com/gosimple/slug"
-	"github.com/mickael-menu/zk/internal/util"
+	"github.com/zk-org/zk/internal/util"
 )
 
 // NewSlugHelper creates a new template helper to slugify text.

internal/adapter/handlebars/helpers/style.go

@@ -4,8 +4,8 @@ import (
 	"strings"
 
 	"github.com/aymerick/raymond"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
 )
 
 // NewStyleHelper creates a new template helper which stylizes the text input

internal/adapter/handlebars/helpers/substring.go

@@ -0,0 +1,31 @@
+package helpers
+
+import (
+	"github.com/aymerick/raymond"
+)
+
+// RegisterSubstring registers a {{substring}} template helper which extracts a
+// substring given a starting index and a length.
+//
+// {{substring 'A full quote' 2 4}} -> "full"
+// {{substring 'A full quote' -5 5}} -> "quote"
+//
+func RegisterSubstring() {
+	raymond.RegisterHelper("substring", func(str string, index int, length int) string {
+		if index < 0 {
+			index = len(str) + index
+		}
+		if index >= len(str) {
+			return ""
+		}
+		end := min(index+length, len(str))
+		return str[index:end]
+	})
+}
+
+func min(a, b int) int {
+	if a < b {
+		return a
+	}
+	return b
+}

internal/adapter/lsp/cmd_index.go

@@ -0,0 +1,27 @@
+package lsp
+
+import (
+	"fmt"
+
+	"github.com/zk-org/zk/internal/core"
+)
+
+const cmdIndex = "zk.index"
+
+func executeCommandIndex(notebook *core.Notebook, args []interface{}) (interface{}, error) {
+	opts := core.NoteIndexOpts{}
+	if len(args) == 2 {
+		options, ok := args[1].(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("zk.index expects a dictionary of options as second argument, got: %v", args[1])
+		}
+		if forceOption, ok := options["force"]; ok {
+			opts.Force = toBool(forceOption)
+		}
+		if verboseOption, ok := options["verbose"]; ok {
+			opts.Verbose = toBool(verboseOption)
+		}
+	}
+
+	return notebook.Index(opts)
+}

internal/adapter/lsp/cmd_link.go

@@ -0,0 +1,64 @@
+package lsp
+
+import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/tliron/glsp"
+	protocol "github.com/tliron/glsp/protocol_3_16"
+)
+
+const cmdLink = "zk.link"
+
+type cmdLinkOpts struct {
+	Path     *string            `json:"path"`
+	Location *protocol.Location `json:"location"`
+	Title    *string            `json:"title"`
+}
+
+func executeCommandLink(notebook *core.Notebook, documents *documentStore, context *glsp.Context, args []interface{}) (interface{}, error) {
+	var opts cmdLinkOpts
+
+	if len(args) > 1 {
+		arg, ok := args[1].(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("%s expects a dictionary of options as second argument, got: %v", cmdLink, args[1])
+		}
+		err := unmarshalJSON(arg, &opts)
+		if err != nil {
+			return nil, errors.Wrapf(err, "failed to parse %s args, got: %v", cmdLink, arg)
+		}
+	}
+
+	if opts.Path == nil {
+		return nil, errors.New("'path' not provided")
+	}
+
+	note, err := notebook.FindByHref(*opts.Path, false)
+
+	if err != nil {
+		return nil, err
+	}
+
+	if note == nil {
+		return nil, errors.New("Requested note to link to not found!")
+	}
+
+	info := &linkInfo{
+		note:     note,
+		location: opts.Location,
+		title:    opts.Title,
+	}
+
+    err = linkNote(notebook, documents, context, info)
+
+    if err != nil {
+        return nil, err
+    }
+
+	return map[string]interface{}{
+		"path": filepath.Join(notebook.Path, note.Path),
+	}, nil
+}

internal/adapter/lsp/cmd_list.go

@@ -0,0 +1,162 @@
+package lsp
+
+import (
+	"fmt"
+	"path/filepath"
+	"time"
+
+	"github.com/zk-org/zk/internal/cli"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	strutil "github.com/zk-org/zk/internal/util/strings"
+)
+
+const cmdList = "zk.list"
+
+type cmdListOpts struct {
+	Select []string `json:"select"`
+	cli.Filtering
+}
+
+func executeCommandList(logger util.Logger, notebook *core.Notebook, args []interface{}) (interface{}, error) {
+	var opts cmdListOpts
+	if len(args) > 1 {
+		arg, ok := args[1].(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("%s expects a dictionary of options as second argument, got: %v", cmdTagList, args[1])
+		}
+		err := unmarshalJSON(arg, &opts)
+		if err != nil {
+			return nil, errors.Wrapf(err, "failed to parse %s args, got: %v", cmdTagList, arg)
+		}
+	}
+
+	if len(opts.Select) == 0 {
+		return nil, fmt.Errorf("%s expects a `select` option with the list of fields to return", cmdTagList)
+	}
+	var selection = newListSelection(opts.Select)
+
+	findOpts, err := opts.NewNoteFindOpts(notebook)
+	if err != nil {
+		return nil, err
+	}
+
+	notes, err := notebook.FindNotes(findOpts)
+	if err != nil {
+		return nil, err
+	}
+
+	listNotes := []listNote{}
+	for _, note := range notes {
+		listNotes = append(listNotes, newListNote(note, selection, notebook.Path))
+	}
+
+	return listNotes, nil
+}
+
+type listSelection struct {
+	Filename     bool
+	FilenameStem bool
+	Path         bool
+	AbsPath      bool
+	Title        bool
+	Lead         bool
+	Body         bool
+	Snippets     bool
+	RawContent   bool
+	WordCount    bool
+	Tags         bool
+	Metadata     bool
+	Created      bool
+	Modified     bool
+	Checksum     bool
+}
+
+func newListSelection(fields []string) listSelection {
+	return listSelection{
+		Filename:     strutil.Contains(fields, "filename"),
+		FilenameStem: strutil.Contains(fields, "filenameStem"),
+		Path:         strutil.Contains(fields, "path"),
+		AbsPath:      strutil.Contains(fields, "absPath"),
+		Title:        strutil.Contains(fields, "title"),
+		Lead:         strutil.Contains(fields, "lead"),
+		Body:         strutil.Contains(fields, "body"),
+		Snippets:     strutil.Contains(fields, "snippets"),
+		RawContent:   strutil.Contains(fields, "rawContent"),
+		WordCount:    strutil.Contains(fields, "wordCount"),
+		Tags:         strutil.Contains(fields, "tags"),
+		Metadata:     strutil.Contains(fields, "metadata"),
+		Created:      strutil.Contains(fields, "created"),
+		Modified:     strutil.Contains(fields, "modified"),
+		Checksum:     strutil.Contains(fields, "checksum"),
+	}
+}
+
+func newListNote(note core.ContextualNote, selection listSelection, basePath string) listNote {
+	var res listNote
+	if selection.Filename {
+		res.Filename = note.Filename()
+	}
+	if selection.FilenameStem {
+		res.FilenameStem = note.FilenameStem()
+	}
+	if selection.Path {
+		res.Path = note.Path
+	}
+	if selection.AbsPath {
+		res.AbsPath = filepath.Join(basePath, note.Path)
+	}
+	if selection.Title {
+		res.Title = note.Title
+	}
+	if selection.Lead {
+		res.Lead = note.Lead
+	}
+	if selection.Body {
+		res.Body = note.Body
+	}
+	if selection.Snippets {
+		res.Snippets = note.Snippets
+	}
+	if selection.RawContent {
+		res.RawContent = note.RawContent
+	}
+	if selection.WordCount {
+		res.WordCount = note.WordCount
+	}
+	if selection.Tags {
+		res.Tags = note.Tags
+	}
+	if selection.Metadata {
+		res.Metadata = note.Metadata
+	}
+	if selection.Created {
+		res.Created = &note.Created
+	}
+	if selection.Modified {
+		res.Modified = &note.Modified
+	}
+	if selection.Checksum {
+		res.Checksum = note.Checksum
+	}
+	return res
+}
+
+type listNote struct {
+	Filename     string                 `json:"filename,omitempty"`
+	FilenameStem string                 `json:"filenameStem,omitempty"`
+	Path         string                 `json:"path,omitempty"`
+	AbsPath      string                 `json:"absPath,omitempty"`
+	Title        string                 `json:"title,omitempty"`
+	Lead         string                 `json:"lead,omitempty"`
+	Body         string                 `json:"body,omitempty"`
+	Snippets     []string               `json:"snippets,omitempty"`
+	RawContent   string                 `json:"rawContent,omitempty"`
+	WordCount    int                    `json:"wordCount,omitempty"`
+	Tags         []string               `json:"tags,omitempty"`
+	Metadata     map[string]interface{} `json:"metadata,omitempty"`
+	Created      *time.Time             `json:"created,omitempty"`
+	Modified     *time.Time             `json:"modified,omitempty"`
+	Checksum     string                 `json:"checksum,omitempty"`
+}

internal/adapter/lsp/cmd_new.go

@@ -0,0 +1,112 @@
+package lsp
+
+import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/zk-org/zk/internal/core"
+	dateutil "github.com/zk-org/zk/internal/util/date"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/opt"
+	"github.com/tliron/glsp"
+	protocol "github.com/tliron/glsp/protocol_3_16"
+)
+
+const cmdNew = "zk.new"
+
+type cmdNewOpts struct {
+	Title                   string             `json:"title"`
+	Content                 string             `json:"content"`
+	Dir                     string             `json:"dir"`
+	Group                   string             `json:"group"`
+	Template                string             `json:"template"`
+	Extra                   map[string]string  `json:"extra"`
+	Date                    string             `json:"date"`
+	Edit                    jsonBoolean        `json:"edit"`
+	DryRun                  jsonBoolean        `json:"dryRun"`
+	InsertLinkAtLocation    *protocol.Location `json:"insertLinkAtLocation"`
+	InsertContentAtLocation *protocol.Location `json:"insertContentAtLocation"`
+}
+
+func executeCommandNew(notebook *core.Notebook, documents *documentStore, context *glsp.Context, args []interface{}) (interface{}, error) {
+	var opts cmdNewOpts
+	if len(args) > 1 {
+		arg, ok := args[1].(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("%s expects a dictionary of options as second argument, got: %v", cmdNew, args[1])
+		}
+		err := unmarshalJSON(arg, &opts)
+		if err != nil {
+			return nil, errors.Wrapf(err, "failed to parse %s args, got: %v", cmdNew, arg)
+		}
+	}
+
+	date, err := dateutil.TimeFromNatural(opts.Date)
+	if err != nil {
+		return nil, errors.Wrapf(err, "%s, failed to parse the `date` option", opts.Date)
+	}
+
+	note, err := notebook.NewNote(core.NewNoteOpts{
+		Title:     opt.NewNotEmptyString(opts.Title),
+		Content:   opts.Content,
+		Directory: opt.NewNotEmptyString(opts.Dir),
+		Group:     opt.NewNotEmptyString(opts.Group),
+		Template:  opt.NewNotEmptyString(opts.Template),
+		Extra:     opts.Extra,
+		DryRun:    bool(opts.DryRun),
+		Date:      date,
+	})
+	if err != nil {
+		var noteExists core.ErrNoteExists
+		if !errors.As(err, &noteExists) {
+			return nil, err
+		}
+		note, err = notebook.FindNote(core.NoteFindOpts{
+			IncludeHrefs: []string{noteExists.Name},
+		})
+		if err != nil {
+			return nil, err
+		}
+	}
+	if note == nil {
+		return nil, errors.New("zk.new could not generate a new note")
+	}
+
+	if opts.InsertContentAtLocation != nil {
+		go context.Call(protocol.ServerWorkspaceApplyEdit, protocol.ApplyWorkspaceEditParams{
+			Edit: protocol.WorkspaceEdit{
+				Changes: map[string][]protocol.TextEdit{
+					opts.InsertContentAtLocation.URI: {{Range: opts.InsertContentAtLocation.Range, NewText: note.RawContent}},
+				},
+			},
+		}, nil)
+	}
+
+	if !opts.DryRun && opts.InsertLinkAtLocation != nil {
+        minNote := note.AsMinimalNote()
+
+        info := &linkInfo{
+            note: &minNote,
+            location: opts.InsertLinkAtLocation,
+            title: &opts.Title,
+        }
+        err := linkNote(notebook, documents, context, info)
+
+        if err != nil {
+            return nil, err
+        }
+	}
+
+	absPath := filepath.Join(notebook.Path, note.Path)
+	if !opts.DryRun && opts.Edit {
+		go context.Call(protocol.ServerWindowShowDocument, protocol.ShowDocumentParams{
+			URI:       pathToURI(absPath),
+			TakeFocus: boolPtr(true),
+		}, nil)
+	}
+
+	return map[string]interface{}{
+		"path":    absPath,
+		"content": note.RawContent,
+	}, nil
+}

internal/adapter/lsp/cmd_tag.go

@@ -0,0 +1,39 @@
+package lsp
+
+import (
+	"fmt"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+)
+
+const cmdTagList = "zk.tag.list"
+
+type cmdTagListOpts struct {
+	Sort []string `json:"sort"`
+}
+
+func executeCommandTagList(logger util.Logger, notebook *core.Notebook, args []interface{}) (interface{}, error) {
+	var opts cmdTagListOpts
+	if len(args) > 1 {
+		arg, ok := args[1].(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("%s expects a dictionary of options as second argument, got: %v", cmdTagList, args[1])
+		}
+		err := unmarshalJSON(arg, &opts)
+		if err != nil {
+			return nil, errors.Wrapf(err, "failed to parse %s args, got: %v", cmdTagList, arg)
+		}
+	}
+
+	var sorters []core.CollectionSorter
+	var err error
+	if opts.Sort != nil {
+		sorters, err = core.CollectionSortersFromStrings(opts.Sort)
+		if err != nil {
+			return nil, err
+		}
+	}
+	return notebook.FindCollections(core.CollectionKindTag, sorters)
+}

internal/adapter/lsp/completion.go

@@ -0,0 +1,66 @@
+package lsp
+
+import (
+	"path/filepath"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util/paths"
+)
+
+// completionTemplates holds templates to render the various elements of an LSP
+// completion item.
+type completionTemplates struct {
+	Label      core.Template
+	FilterText core.Template
+	Detail     core.Template
+}
+
+func newCompletionTemplates(loader core.TemplateLoader, templates core.LSPCompletionTemplates) (result completionTemplates, err error) {
+	if !templates.Label.IsNull() {
+		result.Label, err = loader.LoadTemplate(*templates.Label.Value)
+	}
+	if !templates.FilterText.IsNull() {
+		result.FilterText, err = loader.LoadTemplate(*templates.FilterText.Value)
+	}
+	if !templates.Detail.IsNull() {
+		result.Detail, err = loader.LoadTemplate(*templates.Detail.Value)
+	}
+
+	return
+}
+
+type completionItemRenderContext struct {
+	ID           int64
+	Filename     string
+	FilenameStem string `handlebars:"filename-stem"`
+	Path         string
+	AbsPath      string `handlebars:"abs-path"`
+	RelPath      string `handlebars:"rel-path"`
+	Title        string
+	TitleOrPath  string `handlebars:"title-or-path"`
+	Metadata     map[string]interface{}
+}
+
+func newCompletionItemRenderContext(note core.MinimalNote, notebookDir string, currentDir string) (completionItemRenderContext, error) {
+	absPath := filepath.Join(notebookDir, note.Path)
+	relPath, err := filepath.Rel(currentDir, absPath)
+	if err != nil {
+		return completionItemRenderContext{}, err
+	}
+
+	context := completionItemRenderContext{
+		ID:           int64(note.ID),
+		Filename:     filepath.Base(note.Path),
+		FilenameStem: paths.FilenameStem(note.Path),
+		Path:         note.Path,
+		AbsPath:      absPath,
+		RelPath:      relPath,
+		Title:        note.Title,
+		TitleOrPath:  note.Title,
+		Metadata:     note.Metadata,
+	}
+	if context.TitleOrPath == "" {
+		context.TitleOrPath = note.Path
+	}
+	return context, nil
+}

internal/adapter/lsp/document.go

@@ -2,19 +2,83 @@ package lsp
 
 import (
 	"net/url"
+	"path/filepath"
 	"regexp"
 	"strings"
+	"unicode/utf16"
 
+	"github.com/tliron/glsp"
 	protocol "github.com/tliron/glsp/protocol_3_16"
-	"github.com/tliron/kutil/logging"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	strutil "github.com/zk-org/zk/internal/util/strings"
 )
 
+// documentStore holds opened documents.
+type documentStore struct {
+	documents map[string]*document
+	fs        core.FileStorage
+	logger    util.Logger
+}
+
+func newDocumentStore(fs core.FileStorage, logger util.Logger) *documentStore {
+	return &documentStore{
+		documents: map[string]*document{},
+		fs:        fs,
+		logger:    logger,
+	}
+}
+
+func (s *documentStore) DidOpen(params protocol.DidOpenTextDocumentParams, notify glsp.NotifyFunc) (*document, error) {
+	langID := params.TextDocument.LanguageID
+	if langID != "markdown" && langID != "vimwiki" && langID != "pandoc" {
+		return nil, nil
+	}
+
+	uri := params.TextDocument.URI
+	path, err := s.normalizePath(uri)
+	if err != nil {
+		return nil, err
+	}
+	doc := &document{
+		URI:     uri,
+		Path:    path,
+		Content: params.TextDocument.Text,
+	}
+	s.documents[path] = doc
+	return doc, nil
+}
+
+func (s *documentStore) Close(uri protocol.DocumentUri) {
+	delete(s.documents, uri)
+}
+
+func (s *documentStore) Get(pathOrURI string) (*document, bool) {
+	path, err := s.normalizePath(pathOrURI)
+	if err != nil {
+		s.logger.Err(err)
+		return nil, false
+	}
+	d, ok := s.documents[path]
+	return d, ok
+}
+
+func (s *documentStore) normalizePath(pathOrUri string) (string, error) {
+	path, err := uriToPath(pathOrUri)
+	if err != nil {
+		return "", errors.Wrapf(err, "unable to parse URI: %s", pathOrUri)
+	}
+	return s.fs.Canonical(path), nil
+}
+
 // document represents an opened file.
 type document struct {
-	Path    string
-	Content string
-	Log     logging.Logger
-	lines   []string
+	URI                     protocol.DocumentUri
+	Path                    string
+	NeedsRefreshDiagnostics bool
+	Content                 string
+	lines                   []string
 }
 
 // ApplyChanges updates the content of the document from LSP textDocument/didChange events.
@@ -32,25 +96,19 @@ func (d *document) ApplyChanges(changes []interface{}) {
 	d.lines = nil
 }
 
-var nonEmptyString = regexp.MustCompile(`\S+`)
-
 // WordAt returns the word found at the given location.
-// Credit https://github.com/aca/neuron-language-server/blob/450a7cff71c14e291ee85ff8a0614fa9d4dd5145/utils.go#L13
 func (d *document) WordAt(pos protocol.Position) string {
 	line, ok := d.GetLine(int(pos.Line))
 	if !ok {
 		return ""
 	}
+	return strutil.WordAt(line, int(pos.Character))
+}
 
-	charIdx := int(pos.Character)
-	wordIdxs := nonEmptyString.FindAllStringIndex(line, -1)
-	for _, wordIdx := range wordIdxs {
-		if wordIdx[0] <= charIdx && charIdx <= wordIdx[1] {
-			return line[wordIdx[0]:wordIdx[1]]
-		}
-	}
-
-	return ""
+// ContentAtRange returns the document text at given range.
+func (d *document) ContentAtRange(rng protocol.Range) string {
+	startIndex, endIndex := rng.IndexesIn(d.Content)
+	return d.Content[startIndex:endIndex]
 }
 
 // GetLine returns the line at the given index.
@@ -74,34 +132,46 @@ func (d *document) GetLines() []string {
 // LookBehind returns the n characters before the given position, on the same line.
 func (d *document) LookBehind(pos protocol.Position, length int) string {
 	line, ok := d.GetLine(int(pos.Line))
+	utf16Bytes := utf16.Encode([]rune(line))
 	if !ok {
 		return ""
 	}
 
 	charIdx := int(pos.Character)
 	if length > charIdx {
-		return line[0:charIdx]
+		return string(utf16.Decode(utf16Bytes[0:charIdx]))
 	}
-	return line[(charIdx - length):charIdx]
+	return string(utf16.Decode(utf16Bytes[(charIdx - length):charIdx]))
 }
 
 // LookForward returns the n characters after the given position, on the same line.
 func (d *document) LookForward(pos protocol.Position, length int) string {
 	line, ok := d.GetLine(int(pos.Line))
+	utf16Bytes := utf16.Encode([]rune(line))
 	if !ok {
 		return ""
 	}
 
-	lineLength := len(line)
+	lineLength := len(utf16Bytes)
 	charIdx := int(pos.Character)
 	if lineLength <= charIdx+length {
-		return line[charIdx:]
+		return string(utf16.Decode(utf16Bytes[charIdx:]))
 	}
-	return line[charIdx:(charIdx + length)]
+	return string(utf16.Decode(utf16Bytes[charIdx:(charIdx + length)]))
 }
 
-var wikiLinkRegex = regexp.MustCompile(`\[?\[\[(.+?)(?:\|(.+?))?\]\]`)
-var markdownLinkRegex = regexp.MustCompile(`\[([^\]]+?[^\\])\]\((.+?[^\\])\)`)
+// LinkFromRoot returns a Link to this document from the root of the given
+// notebook.
+func (d *document) LinkFromRoot(nb *core.Notebook) (*documentLink, error) {
+	href, err := nb.RelPath(d.Path)
+	if err != nil {
+		return nil, err
+	}
+	return &documentLink{
+		Href:          href,
+		RelativeToDir: nb.Path,
+	}, nil
+}
 
 // DocumentLinkAt returns the internal or external link found in the document
 // at the given position.
@@ -120,6 +190,66 @@ func (d *document) DocumentLinkAt(pos protocol.Position) (*documentLink, error)
 	return nil, nil
 }
 
+// Recursive function to check whether a link is within inline code.
+func linkWithinInlineCode(strBuffer string, linkStart, linkEnd int, insideInline bool) bool {
+	if backtickId := strings.Index(strBuffer, "`"); backtickId >= 0 && backtickId < linkEnd {
+		return linkWithinInlineCode(strBuffer[backtickId+1:],
+			linkStart-backtickId-1, linkEnd-backtickId-1, !insideInline)
+	} else {
+		return insideInline
+	}
+}
+
+var wikiLinkRegex = regexp.MustCompile(`\[?\[\[(.+?)(?: *\| *(.+?))?\]\]`)
+var markdownLinkRegex = regexp.MustCompile(`\[([^\]]+?[^\\])\]\((.+?[^\\])\)`)
+var fileURIregex = regexp.MustCompile(`file:///`)
+var fencedStartRegex = regexp.MustCompile(`^(` + "```" + `|~~~).*`)
+var fencedEndRegex = regexp.MustCompile(`^(` + "```" + `|~~~)\s*`)
+var indentedRegex = regexp.MustCompile(`^(\s{4}|\t).+`)
+
+var insideInline = false
+var insideFenced = false
+var insideIndented = false
+var currentCodeBlockStart = -1
+
+// check whether the current line in document is within a fenced or indented 
+// code block
+func isLineWithinCodeBlock(lines []string, lineIndex int, line string) bool {
+    // if line is already within code fences or indented code block
+	if insideFenced {
+		if fencedEndRegex.FindStringIndex(line) != nil &&
+			lines[currentCodeBlockStart][:3] == line[:3] {
+			// Fenced code block ends with this line
+			insideFenced = false
+			currentCodeBlockStart = -1
+		}
+		return true
+	} else if insideIndented {
+		if indentedRegex.FindStringIndex(line) == nil && len(line) > 0 {
+			// Indeted code block ends with this line
+			insideIndented = false
+			currentCodeBlockStart = -1
+		} else {
+			return true
+		}
+	} else {
+		// Check whether the current line is the start of a code fence or
+		// indented code block
+		if fencedStartRegex.FindStringIndex(line) != nil {
+			insideFenced = true
+			currentCodeBlockStart = lineIndex
+			return true
+		} else if indentedRegex.FindStringIndex(line) != nil &&
+			(lineIndex > 0 && len(lines[lineIndex-1]) == 0 || lineIndex == 0) {
+			insideIndented = true
+			currentCodeBlockStart = lineIndex
+			return true
+		}
+	}
+	return false
+
+}
+
 // DocumentLinks returns all the internal and external links found in the
 // document.
 func (d *document) DocumentLinks() ([]documentLink, error) {
@@ -128,13 +258,22 @@ func (d *document) DocumentLinks() ([]documentLink, error) {
 	lines := d.GetLines()
 	for lineIndex, line := range lines {
 
-		appendLink := func(href string, start, end int) {
+		if isLineWithinCodeBlock(lines, lineIndex, line) {
+			continue
+		}
+
+		appendLink := func(href string, start, end int, hasTitle bool, isWikiLink bool) {
 			if href == "" {
 				return
 			}
 
+			// Go regexes work with bytes, but the LSP client expects character indexes.
+			start = strutil.ByteIndexToRuneIndex(line, start)
+			end = strutil.ByteIndexToRuneIndex(line, end)
+
 			links = append(links, documentLink{
-				Href: href,
+				Href:          href,
+				RelativeToDir: filepath.Dir(d.Path),
 				Range: protocol.Range{
 					Start: protocol.Position{
 						Line:      protocol.UInteger(lineIndex),
@@ -145,28 +284,94 @@ func (d *document) DocumentLinks() ([]documentLink, error) {
 						Character: protocol.UInteger(end),
 					},
 				},
+				HasTitle:   hasTitle,
+				IsWikiLink: isWikiLink,
 			})
 		}
 
+		// extract link paths from [title](path) patterns
+		// note: match[0:1] is the entire match, match[2:3] is the contents of
+		// brackets, match[4:5] is contents of parentheses
 		for _, match := range markdownLinkRegex.FindAllStringSubmatchIndex(line, -1) {
+			// Ignore when inside backticks: `[title](file)`
+			if linkWithinInlineCode(line, match[0], match[1], insideInline) {
+				continue
+			}
+
+			// Ignore embedded images ![title](file.png)
+			if match[0] > 0 && line[match[0]-1] == '!' {
+				continue
+			}
+
+			// ignore tripple dash file URIs [title](file:///foo.go)
+			if match[5]-match[4] >= 8 {
+				linkURL := line[match[4]:match[5]]
+				fileURIresult := linkURL[:8]
+				if fileURIregex.MatchString(fileURIresult) {
+					continue
+				}
+			}
+
 			href := line[match[4]:match[5]]
-			// Valid Markdown links are percent-encoded.
+
+			// Decode the href if it's percent-encoded
 			if decodedHref, err := url.PathUnescape(href); err == nil {
 				href = decodedHref
 			}
-			appendLink(href, match[0], match[1])
+
+			appendLink(href, match[0], match[1], false, false)
 		}
 
 		for _, match := range wikiLinkRegex.FindAllStringSubmatchIndex(line, -1) {
+			// Ignore when inside backticks: `[[filename]]`
+			if linkWithinInlineCode(line, match[0], match[1], insideInline) {
+				continue
+			}
 			href := line[match[2]:match[3]]
-			appendLink(href, match[0], match[1])
+			hasTitle := match[4] != -1
+			appendLink(href, match[0], match[1], hasTitle, true)
+		}
+		if strings.Count(line, "`")%2 == 1 {
+			insideInline = !insideInline
 		}
 	}
 
 	return links, nil
 }
 
+// IsTagPosition returns whether the given caret position is inside a tag (YAML frontmatter, #hashtag, etc.).
+func (d *document) IsTagPosition(position protocol.Position, noteContentParser core.NoteContentParser) bool {
+	lines := strutil.CopyList(d.GetLines())
+	lineIdx := int(position.Line)
+	charIdx := int(position.Character)
+	line := lines[lineIdx]
+	// https://github.com/zk-org/zk/issues/144#issuecomment-1006108485
+	line = line[:charIdx] + "ZK_PLACEHOLDER" + line[charIdx:]
+	lines[lineIdx] = line
+	targetWord := strutil.WordAt(line, charIdx)
+	if targetWord == "" {
+		return false
+	}
+	if string(targetWord[0]) == "#" {
+		targetWord = targetWord[1:]
+	}
+
+	content := strings.Join(lines, "\n")
+	note, err := noteContentParser.ParseNoteContent(content)
+	if err != nil {
+		return false
+	}
+	return strutil.Contains(note.Tags, targetWord)
+}
+
 type documentLink struct {
-	Href  string
-	Range protocol.Range
+	Href          string
+	RelativeToDir string
+	Range         protocol.Range
+	// HasTitle indicates whether this link has a title information. For
+	// example [[filename]] doesn't but [[filename|title]] does.
+	HasTitle bool
+	// IsWikiLink indicates whether this link is a [[WikiLink]] instead of a
+	// regular Markdown link.
+	IsWikiLink bool
 }

internal/adapter/lsp/server.go

@@ -1,16 +1,18 @@
 package lsp
 
 import (
+	"encoding/json"
 	"fmt"
-	"io/ioutil"
+	"os"
 	"path/filepath"
 	"strings"
+	"time"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/errors"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	strutil "github.com/mickael-menu/zk/internal/util/strings"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/opt"
+	strutil "github.com/zk-org/zk/internal/util/strings"
 	"github.com/tliron/glsp"
 	protocol "github.com/tliron/glsp/protocol_3_16"
 	glspserv "github.com/tliron/glsp/server"
@@ -20,21 +22,25 @@ import (
 
 // Server holds the state of the Language Server.
 type Server struct {
-	server    *glspserv.Server
-	notebooks *core.NotebookStore
-	documents map[protocol.DocumentUri]*document
-	fs        core.FileStorage
-	logger    util.Logger
+	server                 *glspserv.Server
+	notebooks              *core.NotebookStore
+	documents              *documentStore
+	noteContentParser      core.NoteContentParser
+	templateLoader         core.TemplateLoader
+	fs                     core.FileStorage
+	logger                 util.Logger
+	useAdditionalTextEdits opt.Bool
 }
 
 // ServerOpts holds the options to create a new Server.
 type ServerOpts struct {
-	Name      string
-	Version   string
-	LogFile   opt.String
-	Logger    *util.ProxyLogger
-	Notebooks *core.NotebookStore
-	FS        core.FileStorage
+	Name           string
+	Version        string
+	LogFile        opt.String
+	Logger         *util.ProxyLogger
+	Notebooks      *core.NotebookStore
+	TemplateLoader core.TemplateLoader
+	FS             core.FileStorage
 }
 
 // NewServer creates a new Server instance.
@@ -45,20 +51,23 @@ func NewServer(opts ServerOpts) *Server {
 		logging.Configure(10, opts.LogFile.Value)
 	}
 
-	workspace := newWorkspace()
 	handler := protocol.Handler{}
-	server := &Server{
-		server:    glspserv.NewServer(&handler, opts.Name, debug),
-		notebooks: opts.Notebooks,
-		documents: map[string]*document{},
-		fs:        fs,
-	}
+	glspServer := glspserv.NewServer(&handler, opts.Name, debug)
 
 	// Redirect zk's logger to GLSP's to avoid breaking the JSON-RPC protocol
 	// with unwanted output.
 	if opts.Logger != nil {
-		opts.Logger.Logger = newGlspLogger(server.server.Log)
-		server.logger = opts.Logger
+		opts.Logger.Logger = newGlspLogger(glspServer.Log)
+	}
+
+	server := &Server{
+		server:                 glspServer,
+		notebooks:              opts.Notebooks,
+		documents:              newDocumentStore(fs, opts.Logger),
+		templateLoader:         opts.TemplateLoader,
+		fs:                     fs,
+		logger:                 opts.Logger,
+		useAdditionalTextEdits: opt.NullBool,
 	}
 
 	var clientCapabilities protocol.ClientCapabilities
@@ -66,24 +75,25 @@ func NewServer(opts ServerOpts) *Server {
 	handler.Initialize = func(context *glsp.Context, params *protocol.InitializeParams) (interface{}, error) {
 		clientCapabilities = params.Capabilities
 
-		if len(params.WorkspaceFolders) > 0 {
-			for _, f := range params.WorkspaceFolders {
-				workspace.addFolder(f.URI)
-			}
-		} else if params.RootURI != nil {
-			workspace.addFolder(*params.RootURI)
-		} else if params.RootPath != nil {
-			workspace.addFolder(*params.RootPath)
-		}
-
 		// To see the logs with coc.nvim, run :CocCommand workspace.showOutput
 		// https://github.com/neoclide/coc.nvim/wiki/Debug-language-server#using-output-channel
 		if params.Trace != nil {
 			protocol.SetTraceValue(*params.Trace)
 		}
 
+		if params.ClientInfo != nil {
+			if params.ClientInfo.Name == "Visual Studio Code" {
+				// Visual Studio Code doesn't seem to support inl
+				// VSCode doesn't support deleting the trigger characters with
+				// the main TextEdit. We'll use additional text edits instead.
+				server.useAdditionalTextEdits = opt.True
+			}
+		}
+
 		capabilities := handler.CreateServerCapabilities()
 		capabilities.HoverProvider = true
+		capabilities.DefinitionProvider = true
+		capabilities.CodeActionProvider = true
 
 		change := protocol.TextDocumentSyncKindIncremental
 		capabilities.TextDocumentSync = protocol.TextDocumentSyncOptions{
@@ -95,14 +105,22 @@ func NewServer(opts ServerOpts) *Server {
 			ResolveProvider: boolPtr(true),
 		}
 
-		triggerChars := []string{"[", "#", ":"}
+		triggerChars := []string{"(", "[", "#", ":"}
 
+		capabilities.ExecuteCommandProvider = &protocol.ExecuteCommandOptions{
+			Commands: []string{
+				cmdIndex,
+				cmdNew,
+				cmdList,
+				cmdTagList,
+			},
+		}
 		capabilities.CompletionProvider = &protocol.CompletionOptions{
 			TriggerCharacters: triggerChars,
 			ResolveProvider:   boolPtr(true),
 		}
 
-		capabilities.DefinitionProvider = boolPtr(true)
+		capabilities.ReferencesProvider = &protocol.ReferenceOptions{}
 
 		return protocol.InitializeResult{
 			Capabilities: capabilities,
@@ -127,59 +145,52 @@ func NewServer(opts ServerOpts) *Server {
 		return nil
 	}
 
-	handler.WorkspaceDidChangeWorkspaceFolders = func(context *glsp.Context, params *protocol.DidChangeWorkspaceFoldersParams) error {
-		for _, f := range params.Event.Added {
-			workspace.addFolder(f.URI)
-		}
-		for _, f := range params.Event.Removed {
-			workspace.removeFolder(f.URI)
-		}
-		return nil
-	}
-
 	handler.TextDocumentDidOpen = func(context *glsp.Context, params *protocol.DidOpenTextDocumentParams) error {
-		langID := params.TextDocument.LanguageID
-		if langID != "markdown" && langID != "vimwiki" {
-			return nil
+		doc, err := server.documents.DidOpen(*params, context.Notify)
+		if err != nil {
+			return err
 		}
-
-		path := fs.Canonical(strings.TrimPrefix(params.TextDocument.URI, "file://"))
-
-		server.documents[params.TextDocument.URI] = &document{
-			Path:    path,
-			Content: params.TextDocument.Text,
-			Log:     server.server.Log,
+		if doc != nil {
+			server.refreshDiagnosticsOfDocument(doc, context.Notify, false)
 		}
-
 		return nil
 	}
 
 	handler.TextDocumentDidChange = func(context *glsp.Context, params *protocol.DidChangeTextDocumentParams) error {
-		doc, ok := server.documents[params.TextDocument.URI]
+		doc, ok := server.documents.Get(params.TextDocument.URI)
 		if !ok {
 			return nil
 		}
 
 		doc.ApplyChanges(params.ContentChanges)
+		server.refreshDiagnosticsOfDocument(doc, context.Notify, true)
 		return nil
 	}
 
 	handler.TextDocumentDidClose = func(context *glsp.Context, params *protocol.DidCloseTextDocumentParams) error {
-		delete(server.documents, params.TextDocument.URI)
+		server.documents.Close(params.TextDocument.URI)
 		return nil
 	}
 
 	handler.TextDocumentDidSave = func(context *glsp.Context, params *protocol.DidSaveTextDocumentParams) error {
+		doc, ok := server.documents.Get(params.TextDocument.URI)
+		if !ok {
+			return nil
+		}
+
+		notebook, err := server.notebookOf(doc)
+		if err != nil {
+			server.logger.Err(err)
+			return nil
+		}
+
+		_, err = notebook.Index(core.NoteIndexOpts{})
+		server.logger.Err(err)
 		return nil
 	}
 
 	handler.TextDocumentCompletion = func(context *glsp.Context, params *protocol.CompletionParams) (interface{}, error) {
-		triggerChar := params.Context.TriggerCharacter
-		if params.Context.TriggerKind != protocol.CompletionTriggerKindTriggerCharacter || triggerChar == nil {
-			return nil, nil
-		}
-
-		doc, ok := server.documents[params.TextDocument.URI]
+		doc, ok := server.documents.Get(params.TextDocument.URI)
 		if !ok {
 			return nil, nil
 		}
@@ -189,27 +200,16 @@ func NewServer(opts ServerOpts) *Server {
 			return nil, err
 		}
 
-		switch *triggerChar {
-		case "#":
-			if notebook.Config.Format.Markdown.Hashtags {
-				return server.buildTagCompletionList(notebook, "#")
-			}
-		case ":":
-			if notebook.Config.Format.Markdown.ColonTags {
-				return server.buildTagCompletionList(notebook, ":")
-			}
-		case "[":
-			if doc.LookBehind(params.Position, 2) == "[[" {
-				return server.buildLinkCompletionList(doc, notebook, params)
-			}
+		if params.Context != nil && params.Context.TriggerKind == protocol.CompletionTriggerKindInvoked {
+			return server.buildInvokedCompletionList(notebook, doc, params.Position)
+		} else {
+			return server.buildTriggerCompletionList(notebook, doc, params.Position)
 		}
-
-		return nil, nil
 	}
 
 	handler.CompletionItemResolve = func(context *glsp.Context, params *protocol.CompletionItem) (*protocol.CompletionItem, error) {
 		if path, ok := params.Data.(string); ok {
-			content, err := ioutil.ReadFile(path)
+			content, err := os.ReadFile(path)
 			if err != nil {
 				return params, err
 			}
@@ -223,7 +223,7 @@ func NewServer(opts ServerOpts) *Server {
 	}
 
 	handler.TextDocumentHover = func(context *glsp.Context, params *protocol.HoverParams) (*protocol.Hover, error) {
-		doc, ok := server.documents[params.TextDocument.URI]
+		doc, ok := server.documents.Get(params.TextDocument.URI)
 		if !ok {
 			return nil, nil
 		}
@@ -238,13 +238,19 @@ func NewServer(opts ServerOpts) *Server {
 			return nil, err
 		}
 
-		target, err := server.targetForHref(link.Href, doc, notebook)
-		if err != nil || target == "" || strutil.IsURL(target) {
+		target, err := server.noteForLink(*link, notebook)
+		if err != nil || target == nil {
+			return nil, err
+		}
+
+		path, err := uriToPath(target.URI)
+		if err != nil {
+			server.logger.Printf("unable to parse URI: %v", err)
 			return nil, err
 		}
+		path = fs.Canonical(path)
 
-		target = strings.TrimPrefix(target, "file://")
-		contents, err := ioutil.ReadFile(target)
+		contents, err := os.ReadFile(path)
 		if err != nil {
 			return nil, err
 		}
@@ -258,7 +264,7 @@ func NewServer(opts ServerOpts) *Server {
 	}
 
 	handler.TextDocumentDocumentLink = func(context *glsp.Context, params *protocol.DocumentLinkParams) ([]protocol.DocumentLink, error) {
-		doc, ok := server.documents[params.TextDocument.URI]
+		doc, ok := server.documents.Get(params.TextDocument.URI)
 		if !ok {
 			return nil, nil
 		}
@@ -275,22 +281,31 @@ func NewServer(opts ServerOpts) *Server {
 
 		documentLinks := []protocol.DocumentLink{}
 		for _, link := range links {
-			target, err := server.targetForHref(link.Href, doc, notebook)
-			if target == "" || err != nil {
-				continue
+			var target string
+			if strutil.IsURL(link.Href) {
+				// External link
+				target = link.Href
+			} else {
+				// Internal note link
+				targetNote, err := server.noteForLink(link, notebook)
+				if targetNote != nil && err == nil {
+					target = targetNote.URI
+				}
 			}
 
-			documentLinks = append(documentLinks, protocol.DocumentLink{
-				Range:  link.Range,
-				Target: &target,
-			})
+			if target != "" {
+				documentLinks = append(documentLinks, protocol.DocumentLink{
+					Range:  link.Range,
+					Target: &target,
+				})
+			}
 		}
 
 		return documentLinks, err
 	}
 
 	handler.TextDocumentDefinition = func(context *glsp.Context, params *protocol.DefinitionParams) (interface{}, error) {
-		doc, ok := server.documents[params.TextDocument.URI]
+		doc, ok := server.documents.Get(params.TextDocument.URI)
 		if !ok {
 			return nil, nil
 		}
@@ -305,8 +320,8 @@ func NewServer(opts ServerOpts) *Server {
 			return nil, err
 		}
 
-		target, err := server.targetForHref(link.Href, doc, notebook)
-		if link == nil || target == "" || err != nil {
+		target, err := server.noteForLink(*link, notebook)
+		if link == nil || target == nil || err != nil {
 			return nil, err
 		}
 
@@ -315,51 +330,362 @@ func NewServer(opts ServerOpts) *Server {
 		if false && isTrue(clientCapabilities.TextDocument.Definition.LinkSupport) {
 			return protocol.LocationLink{
 				OriginSelectionRange: &link.Range,
-				TargetURI:            target,
+				TargetURI:            target.URI,
 			}, nil
 		} else {
 			return protocol.Location{
-				URI: target,
+				URI: target.URI,
 			}, nil
 		}
 	}
 
+	handler.WorkspaceExecuteCommand = func(context *glsp.Context, params *protocol.ExecuteCommandParams) (interface{}, error) {
+
+		openNotebook := func() (*core.Notebook, error) {
+			args := params.Arguments
+			if len(args) == 0 {
+				return nil, fmt.Errorf("%s expects a notebook path as first argument", params.Command)
+			}
+			path, ok := args[0].(string)
+			if !ok {
+				return nil, fmt.Errorf("%s expects a notebook path as first argument, got: %v", params.Command, args[0])
+			}
+
+			return server.notebooks.Open(path)
+		}
+
+		switch params.Command {
+		case cmdIndex:
+			nb, err := openNotebook()
+			if err != nil {
+				return nil, err
+			}
+			return executeCommandIndex(nb, params.Arguments)
+
+		case cmdNew:
+			nb, err := openNotebook()
+			if err != nil {
+				return nil, err
+			}
+			return executeCommandNew(nb, server.documents, context, params.Arguments)
+
+		case cmdLink:
+			nb, err := openNotebook()
+			if err != nil {
+				return nil, err
+			}
+			return executeCommandLink(nb, server.documents, context, params.Arguments)
+
+		case cmdList:
+			nb, err := openNotebook()
+			if err != nil {
+				return nil, err
+			}
+			return executeCommandList(server.logger, nb, params.Arguments)
+
+		case cmdTagList:
+			nb, err := openNotebook()
+			if err != nil {
+				return nil, err
+			}
+			return executeCommandTagList(server.logger, nb, params.Arguments)
+
+		default:
+			return nil, fmt.Errorf("unknown zk LSP command: %s", params.Command)
+		}
+	}
+
+	handler.TextDocumentCodeAction = func(context *glsp.Context, params *protocol.CodeActionParams) (interface{}, error) {
+		if isRangeEmpty(params.Range) {
+			return nil, nil
+		}
+
+		doc, ok := server.documents.Get(params.TextDocument.URI)
+		if !ok {
+			return nil, nil
+		}
+		wd := filepath.Dir(doc.Path)
+
+		actions := []protocol.CodeAction{}
+
+		addAction := func(dir string, actionTitle string) error {
+			opts := cmdNewOpts{
+				Title: doc.ContentAtRange(params.Range),
+				Dir:   dir,
+				InsertLinkAtLocation: &protocol.Location{
+					URI:   params.TextDocument.URI,
+					Range: params.Range,
+				},
+			}
+
+			var jsonOpts map[string]interface{}
+			err := unmarshalJSON(opts, &jsonOpts)
+			if err != nil {
+				return err
+			}
+
+			actions = append(actions, protocol.CodeAction{
+				Title: actionTitle,
+				Kind:  stringPtr(protocol.CodeActionKindRefactor),
+				Command: &protocol.Command{
+					Title:     actionTitle,
+					Command:   cmdNew,
+					Arguments: []interface{}{wd, jsonOpts},
+				},
+			})
+
+			return nil
+		}
+
+		addAction(wd, "New note in current directory")
+		addAction("", "New note in top directory")
+
+		return actions, nil
+	}
+
+	handler.TextDocumentReferences = func(context *glsp.Context, params *protocol.ReferenceParams) ([]protocol.Location, error) {
+		doc, ok := server.documents.Get(params.TextDocument.URI)
+		if !ok {
+			return nil, nil
+		}
+
+		notebook, err := server.notebookOf(doc)
+		if err != nil {
+			return nil, err
+		}
+
+		link, err := doc.DocumentLinkAt(params.Position)
+		if err != nil {
+			return nil, err
+		}
+		if link == nil {
+			link, err = doc.LinkFromRoot(notebook)
+			if err != nil {
+				return nil, err
+			}
+		}
+
+		target, err := server.noteForLink(*link, notebook)
+		if link == nil || target == nil || err != nil {
+			return nil, err
+		}
+
+		opts := core.NoteFindOpts{
+			LinkTo: &core.LinkFilter{Hrefs: []string{target.Path}},
+		}
+
+		notes, err := notebook.FindNotes(opts)
+		if err != nil {
+			return nil, err
+		}
+
+		var locations []protocol.Location
+
+		for _, note := range notes {
+			pos := strings.Index(note.RawContent, target.Path[0:len(target.Path)-3])
+			var line uint32 = 0
+			if pos < 0 {
+				line = 0
+			} else {
+				linePos := strings.Count(note.RawContent[0:pos], "\n")
+				line = uint32(linePos)
+			}
+
+			locations = append(locations, protocol.Location{
+				URI: pathToURI(filepath.Join(notebook.Path, note.Path)),
+				Range: protocol.Range{
+					Start: protocol.Position{
+						Line:      line,
+						Character: 0,
+					},
+					End: protocol.Position{
+						Line:      line,
+						Character: 0,
+					},
+				},
+			})
+		}
+
+		return locations, nil
+	}
+
 	return server
 }
 
+// Run starts the Language Server in stdio mode.
+func (s *Server) Run() error {
+	return errors.Wrap(s.server.RunStdio(), "lsp")
+}
+
 func (s *Server) notebookOf(doc *document) (*core.Notebook, error) {
 	return s.notebooks.Open(doc.Path)
 }
 
-// targetForHref returns the LSP documentUri for the note at the given HREF.
-func (s *Server) targetForHref(href string, doc *document, notebook *core.Notebook) (string, error) {
+// noteForLink returns the Note object for the note targeted by the given link.
+//
+// Match by order of precedence:
+//  1. Prefix of relative path
+//  2. Find any occurrence of the href in a note path (substring)
+//  3. Match the href as a term in the note titles
+func (s *Server) noteForLink(link documentLink, notebook *core.Notebook) (*Note, error) {
+	note, err := s.noteForHref(link.Href, link.RelativeToDir, notebook)
+	if note == nil && err == nil && link.IsWikiLink {
+		// Try to find a partial href match.
+		note, err = notebook.FindByHref(link.Href, true)
+	}
+	if note == nil || err != nil {
+		return nil, err
+	}
+
+	joined_path := filepath.Join(notebook.Path, note.Path)
+	return &Note{*note, pathToURI(joined_path)}, nil
+}
+
+// noteForHref returns the Note object for the note targeted by the given HREF
+// relative to relativeToDir.
+func (s *Server) noteForHref(href string, relativeToDir string, notebook *core.Notebook) (*core.MinimalNote, error) {
 	if strutil.IsURL(href) {
-		return href, nil
-	} else {
-		path := filepath.Clean(filepath.Join(filepath.Dir(doc.Path), href))
-		path, err := filepath.Rel(notebook.Path, path)
-		if err != nil {
-			return "", errors.Wrapf(err, "failed to resolve href: %s", href)
+		return nil, nil
+	}
+
+	path := href
+	if relativeToDir != "" {
+		path = filepath.Clean(filepath.Join(relativeToDir, path))
+	}
+	path, err := filepath.Rel(notebook.Path, path)
+	if err != nil {
+		return nil, errors.Wrapf(err, "failed to resolve href: %s", href)
+	}
+	note, err := notebook.FindByHref(path, false)
+	if err != nil {
+		s.logger.Printf("findByHref(%s): %s", href, err.Error())
+	}
+	return note, err
+}
+
+type Note struct {
+	core.MinimalNote
+	URI protocol.DocumentUri
+}
+
+func (s *Server) refreshDiagnosticsOfDocument(doc *document, notify glsp.NotifyFunc, delay bool) {
+	if doc.NeedsRefreshDiagnostics { // Already refreshing
+		return
+	}
+
+	notebook, err := s.notebookOf(doc)
+	if err != nil {
+		s.logger.Err(err)
+		return
+	}
+
+	diagConfig := notebook.Config.LSP.Diagnostics
+	if diagConfig.WikiTitle == core.LSPDiagnosticNone && diagConfig.DeadLink == core.LSPDiagnosticNone {
+		// No diagnostic enabled.
+		return
+	}
+
+	doc.NeedsRefreshDiagnostics = true
+	go func() {
+		if delay {
+			time.Sleep(1 * time.Second)
 		}
-		note, err := notebook.FindByHref(path)
+		doc.NeedsRefreshDiagnostics = false
+
+		diagnostics := []protocol.Diagnostic{}
+		links, err := doc.DocumentLinks()
 		if err != nil {
-			s.logger.Printf("findByHref(%s): %s", href, err.Error())
-			return "", err
+			s.logger.Err(err)
+			return
 		}
-		if note == nil {
-			return "", nil
+
+		for _, link := range links {
+			if strutil.IsURL(link.Href) {
+				continue
+			}
+			target, err := s.noteForLink(link, notebook)
+			if err != nil {
+				s.logger.Err(err)
+				continue
+			}
+
+			var severity protocol.DiagnosticSeverity
+			var message string
+			if target == nil {
+				if diagConfig.DeadLink == core.LSPDiagnosticNone {
+					continue
+				}
+				severity = protocol.DiagnosticSeverity(diagConfig.DeadLink)
+				message = "not found"
+			} else {
+				if diagConfig.WikiTitle == core.LSPDiagnosticNone {
+					continue
+				}
+				severity = protocol.DiagnosticSeverity(diagConfig.WikiTitle)
+				message = target.Title
+			}
+
+			diagnostics = append(diagnostics, protocol.Diagnostic{
+				Range:    link.Range,
+				Severity: &severity,
+				Source:   stringPtr("zk"),
+				Message:  message,
+			})
 		}
-		return "file://" + filepath.Join(notebook.Path, note.Path), nil
+
+		go notify(protocol.ServerTextDocumentPublishDiagnostics, protocol.PublishDiagnosticsParams{
+			URI:         doc.URI,
+			Diagnostics: diagnostics,
+		})
+	}()
+}
+
+// buildInvokedCompletionList builds the completion item response for a
+// completion started automatically when typing an identifier, or manually.
+func (s *Server) buildInvokedCompletionList(notebook *core.Notebook, doc *document, position protocol.Position) ([]protocol.CompletionItem, error) {
+	currentWord := doc.WordAt(position)
+	if strings.HasPrefix(doc.LookBehind(position, len(currentWord)+2), "[[") {
+		return s.buildLinkCompletionList(notebook, doc, position)
+	}
+
+	if doc.IsTagPosition(position, notebook.Parser) {
+		return s.buildTagCompletionList(notebook, doc.WordAt(position))
 	}
+
+	return nil, nil
 }
 
-// Run starts the Language Server in stdio mode.
-func (s *Server) Run() error {
-	return errors.Wrap(s.server.RunStdio(), "lsp")
+// buildTriggerCompletionList builds the completion item response for a
+// completion started with a trigger character.
+func (s *Server) buildTriggerCompletionList(notebook *core.Notebook, doc *document, position protocol.Position) ([]protocol.CompletionItem, error) {
+	// We don't use the context because clients might not send it. Instead,
+	// we'll look for trigger patterns in the document.
+	switch doc.LookBehind(position, 3) {
+	case "]((":
+		return s.buildLinkCompletionList(notebook, doc, position)
+	}
+
+	switch doc.LookBehind(position, 2) {
+	case "[[":
+		return s.buildLinkCompletionList(notebook, doc, position)
+	}
+
+	switch doc.LookBehind(position, 1) {
+	case "#":
+		if notebook.Config.Format.Markdown.Hashtags {
+			return s.buildTagCompletionList(notebook, "#")
+		}
+	case ":":
+		if notebook.Config.Format.Markdown.ColonTags {
+			return s.buildTagCompletionList(notebook, ":")
+		}
+	}
+
+	return nil, nil
 }
 
-func (s *Server) buildTagCompletionList(notebook *core.Notebook, triggerChar string) ([]protocol.CompletionItem, error) {
-	tags, err := notebook.FindCollections(core.CollectionKindTag)
+func (s *Server) buildTagCompletionList(notebook *core.Notebook, prefix string) ([]protocol.CompletionItem, error) {
+	tags, err := notebook.FindCollections(core.CollectionKindTag, nil)
 	if err != nil {
 		return nil, err
 	}
@@ -368,7 +694,7 @@ func (s *Server) buildTagCompletionList(notebook *core.Notebook, triggerChar str
 	for _, tag := range tags {
 		items = append(items, protocol.CompletionItem{
 			Label:      tag.Name,
-			InsertText: s.buildInsertForTag(tag.Name, triggerChar, notebook.Config),
+			InsertText: s.buildInsertForTag(tag.Name, prefix, notebook.Config),
 			Detail:     stringPtr(fmt.Sprintf("%d %s", tag.NoteCount, strutil.Pluralize("note", tag.NoteCount))),
 		})
 	}
@@ -376,8 +702,8 @@ func (s *Server) buildTagCompletionList(notebook *core.Notebook, triggerChar str
 	return items, nil
 }
 
-func (s *Server) buildInsertForTag(name string, triggerChar string, config core.Config) *string {
-	switch triggerChar {
+func (s *Server) buildInsertForTag(name string, prefix string, config core.Config) *string {
+	switch prefix {
 	case ":":
 		name += ":"
 	case "#":
@@ -392,8 +718,13 @@ func (s *Server) buildInsertForTag(name string, triggerChar string, config core.
 	return &name
 }
 
-func (s *Server) buildLinkCompletionList(doc *document, notebook *core.Notebook, params *protocol.CompletionParams) ([]protocol.CompletionItem, error) {
-	linkFormatter, err := notebook.NewLinkFormatter()
+func (s *Server) buildLinkCompletionList(notebook *core.Notebook, doc *document, position protocol.Position) ([]protocol.CompletionItem, error) {
+	linkFormatter, err := newLinkFormatter(notebook, doc, position)
+	if err != nil {
+		return nil, err
+	}
+
+	templates, err := newCompletionTemplates(s.templateLoader, notebook.Config.LSP.Completion.Note)
 	if err != nil {
 		return nil, err
 	}
@@ -405,7 +736,7 @@ func (s *Server) buildLinkCompletionList(doc *document, notebook *core.Notebook,
 
 	var items []protocol.CompletionItem
 	for _, note := range notes {
-		item, err := s.newCompletionItem(notebook, note, doc, params.Position, linkFormatter)
+		item, err := s.newCompletionItem(notebook, note, doc, position, linkFormatter, templates)
 		if err != nil {
 			s.logger.Err(err)
 			continue
@@ -417,67 +748,135 @@ func (s *Server) buildLinkCompletionList(doc *document, notebook *core.Notebook,
 	return items, nil
 }
 
-func (s *Server) newCompletionItem(notebook *core.Notebook, note core.MinimalNote, doc *document, pos protocol.Position, linkFormatter core.LinkFormatter) (item protocol.CompletionItem, err error) {
+func newLinkFormatter(notebook *core.Notebook, doc *document, position protocol.Position) (core.LinkFormatter, error) {
+	if doc.LookBehind(position, 3) == "]((" {
+		return core.NewMarkdownLinkFormatter(notebook.Config.Format.Markdown, true)
+	} else {
+		return notebook.NewLinkFormatter()
+	}
+}
+
+func (s *Server) newCompletionItem(notebook *core.Notebook, note core.MinimalNote, doc *document, pos protocol.Position, linkFormatter core.LinkFormatter, templates completionTemplates) (protocol.CompletionItem, error) {
 	kind := protocol.CompletionItemKindReference
-	item.Kind = &kind
-	item.Data = filepath.Join(notebook.Path, note.Path)
+	item := protocol.CompletionItem{
+		Kind: &kind,
+		Data: filepath.Join(notebook.Path, note.Path),
+	}
 
-	if note.Title != "" {
-		item.Label = note.Title
+	templateContext, err := newCompletionItemRenderContext(note, notebook.Path, doc.Path)
+	if err != nil {
+		return item, err
+	}
+
+	if templates.Label != nil {
+		item.Label, err = templates.Label.Render(templateContext)
+		if err != nil {
+			return item, err
+		}
 	} else {
+		item.Label = note.Title
+	}
+	// Fallback on the note path to never have empty labels.
+	if item.Label == "" {
 		item.Label = note.Path
 	}
 
-	// Add the path to the filter text to be able to complete by it.
-	item.FilterText = stringPtr(item.Label + " " + note.Path)
+	if templates.FilterText != nil {
+		filterText, err := templates.FilterText.Render(templateContext)
+		if err != nil {
+			return item, err
+		}
+		item.FilterText = &filterText
+	}
+	if item.FilterText == nil || *item.FilterText == "" {
+		// Add the path to the filter text to be able to complete by it.
+		item.FilterText = stringPtr(item.Label + " " + note.Path)
+	}
+
+	if templates.Detail != nil {
+		detail, err := templates.Detail.Render(templateContext)
+		if err != nil {
+			return item, err
+		}
+		item.Detail = &detail
+	}
 
 	item.TextEdit, err = s.newTextEditForLink(notebook, note, doc, pos, linkFormatter)
 	if err != nil {
 		err = errors.Wrapf(err, "failed to build TextEdit for note at %s", note.Path)
-		return
+		return item, err
 	}
 
-	addTextEdits := []protocol.TextEdit{}
+	if s.useAdditionalTextEditsWithNotebook(notebook) {
+		addTextEdits := []protocol.TextEdit{}
 
-	// Some LSP clients (e.g. VSCode) don't support deleting the trigger
-	// characters with the main TextEdit. So let's add an additional
-	// TextEdit for that.
-	addTextEdits = append(addTextEdits, protocol.TextEdit{
-		NewText: "",
-		Range:   rangeFromPosition(pos, -2, 0),
-	})
+		startOffset := -2
+		if doc.LookBehind(pos, 2) != "[[" {
+			currentWord := doc.WordAt(pos)
+			startOffset = -2 - len(currentWord)
+		}
 
-	item.AdditionalTextEdits = addTextEdits
+		// Some LSP clients (e.g. VSCode) don't support deleting the trigger
+		// characters with the main TextEdit. So let's add an additional
+		// TextEdit for that.
+		addTextEdits = append(addTextEdits, protocol.TextEdit{
+			NewText: "",
+			Range:   rangeFromPosition(pos, startOffset, 0),
+		})
+
+		item.AdditionalTextEdits = addTextEdits
+	}
 
 	return item, nil
 }
 
 func (s *Server) newTextEditForLink(notebook *core.Notebook, note core.MinimalNote, doc *document, pos protocol.Position, linkFormatter core.LinkFormatter) (interface{}, error) {
-	path := filepath.Join(notebook.Path, note.Path)
-	path = s.fs.Canonical(path)
-	path, err := filepath.Rel(filepath.Dir(doc.Path), path)
+	path := core.NotebookPath{
+		Path:       note.Path,
+		BasePath:   notebook.Path,
+		WorkingDir: filepath.Dir(doc.Path),
+	}
+	context, err := core.NewLinkFormatterContext(path, note.Title, note.Metadata)
 	if err != nil {
-		path = note.Path
+		return nil, err
 	}
-
-	link, err := linkFormatter(path, note.Title)
+	link, err := linkFormatter(context)
 	if err != nil {
 		return nil, err
 	}
 
+	// Overwrite [[ trigger directly if the additional text edits are disabled.
+	startOffset := 0
+	if !s.useAdditionalTextEditsWithNotebook(notebook) {
+		if doc.LookBehind(pos, 2) == "[[" {
+			startOffset = -2
+		} else {
+			currentWord := doc.WordAt(pos)
+			startOffset = -2 - len(currentWord) 
+		}
+	}
+
 	// Some LSP clients (e.g. VSCode) auto-pair brackets, so we need to
-	// remove the closing ]] after the completion.
+	// remove the closing ]] or )) after the completion.
 	endOffset := 0
-	if doc.LookForward(pos, 2) == "]]" {
+	suffix := doc.LookForward(pos, 2)
+	if suffix == "]]" || suffix == "))" {
 		endOffset = 2
 	}
 
 	return protocol.TextEdit{
 		NewText: link,
-		Range:   rangeFromPosition(pos, 0, endOffset),
+		Range:   rangeFromPosition(pos, startOffset, endOffset),
 	}, nil
 }
 
+func (s *Server) useAdditionalTextEditsWithNotebook(nb *core.Notebook) bool {
+	return nb.Config.LSP.Completion.UseAdditionalTextEdits.
+		Or(s.useAdditionalTextEdits).
+		OrBool(false).
+		Unwrap()
+}
+
 func positionInRange(content string, rng protocol.Range, pos protocol.Position) bool {
 	start, end := rng.IndexesIn(content)
 	i := pos.IndexIn(content)
@@ -501,6 +900,10 @@ func rangeFromPosition(pos protocol.Position, startOffset, endOffset int) protoc
 	}
 }
 
+func isRangeEmpty(pos protocol.Range) bool {
+	return pos.Start == pos.End
+}
+
 func boolPtr(v bool) *bool {
 	b := v
 	return &b
@@ -518,3 +921,16 @@ func stringPtr(v string) *string {
 	s := v
 	return &s
 }
+
+func unmarshalJSON(obj interface{}, v interface{}) error {
+	js, err := json.Marshal(obj)
+	if err != nil {
+		return err
+	}
+	return json.Unmarshal(js, v)
+}
+
+func toBool(obj interface{}) bool {
+	s := strings.ToLower(fmt.Sprint(obj))
+	return s == "true" || s == "1"
+}

internal/adapter/lsp/util.go

@@ -0,0 +1,118 @@
+package lsp
+
+import (
+	"fmt"
+	"net/url"
+	"path/filepath"
+	"runtime"
+	"strings"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/tliron/glsp"
+	protocol "github.com/tliron/glsp/protocol_3_16"
+)
+
+func pathToURI(path string) string {
+	u := &url.URL{
+		Scheme: "file",
+		Path:   path,
+	}
+	return u.String()
+}
+
+func uriToPath(uri string) (string, error) {
+	s := strings.ReplaceAll(uri, "%5C", "/")
+	parsed, err := url.Parse(s)
+	if err != nil {
+		return "", err
+	}
+	if parsed.Scheme != "file" {
+		return "", errors.New("URI was not a file:// URI")
+	}
+
+	if runtime.GOOS == "windows" {
+		// In Windows "file:///c:/tmp/foo.md" is parsed to "/c:/tmp/foo.md".
+		// Strip the first character to get a valid path.
+		if strings.Contains(parsed.Path[1:], ":") {
+			// url.Parse() behaves differently with "file:///c:/..." and "file://c:/..."
+			return parsed.Path[1:], nil
+		} else {
+			// if the windows drive is not included in Path it will be in Host
+			return parsed.Host + "/" + parsed.Path[1:], nil
+		}
+	}
+	return parsed.Path, nil
+}
+
+// jsonBoolean can be unmarshalled from integers or strings.
+// Neovim cannot send a boolean easily, so it's useful to support integers too.
+type jsonBoolean bool
+
+func (b *jsonBoolean) UnmarshalJSON(data []byte) error {
+	s := string(data)
+	if s == "1" || s == "true" {
+		*b = true
+	} else if s == "0" || s == "false" {
+		*b = false
+	} else {
+		return fmt.Errorf("%s: failed to unmarshal as boolean", s)
+	}
+	return nil
+}
+
+type linkInfo struct {
+    note *core.MinimalNote
+	location *protocol.Location
+	title    *string
+}
+
+func linkNote(notebook *core.Notebook, documents *documentStore, context *glsp.Context, info *linkInfo) error {
+	if info.location == nil {
+		return errors.New("'location' not provided")
+	}
+
+	// Get current document to edit
+	doc, ok := documents.Get(info.location.URI)
+	if !ok {
+		return fmt.Errorf("Cannot insert link in '%s'", info.location.URI)
+	}
+
+	formatter, err := notebook.NewLinkFormatter()
+	if err != nil {
+		return err
+	}
+
+	path := core.NotebookPath{
+		Path:       info.note.Path,
+		BasePath:   notebook.Path,
+		WorkingDir: filepath.Dir(doc.Path),
+	}
+
+	var title *string
+	title = info.title
+
+	if title == nil {
+		title = &info.note.Title
+	}
+
+	formatterContext, err := core.NewLinkFormatterContext(path, *title, info.note.Metadata)
+	if err != nil {
+		return err
+	}
+
+	link, err := formatter(formatterContext)
+	if err != nil {
+		return err
+	}
+
+	go context.Call(protocol.ServerWorkspaceApplyEdit, protocol.ApplyWorkspaceEditParams{
+		Edit: protocol.WorkspaceEdit{
+			Changes: map[string][]protocol.TextEdit{
+				info.location.URI: {{Range: info.location.Range, NewText: link}},
+			},
+		},
+	}, nil)
+
+	return nil
+}

internal/adapter/lsp/workspace.go

@@ -1,28 +0,0 @@
-package lsp
-
-import "strings"
-
-type workspace struct {
-	folders []string
-}
-
-func newWorkspace() *workspace {
-	return &workspace{
-		folders: []string{},
-	}
-}
-
-func (w *workspace) addFolder(folder string) {
-	folder = strings.TrimPrefix(folder, "file://")
-	w.folders = append(w.folders, folder)
-}
-
-func (w *workspace) removeFolder(folder string) {
-	folder = strings.TrimPrefix(folder, "file://")
-	for i, f := range w.folders {
-		if f == folder {
-			w.folders = append(w.folders[:i], w.folders[i+1:]...)
-			break
-		}
-	}
-}

internal/adapter/markdown/extensions/tag.go

@@ -6,7 +6,6 @@ import (
 
 	"github.com/yuin/goldmark"
 	"github.com/yuin/goldmark/ast"
-	gast "github.com/yuin/goldmark/ast"
 	"github.com/yuin/goldmark/parser"
 	"github.com/yuin/goldmark/text"
 	"github.com/yuin/goldmark/util"
@@ -14,7 +13,7 @@ import (
 
 // Tags represents a list of inline tags in a Markdown document.
 type Tags struct {
-	gast.BaseInline
+	ast.BaseInline
 	// Tags in this list.
 	Tags []string
 }
@@ -22,13 +21,13 @@ type Tags struct {
 func (n *Tags) Dump(source []byte, level int) {
 	m := map[string]string{}
 	m["Tags"] = strings.Join(n.Tags, ", ")
-	gast.DumpHelper(n, source, level, m, nil)
+	ast.DumpHelper(n, source, level, m, nil)
 }
 
 // KindTags is a NodeKind of the Tags node.
-var KindTags = gast.NewNodeKind("Tags")
+var KindTags = ast.NewNodeKind("Tags")
 
-func (n *Tags) Kind() gast.NodeKind {
+func (n *Tags) Kind() ast.NodeKind {
 	return KindTags
 }
 
@@ -106,7 +105,11 @@ func (p *hashtagParser) Parse(parent ast.Node, block text.Reader, pc parser.Cont
 		}
 	}
 
-	for i, char := range string(line[1:]) {
+	for i, char := range string(line) {
+		if i == 0 {
+			// Skip the first character, as it is #
+			continue
+		}
 		if parsingMultiWordTag {
 			multiWordTagEndPos = i
 		} else {
@@ -164,7 +167,7 @@ func (p *hashtagParser) Parse(parent ast.Node, block text.Reader, pc parser.Cont
 	block.Advance(endPos)
 
 	return &Tags{
-		BaseInline: gast.BaseInline{},
+		BaseInline: ast.BaseInline{},
 		Tags:       []string{tag},
 	}
 }
@@ -222,7 +225,7 @@ func (p *colontagParser) Parse(parent ast.Node, block text.Reader, pc parser.Con
 
 		} else if char == ':' {
 			tag = strings.TrimSpace(tag)
-			if len(tag) == 0 {
+			if !isValidTag(tag) {
 				break
 			}
 			tags = append(tags, tag)
@@ -244,7 +247,7 @@ func (p *colontagParser) Parse(parent ast.Node, block text.Reader, pc parser.Con
 	block.Advance(endPos)
 
 	return &Tags{
-		BaseInline: gast.BaseInline{},
+		BaseInline: ast.BaseInline{},
 		Tags:       tags,
 	}
 }
@@ -256,3 +259,19 @@ func isValidTagChar(r rune, excluded rune) bool {
 		r == '&' || r == '+' || r == '=' || r == ':' ||
 		r == '#')
 }
+
+func isValidTag(tag string) bool {
+	if len(tag) == 0 {
+		return false
+	}
+
+	// Prevent Markdown table syntax to be parsed a a colon tag, e.g. |:---:|
+	// https://github.com/zk-org/zk/issues/185
+	for _, c := range tag {
+		if c != '-' {
+			return true
+		}
+	}
+
+	return false
+}

internal/adapter/markdown/extensions/wikilink.go

@@ -3,7 +3,7 @@ package extensions
 import (
 	"strings"
 
-	"github.com/mickael-menu/zk/internal/core"
+	"github.com/zk-org/zk/internal/core"
 	"github.com/yuin/goldmark"
 	"github.com/yuin/goldmark/ast"
 	"github.com/yuin/goldmark/parser"
@@ -18,6 +18,11 @@ var WikiLinkExt = &wikiLink{}
 
 type wikiLink struct{}
 
+// WikiLink represents a wiki link found in a Markdown document.
+type WikiLink struct {
+	ast.Link
+}
+
 func (w *wikiLink) Extend(m goldmark.Markdown) {
 	m.Parser().AddOptions(
 		parser.WithInlineParsers(
@@ -51,7 +56,7 @@ func (p *wlParser) Parse(parent ast.Node, block text.Reader, pc parser.Context)
 		endPos          = 0     // Last position of the link in the line
 	)
 
-	appendChar := func(c byte) {
+	appendRune := func(c rune) {
 		if parsingLabel {
 			label += string(c)
 		} else {
@@ -59,7 +64,7 @@ func (p *wlParser) Parse(parent ast.Node, block text.Reader, pc parser.Context)
 		}
 	}
 
-	for i, char := range line {
+	for i, char := range string(line) {
 		endPos = i
 
 		if closed {
@@ -116,11 +121,11 @@ func (p *wlParser) Parse(parent ast.Node, block text.Reader, pc parser.Context)
 		// We add them to the HREF and reset the count.
 		if closerCharCount > 0 {
 			for i := 0; i < closerCharCount; i++ {
-				appendChar(']')
+				appendRune(']')
 			}
 			closerCharCount = 0
 		}
-		appendChar(char)
+		appendRune(char)
 	}
 
 	if !closed || len(href) == 0 {
@@ -135,7 +140,7 @@ func (p *wlParser) Parse(parent ast.Node, block text.Reader, pc parser.Context)
 		label = href
 	}
 
-	link := ast.NewLink()
+	link := &WikiLink{Link: *ast.NewLink()}
 	link.Destination = []byte(href)
 	// Title will be parsed as the link's rel by the Markdown parser.
 	link.Title = []byte(rel)

internal/adapter/markdown/markdown.go

@@ -3,14 +3,16 @@ package markdown
 import (
 	"bufio"
 	"fmt"
+	"net/url"
 	"regexp"
 	"strings"
 
-	"github.com/mickael-menu/zk/internal/adapter/markdown/extensions"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	strutil "github.com/mickael-menu/zk/internal/util/strings"
-	"github.com/mickael-menu/zk/internal/util/yaml"
+	"github.com/zk-org/zk/internal/adapter/markdown/extensions"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/opt"
+	strutil "github.com/zk-org/zk/internal/util/strings"
+	"github.com/zk-org/zk/internal/util/yaml"
 	"github.com/mvdan/xurls"
 	"github.com/yuin/goldmark"
 	meta "github.com/yuin/goldmark-meta"
@@ -22,7 +24,8 @@ import (
 
 // Parser parses the content of Markdown notes.
 type Parser struct {
-	md goldmark.Markdown
+	md     goldmark.Markdown
+	logger util.Logger
 }
 
 type ParserOpts struct {
@@ -35,7 +38,7 @@ type ParserOpts struct {
 }
 
 // NewParser creates a new Markdown Parser.
-func NewParser(options ParserOpts) *Parser {
+func NewParser(options ParserOpts, logger util.Logger) *Parser {
 	return &Parser{
 		md: goldmark.New(
 			goldmark.WithExtensions(
@@ -57,11 +60,12 @@ func NewParser(options ParserOpts) *Parser {
 				},
 			),
 		),
+		logger: logger,
 	}
 }
 
-// Parse implements core.NoteParser.
-func (p *Parser) Parse(content string) (*core.ParsedNote, error) {
+// ParseNoteContent implements core.NoteContentParser.
+func (p *Parser) ParseNoteContent(content string) (*core.NoteContent, error) {
 	bytes := []byte(content)
 
 	context := parser.NewContext()
@@ -70,7 +74,7 @@ func (p *Parser) Parse(content string) (*core.ParsedNote, error) {
 		parser.WithContext(context),
 	)
 
-	links, err := parseLinks(root, bytes)
+	links, err := p.parseLinks(root, bytes)
 	if err != nil {
 		return nil, err
 	}
@@ -91,7 +95,7 @@ func (p *Parser) Parse(content string) (*core.ParsedNote, error) {
 		return nil, err
 	}
 
-	return &core.ParsedNote{
+	return &core.NoteContent{
 		Title:    title,
 		Body:     body,
 		Lead:     parseLead(body),
@@ -208,19 +212,21 @@ func parseTags(frontmatter frontmatter, root ast.Node, source []byte) ([]string,
 }
 
 // parseLinks extracts outbound links from the note.
-func parseLinks(root ast.Node, source []byte) ([]core.Link, error) {
+func (p *Parser) parseLinks(root ast.Node, source []byte) ([]core.Link, error) {
 	links := make([]core.Link, 0)
 
 	err := ast.Walk(root, func(n ast.Node, entering bool) (ast.WalkStatus, error) {
 		if entering {
 			switch link := n.(type) {
 			case *ast.Link:
-				href := string(link.Destination)
+				href, err := url.PathUnescape(string(link.Destination))
+				p.logger.Err(err)
 				if href != "" {
 					snippet, snStart, snEnd := extractLines(n, source)
 					links = append(links, core.Link{
 						Title:        string(link.Text(source)),
 						Href:         href,
+						Type:         core.LinkTypeMarkdown,
 						Rels:         core.LinkRels(strings.Fields(string(link.Title))...),
 						IsExternal:   strutil.IsURL(href),
 						Snippet:      snippet,
@@ -235,6 +241,7 @@ func parseLinks(root ast.Node, source []byte) ([]core.Link, error) {
 					links = append(links, core.Link{
 						Title:        string(link.Label(source)),
 						Href:         href,
+						Type:         core.LinkTypeImplicit,
 						Rels:         []core.LinkRelation{},
 						IsExternal:   true,
 						Snippet:      snippet,
@@ -242,6 +249,22 @@ func parseLinks(root ast.Node, source []byte) ([]core.Link, error) {
 						SnippetEnd:   snEnd,
 					})
 				}
+
+			case *extensions.WikiLink:
+				href := string(link.Destination)
+				if href != "" {
+					snippet, snStart, snEnd := extractLines(n, source)
+					links = append(links, core.Link{
+						Title:        string(link.Text(source)),
+						Href:         href,
+						Type:         core.LinkTypeWikiLink,
+						Rels:         core.LinkRels(strings.Fields(string(link.Title))...),
+						IsExternal:   strutil.IsURL(href),
+						Snippet:      snippet,
+						SnippetStart: snStart,
+						SnippetEnd:   snEnd,
+					})
+				}
 			}
 		}
 		return ast.WalkContinue, nil

internal/adapter/markdown/markdown_test.go

@@ -3,9 +3,10 @@ package markdown
 import (
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/opt"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestParseTitle(t *testing.T) {
@@ -187,6 +188,10 @@ func TestParseHashtags(t *testing.T) {
 	test("##invalid also#invalid", []string{})
 	// Bear's multi multi-word tags are disabled
 	test("#multi word# end", []string{"multi"})
+
+	// Single character
+	// See https://github.com/zk-org/zk/issues/118
+	test("#a", []string{"a"})
 }
 
 func TestParseWordtags(t *testing.T) {
@@ -364,6 +369,8 @@ An https://inline-link.com and http://another-inline-link.com.
 
 A [[Wiki link]] is surrounded by [[2-brackets | two brackets]].
 
+[[lien accentué]]
+
 It can contain [[esca]\]ped \[chara\\cters]].
 
 A [[[Folgezettel link]]] is surrounded by three brackets.
@@ -379,6 +386,7 @@ Neuron links with titles: [[trailing|Trailing link]]# #[[leading |  Leading link
 		{
 			Title:        "link",
 			Href:         "heading",
+			Type:         core.LinkTypeMarkdown,
 			Rels:         []core.LinkRelation{},
 			IsExternal:   false,
 			Snippet:      "Heading with a [link](heading)",
@@ -388,6 +396,7 @@ Neuron links with titles: [[trailing|Trailing link]]# #[[leading |  Leading link
 		{
 			Title:      "multiple links",
 			Href:       "stripped-formatting",
+			Type:       core.LinkTypeMarkdown,
 			Rels:       []core.LinkRelation{},
 			IsExternal: false,
 			Snippet: `Paragraph containing [multiple **links**](stripped-formatting), here's one [relative](../other).
@@ -398,6 +407,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:      "relative",
 			Href:       "../other",
+			Type:       core.LinkTypeMarkdown,
 			Rels:       []core.LinkRelation{},
 			IsExternal: false,
 			Snippet: `Paragraph containing [multiple **links**](stripped-formatting), here's one [relative](../other).
@@ -408,6 +418,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:      "one relation",
 			Href:       "one",
+			Type:       core.LinkTypeMarkdown,
 			Rels:       core.LinkRels("rel-1"),
 			IsExternal: false,
 			Snippet: `Paragraph containing [multiple **links**](stripped-formatting), here's one [relative](../other).
@@ -418,6 +429,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:      "several relations",
 			Href:       "several",
+			Type:       core.LinkTypeMarkdown,
 			Rels:       core.LinkRels("rel-1", "rel-2"),
 			IsExternal: false,
 			Snippet: `Paragraph containing [multiple **links**](stripped-formatting), here's one [relative](../other).
@@ -428,6 +440,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:        "https://inline-link.com",
 			Href:         "https://inline-link.com",
+			Type:         core.LinkTypeImplicit,
 			IsExternal:   true,
 			Rels:         []core.LinkRelation{},
 			Snippet:      "An https://inline-link.com and http://another-inline-link.com.",
@@ -437,6 +450,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:        "http://another-inline-link.com",
 			Href:         "http://another-inline-link.com",
+			Type:         core.LinkTypeImplicit,
 			IsExternal:   true,
 			Rels:         []core.LinkRelation{},
 			Snippet:      "An https://inline-link.com and http://another-inline-link.com.",
@@ -446,6 +460,7 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:        "Wiki link",
 			Href:         "Wiki link",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         []core.LinkRelation{},
 			Snippet:      "A [[Wiki link]] is surrounded by [[2-brackets | two brackets]].",
@@ -455,83 +470,129 @@ A link can have [one relation](one "rel-1") or [several relations](several "rel-
 		{
 			Title:        "two brackets",
 			Href:         "2-brackets",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         []core.LinkRelation{},
 			Snippet:      "A [[Wiki link]] is surrounded by [[2-brackets | two brackets]].",
 			SnippetStart: 288,
 			SnippetEnd:   351,
 		},
+		{
+			Title:        "lien accentué",
+			Href:         "lien accentué",
+			Type:         core.LinkTypeWikiLink,
+			IsExternal:   false,
+			Rels:         []core.LinkRelation{},
+			Snippet:      "[[lien accentué]]",
+			SnippetStart: 353,
+			SnippetEnd:   371,
+		},
 		{
 			Title:        `esca]]ped [chara\cters`,
 			Href:         `esca]]ped [chara\cters`,
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         []core.LinkRelation{},
 			Snippet:      `It can contain [[esca]\]ped \[chara\\cters]].`,
-			SnippetStart: 353,
-			SnippetEnd:   398,
+			SnippetStart: 373,
+			SnippetEnd:   418,
 		},
 		{
 			Title:        "Folgezettel link",
 			Href:         "Folgezettel link",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         core.LinkRels("down"),
 			Snippet:      "A [[[Folgezettel link]]] is surrounded by three brackets.",
-			SnippetStart: 400,
-			SnippetEnd:   457,
+			SnippetStart: 420,
+			SnippetEnd:   477,
 		},
 		{
 			Title:        "trailing hash",
 			Href:         "trailing hash",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         core.LinkRels("down"),
 			Snippet:      "Neuron also supports a [[trailing hash]]# for Folgezettel links.",
-			SnippetStart: 459,
-			SnippetEnd:   523,
+			SnippetStart: 479,
+			SnippetEnd:   543,
 		},
 		{
 			Title:        "leading hash",
 			Href:         "leading hash",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         core.LinkRels("up"),
 			Snippet:      "A #[[leading hash]] is used for #uplinks.",
-			SnippetStart: 525,
-			SnippetEnd:   566,
+			SnippetStart: 545,
+			SnippetEnd:   586,
 		},
 		{
 			Title:        "Trailing link",
 			Href:         "trailing",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         core.LinkRels("down"),
 			Snippet:      "Neuron links with titles: [[trailing|Trailing link]]# #[[leading |  Leading link]]",
-			SnippetStart: 568,
-			SnippetEnd:   650,
+			SnippetStart: 588,
+			SnippetEnd:   670,
 		},
 		{
 			Title:        "Leading link",
 			Href:         "leading",
+			Type:         core.LinkTypeWikiLink,
 			IsExternal:   false,
 			Rels:         core.LinkRels("up"),
 			Snippet:      "Neuron links with titles: [[trailing|Trailing link]]# #[[leading |  Leading link]]",
-			SnippetStart: 568,
-			SnippetEnd:   650,
+			SnippetStart: 588,
+			SnippetEnd:   670,
 		},
 		{
 			Title:        "External links",
 			Href:         "http://example.com",
+			Type:         core.LinkTypeMarkdown,
 			Rels:         []core.LinkRelation{},
 			IsExternal:   true,
 			Snippet:      `[External links](http://example.com) are marked [as such](ftp://domain).`,
-			SnippetStart: 652,
-			SnippetEnd:   724,
+			SnippetStart: 672,
+			SnippetEnd:   744,
 		},
 		{
 			Title:        "as such",
 			Href:         "ftp://domain",
+			Type:         core.LinkTypeMarkdown,
 			Rels:         []core.LinkRelation{},
 			IsExternal:   true,
 			Snippet:      `[External links](http://example.com) are marked [as such](ftp://domain).`,
-			SnippetStart: 652,
-			SnippetEnd:   724,
+			SnippetStart: 672,
+			SnippetEnd:   744,
+		},
+	})
+
+	// Markdown links are decoded, but not WikiLinks.
+	// i.e. https://github.com/zk-org/zk/issues/86
+	test("[foo%20bar](202110031652%20foo%20bar)", []core.Link{
+		{
+			Title:        "foo%20bar",
+			Href:         "202110031652 foo bar",
+			Type:         core.LinkTypeMarkdown,
+			IsExternal:   false,
+			Rels:         []core.LinkRelation{},
+			Snippet:      "[foo%20bar](202110031652%20foo%20bar)",
+			SnippetStart: 0,
+			SnippetEnd:   37,
+		},
+	})
+	test("[[202110031652%20foo%20bar]]", []core.Link{
+		{
+			Title:        "202110031652%20foo%20bar",
+			Href:         "202110031652%20foo%20bar",
+			Type:         core.LinkTypeWikiLink,
+			IsExternal:   false,
+			Rels:         []core.LinkRelation{},
+			Snippet:      "[[202110031652%20foo%20bar]]",
+			SnippetStart: 0,
+			SnippetEnd:   28,
 		},
 	})
 }
@@ -564,7 +625,7 @@ Paragraph
 	})
 }
 
-func parse(t *testing.T, source string) core.ParsedNote {
+func parse(t *testing.T, source string) core.NoteContent {
 	return parseWithOptions(t, source, ParserOpts{
 		HashtagEnabled:      true,
 		MultiWordTagEnabled: true,
@@ -572,8 +633,8 @@ func parse(t *testing.T, source string) core.ParsedNote {
 	})
 }
 
-func parseWithOptions(t *testing.T, source string, options ParserOpts) core.ParsedNote {
-	content, err := NewParser(options).Parse(source)
+func parseWithOptions(t *testing.T, source string, options ParserOpts) core.NoteContent {
+	content, err := NewParser(options, &util.NullLogger).ParseNoteContent(source)
 	assert.Nil(t, err)
 	return *content
 }

internal/adapter/sqlite/collection_dao.go

@@ -3,10 +3,11 @@ package sqlite
 import (
 	"database/sql"
 	"fmt"
+	"strings"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
 )
 
 // CollectionDAO persists collections (e.g. tags) in the SQLite database.
@@ -17,7 +18,6 @@ type CollectionDAO struct {
 	// Prepared SQL statements
 	createCollectionStmt   *LazyStmt
 	findCollectionStmt     *LazyStmt
-	findAllCollectionsStmt *LazyStmt
 	findAssociationStmt    *LazyStmt
 	createAssociationStmt  *LazyStmt
 	removeAssociationsStmt *LazyStmt
@@ -42,16 +42,6 @@ func NewCollectionDAO(tx Transaction, logger util.Logger) *CollectionDAO {
 			 WHERE kind = ? AND name = ?
 		`),
 
-		// Find all collections.
-		findAllCollectionsStmt: tx.PrepareLazy(`
-			SELECT c.name, COUNT(nc.id) as count
-			  FROM collections c
-			 INNER JOIN notes_collections nc ON nc.collection_id = c.id
-			 WHERE kind = ?
-			 GROUP BY c.id
-			 ORDER BY c.name
-		`),
-
 		// Returns whether a note and a collection are associated.
 		findAssociationStmt: tx.PrepareLazy(`
 			SELECT id FROM notes_collections
@@ -87,8 +77,25 @@ func (d *CollectionDAO) FindOrCreate(kind core.CollectionKind, name string) (cor
 	}
 }
 
-func (d *CollectionDAO) FindAll(kind core.CollectionKind) ([]core.Collection, error) {
-	rows, err := d.findAllCollectionsStmt.Query(kind)
+func (d *CollectionDAO) FindAll(kind core.CollectionKind, sorters []core.CollectionSorter) ([]core.Collection, error) {
+	query := `
+		SELECT c.id, c.name, COUNT(nc.id) as count
+		  FROM collections c
+		 INNER JOIN notes_collections nc ON nc.collection_id = c.id
+		 WHERE kind = ?
+		 GROUP BY c.id
+	`
+
+	orderTerms := []string{}
+	if sorters != nil {
+		for _, sorter := range sorters {
+			orderTerms = append(orderTerms, collectionOrderTerm(sorter))
+		}
+	}
+	orderTerms = append(orderTerms, `c.name ASC`)
+	query += "ORDER BY " + strings.Join(orderTerms, ", ") + "\n"
+
+	rows, err := d.tx.Query(query, kind)
 	if err != nil {
 		return []core.Collection{}, err
 	}
@@ -97,14 +104,16 @@ func (d *CollectionDAO) FindAll(kind core.CollectionKind) ([]core.Collection, er
 	collections := []core.Collection{}
 
 	for rows.Next() {
+		var id sql.NullInt64
 		var name string
 		var count int
-		err := rows.Scan(&name, &count)
+		err := rows.Scan(&id, &name, &count)
 		if err != nil {
 			return collections, err
 		}
 
 		collections = append(collections, core.Collection{
+			ID:        core.CollectionID(id.Int64),
 			Kind:      kind,
 			Name:      name,
 			NoteCount: count,
@@ -114,6 +123,22 @@ func (d *CollectionDAO) FindAll(kind core.CollectionKind) ([]core.Collection, er
 	return collections, nil
 }
 
+func collectionOrderTerm(sorter core.CollectionSorter) string {
+	order := " ASC"
+	if !sorter.Ascending {
+		order = " DESC"
+	}
+
+	switch sorter.Field {
+	case core.CollectionSortName:
+		return "c.name COLLATE NOCASE" + order
+	case core.CollectionSortNoteCount:
+		return "count" + order
+	default:
+		panic(fmt.Sprintf("%v: unknown core.CollectionSortField", sorter.Field))
+	}
+}
+
 func (d *CollectionDAO) findCollection(kind core.CollectionKind, name string) (core.CollectionID, error) {
 	wrap := errors.Wrapperf("failed to get %s named %s", kind, name)
 

internal/adapter/sqlite/collection_dao_test.go

@@ -3,9 +3,9 @@ package sqlite
 import (
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestCollectionDAOFindOrCreate(t *testing.T) {
@@ -35,18 +35,51 @@ func TestCollectionDAOFindOrCreate(t *testing.T) {
 func TestCollectionDaoFindAll(t *testing.T) {
 	testCollectionDAO(t, func(tx Transaction, dao *CollectionDAO) {
 		// Finds none
-		cs, err := dao.FindAll("missing")
+		cs, err := dao.FindAll("missing", nil)
 		assert.Nil(t, err)
 		assert.Equal(t, len(cs), 0)
 
 		// Finds existing
-		cs, err = dao.FindAll("tag")
+		cs, err = dao.FindAll("tag", nil)
 		assert.Nil(t, err)
 		assert.Equal(t, cs, []core.Collection{
-			{Kind: "tag", Name: "adventure", NoteCount: 2},
-			{Kind: "tag", Name: "fantasy", NoteCount: 1},
-			{Kind: "tag", Name: "fiction", NoteCount: 1},
-			{Kind: "tag", Name: "history", NoteCount: 1},
+			{ID: 2, Kind: "tag", Name: "adventure", NoteCount: 2},
+			{ID: 4, Kind: "tag", Name: "fantasy", NoteCount: 1},
+			{ID: 1, Kind: "tag", Name: "fiction", NoteCount: 1},
+			{ID: 5, Kind: "tag", Name: "history", NoteCount: 1},
+			{ID: 7, Kind: "tag", Name: "science", NoteCount: 3},
+		})
+	})
+}
+
+func TestCollectionDaoFindAllSortedByName(t *testing.T) {
+	testCollectionDAO(t, func(tx Transaction, dao *CollectionDAO) {
+		cs, err := dao.FindAll("tag", []core.CollectionSorter{
+			{Field: core.CollectionSortName, Ascending: false},
+		})
+		assert.Nil(t, err)
+		assert.Equal(t, cs, []core.Collection{
+			{ID: 7, Kind: "tag", Name: "science", NoteCount: 3},
+			{ID: 5, Kind: "tag", Name: "history", NoteCount: 1},
+			{ID: 1, Kind: "tag", Name: "fiction", NoteCount: 1},
+			{ID: 4, Kind: "tag", Name: "fantasy", NoteCount: 1},
+			{ID: 2, Kind: "tag", Name: "adventure", NoteCount: 2},
+		})
+	})
+}
+
+func TestCollectionDaoFindAllSortedByNoteCount(t *testing.T) {
+	testCollectionDAO(t, func(tx Transaction, dao *CollectionDAO) {
+		cs, err := dao.FindAll("tag", []core.CollectionSorter{
+			{Field: core.CollectionSortNoteCount, Ascending: false},
+		})
+		assert.Nil(t, err)
+		assert.Equal(t, cs, []core.Collection{
+			{ID: 7, Kind: "tag", Name: "science", NoteCount: 3},
+			{ID: 2, Kind: "tag", Name: "adventure", NoteCount: 2},
+			{ID: 4, Kind: "tag", Name: "fantasy", NoteCount: 1},
+			{ID: 1, Kind: "tag", Name: "fiction", NoteCount: 1},
+			{ID: 5, Kind: "tag", Name: "history", NoteCount: 1},
 		})
 	})
 }

internal/adapter/sqlite/db.go

@@ -2,10 +2,12 @@ package sqlite
 
 import (
 	"database/sql"
+	"fmt"
+	"regexp"
 
 	sqlite "github.com/mattn/go-sqlite3"
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util/errors"
 )
 
 func init() {
@@ -15,6 +17,9 @@ func init() {
 			if err := conn.RegisterFunc("mention_query", buildMentionQuery, true); err != nil {
 				return err
 			}
+			if err := conn.RegisterFunc("regexp", regexp.MatchString, true); err != nil {
+				return err
+			}
 			return nil
 		},
 	})
@@ -75,133 +80,159 @@ func (db *DB) migrate() error {
 			return err
 		}
 
-		needsReindexing := false
-
-		if version <= 0 {
-			err = tx.ExecStmts([]string{
-				// Notes
-				`CREATE TABLE IF NOT EXISTS notes (
-					id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-					path TEXT NOT NULL,
-					sortable_path TEXT NOT NULL,
-					title TEXT DEFAULT('') NOT NULL,
-					lead TEXT DEFAULT('') NOT NULL,
-					body TEXT DEFAULT('') NOT NULL,
-					raw_content TEXT DEFAULT('') NOT NULL,
-					word_count INTEGER DEFAULT(0) NOT NULL,
-					checksum TEXT NOT NULL,
-					created DATETIME DEFAULT(CURRENT_TIMESTAMP) NOT NULL,
-					modified DATETIME DEFAULT(CURRENT_TIMESTAMP) NOT NULL,
-					UNIQUE(path)
-				)`,
-				`CREATE INDEX IF NOT EXISTS index_notes_checksum ON notes (checksum)`,
-				`CREATE INDEX IF NOT EXISTS index_notes_path ON notes (path)`,
-
-				// Links
-				`CREATE TABLE IF NOT EXISTS links (
-					id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-					source_id INTEGER NOT NULL REFERENCES notes(id)
-						ON DELETE CASCADE,
-					target_id INTEGER REFERENCES notes(id)
-						ON DELETE SET NULL,
-					title TEXT DEFAULT('') NOT NULL,
-					href TEXT NOT NULL,
-					external INT DEFAULT(0) NOT NULL,
-					rels TEXT DEFAULT('') NOT NULL,
-					snippet TEXT DEFAULT('') NOT NULL
-				)`,
-				`CREATE INDEX IF NOT EXISTS index_links_source_id_target_id ON links (source_id, target_id)`,
-
-				// FTS index
-				`CREATE VIRTUAL TABLE IF NOT EXISTS notes_fts USING fts5(
-					path, title, body,
-					content = notes,
-					content_rowid = id,
-					tokenize = "porter unicode61 remove_diacritics 1 tokenchars '''&/'"
-				)`,
-				// Triggers to keep the FTS index up to date.
-				`CREATE TRIGGER IF NOT EXISTS trigger_notes_ai AFTER INSERT ON notes BEGIN
-					INSERT INTO notes_fts(rowid, path, title, body) VALUES (new.id, new.path, new.title, new.body);
-				END`,
-				`CREATE TRIGGER IF NOT EXISTS trigger_notes_ad AFTER DELETE ON notes BEGIN
-					INSERT INTO notes_fts(notes_fts, rowid, path, title, body) VALUES('delete', old.id, old.path, old.title, old.body);
-				END`,
-				`CREATE TRIGGER IF NOT EXISTS trigger_notes_au AFTER UPDATE ON notes BEGIN
-					INSERT INTO notes_fts(notes_fts, rowid, path, title, body) VALUES('delete', old.id, old.path, old.title, old.body);
-					INSERT INTO notes_fts(rowid, path, title, body) VALUES (new.id, new.path, new.title, new.body);
-				END`,
-				`PRAGMA user_version = 1`,
-			})
-			if err != nil {
-				return err
-			}
+		migrations := []struct {
+			SQL             []string
+			NeedsReindexing bool
+		}{
+			{ // 1
+				SQL: []string{
+					// Notes
+					`CREATE TABLE IF NOT EXISTS notes (
+						id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+						path TEXT NOT NULL,
+						sortable_path TEXT NOT NULL,
+						title TEXT DEFAULT('') NOT NULL,
+						lead TEXT DEFAULT('') NOT NULL,
+						body TEXT DEFAULT('') NOT NULL,
+						raw_content TEXT DEFAULT('') NOT NULL,
+						word_count INTEGER DEFAULT(0) NOT NULL,
+						checksum TEXT NOT NULL,
+						created DATETIME DEFAULT(CURRENT_TIMESTAMP) NOT NULL,
+						modified DATETIME DEFAULT(CURRENT_TIMESTAMP) NOT NULL,
+						UNIQUE(path)
+					)`,
+					`CREATE INDEX IF NOT EXISTS index_notes_checksum ON notes (checksum)`,
+					`CREATE INDEX IF NOT EXISTS index_notes_path ON notes (path)`,
+
+					// Links
+					`CREATE TABLE IF NOT EXISTS links (
+						id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+						source_id INTEGER NOT NULL REFERENCES notes(id)
+							ON DELETE CASCADE,
+						target_id INTEGER REFERENCES notes(id)
+							ON DELETE SET NULL,
+						title TEXT DEFAULT('') NOT NULL,
+						href TEXT NOT NULL,
+						external INT DEFAULT(0) NOT NULL,
+						rels TEXT DEFAULT('') NOT NULL,
+						snippet TEXT DEFAULT('') NOT NULL
+					)`,
+					`CREATE INDEX IF NOT EXISTS index_links_source_id_target_id ON links (source_id, target_id)`,
+
+					// FTS index
+					`CREATE VIRTUAL TABLE IF NOT EXISTS notes_fts USING fts5(
+						path, title, body,
+						content = notes,
+						content_rowid = id,
+						tokenize = "porter unicode61 remove_diacritics 1 tokenchars '''&/'"
+					)`,
+					// Triggers to keep the FTS index up to date.
+					`CREATE TRIGGER IF NOT EXISTS trigger_notes_ai AFTER INSERT ON notes BEGIN
+						INSERT INTO notes_fts(rowid, path, title, body) VALUES (new.id, new.path, new.title, new.body);
+					END`,
+					`CREATE TRIGGER IF NOT EXISTS trigger_notes_ad AFTER DELETE ON notes BEGIN
+						INSERT INTO notes_fts(notes_fts, rowid, path, title, body) VALUES('delete', old.id, old.path, old.title, old.body);
+					END`,
+					`CREATE TRIGGER IF NOT EXISTS trigger_notes_au AFTER UPDATE ON notes BEGIN
+						INSERT INTO notes_fts(notes_fts, rowid, path, title, body) VALUES('delete', old.id, old.path, old.title, old.body);
+						INSERT INTO notes_fts(rowid, path, title, body) VALUES (new.id, new.path, new.title, new.body);
+					END`,
+				},
+			},
+
+			{ // 2
+				SQL: []string{
+					// Collections
+					`CREATE TABLE IF NOT EXISTS collections (
+						id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+						kind TEXT NO NULL,
+						name TEXT NOT NULL,
+						UNIQUE(kind, name)
+					)`,
+					`CREATE INDEX IF NOT EXISTS index_collections ON collections (kind, name)`,
+
+					// Note-Collection association
+					`CREATE TABLE IF NOT EXISTS notes_collections (
+						id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+						note_id INTEGER NOT NULL REFERENCES notes(id)
+							ON DELETE CASCADE,
+						collection_id INTEGER NOT NULL REFERENCES collections(id)
+							ON DELETE CASCADE
+					)`,
+					`CREATE INDEX IF NOT EXISTS index_notes_collections ON notes_collections (note_id, collection_id)`,
+
+					// View of notes with their associated metadata (e.g. tags), for simpler queries.
+					`CREATE VIEW notes_with_metadata AS
+					 SELECT n.*, GROUP_CONCAT(c.name, '` + "\x01" + `') AS tags
+					   FROM notes n
+					   LEFT JOIN notes_collections nc ON nc.note_id = n.id
+					   LEFT JOIN collections c ON nc.collection_id = c.id AND c.kind = '` + string(core.CollectionKindTag) + `'
+					  GROUP BY n.id`,
+				},
+			},
+
+			{ // 3
+				SQL: []string{
+					// Add a `metadata` column to `notes`
+					`ALTER TABLE notes ADD COLUMN metadata TEXT DEFAULT('{}') NOT NULL`,
+
+					// Add snippet's start and end offsets to `links`
+					`ALTER TABLE links ADD COLUMN snippet_start INTEGER DEFAULT(0) NOT NULL`,
+					`ALTER TABLE links ADD COLUMN snippet_end INTEGER DEFAULT(0) NOT NULL`,
+				},
+				NeedsReindexing: true,
+			},
+
+			{ // 4
+				SQL: []string{
+					// Metadata
+					`CREATE TABLE IF NOT EXISTS metadata (
+						key TEXT PRIMARY KEY NOT NULL,
+						value TEXT NO NULL
+					)`,
+				},
+			},
+
+			{ // 5
+				SQL: []string{
+					// Add a `type` column to `links`
+					`ALTER TABLE links ADD COLUMN type TEXT DEFAULT('') NOT NULL`,
+				},
+				NeedsReindexing: true,
+			},
+
+			{ // 6
+				SQL: []string{
+					// View of links with the source and target notes metadata, for simpler queries.
+					`CREATE VIEW resolved_links AS
+					 SELECT l.*, s.path AS source_path, s.title AS source_title, t.path AS target_path, t.title AS target_title
+					   FROM links l
+					   LEFT JOIN notes s ON l.source_id = s.id
+					   LEFT JOIN notes t ON l.target_id = t.id`,
+				},
+			},
+
+			{ // 7
+				SQL: []string{},
+				// https://github.com/zk-org/zk/issues/170#issuecomment-1107848441
+				NeedsReindexing: true,
+			},
 		}
 
-		if version <= 1 {
-			err = tx.ExecStmts([]string{
-				// Collections
-				`CREATE TABLE IF NOT EXISTS collections (
-					id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-					kind TEXT NO NULL,
-					name TEXT NOT NULL,
-					UNIQUE(kind, name)
-				)`,
-				`CREATE INDEX IF NOT EXISTS index_collections ON collections (kind, name)`,
-
-				// Note-Collection association
-				`CREATE TABLE IF NOT EXISTS notes_collections (
-					id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-					note_id INTEGER NOT NULL REFERENCES notes(id)
-						ON DELETE CASCADE,
-					collection_id INTEGER NOT NULL REFERENCES collections(id)
-						ON DELETE CASCADE
-				)`,
-				`CREATE INDEX IF NOT EXISTS index_notes_collections ON notes_collections (note_id, collection_id)`,
-
-				// View of notes with their associated metadata (e.g. tags), for simpler queries.
-				`CREATE VIEW notes_with_metadata AS
-				 SELECT n.*, GROUP_CONCAT(c.name, '` + "\x01" + `') AS tags
-				   FROM notes n
-				   LEFT JOIN notes_collections nc ON nc.note_id = n.id
-				   LEFT JOIN collections c ON nc.collection_id = c.id AND c.kind = '` + string(core.CollectionKindTag) + `'
-				  GROUP BY n.id`,
-
-				`PRAGMA user_version = 2`,
-			})
-			if err != nil {
-				return err
-			}
-		}
-
-		if version <= 2 {
-			err = tx.ExecStmts([]string{
-				// Add a `metadata` column to `notes`
-				`ALTER TABLE notes ADD COLUMN metadata TEXT DEFAULT('{}') NOT NULL`,
-
-				// Add snippet's start and end offsets to `links`
-				`ALTER TABLE links ADD COLUMN snippet_start INTEGER DEFAULT(0) NOT NULL`,
-				`ALTER TABLE links ADD COLUMN snippet_end INTEGER DEFAULT(0) NOT NULL`,
+		needsReindexing := false
 
-				`PRAGMA user_version = 3`,
-			})
-			if err != nil {
-				return err
+		for i, migration := range migrations {
+			if version > i {
+				continue
 			}
 
-			needsReindexing = true
-		}
-
-		if version <= 3 {
-			err = tx.ExecStmts([]string{
-				// Metadata
-				`CREATE TABLE IF NOT EXISTS metadata (
-					key TEXT PRIMARY KEY NOT NULL,
-					value TEXT NO NULL
-				)`,
-			})
+			stmts := append(migration.SQL, fmt.Sprintf("PRAGMA user_version = %d", i+1))
+			err = tx.ExecStmts(stmts)
 			if err != nil {
 				return err
 			}
+
+			needsReindexing = needsReindexing || migration.NeedsReindexing
 		}
 
 		if needsReindexing {

internal/adapter/sqlite/db_test.go

@@ -3,8 +3,8 @@ package sqlite
 import (
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/util/fixtures"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/util/fixtures"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestOpen(t *testing.T) {
@@ -27,7 +27,7 @@ func TestMigrateFrom0(t *testing.T) {
 		var version int
 		err := tx.QueryRow("PRAGMA user_version").Scan(&version)
 		assert.Nil(t, err)
-		assert.Equal(t, version, 3)
+		assert.Equal(t, version, 7)
 
 		_, err = tx.Exec(`
 			INSERT INTO notes (path, sortable_path, title, body, word_count, checksum)

internal/adapter/sqlite/link_dao.go

@@ -0,0 +1,171 @@
+package sqlite
+
+import (
+	"database/sql"
+	"fmt"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+)
+
+// LinkDAO persists links in the SQLite database.
+type LinkDAO struct {
+	tx     Transaction
+	logger util.Logger
+
+	// Prepared SQL statements
+	addLinkStmt        *LazyStmt
+	removeLinksStmt    *LazyStmt
+	updateTargetIDStmt *LazyStmt
+}
+
+// NewLinkDAO creates a new instance of a DAO working on the given database
+// transaction.
+func NewLinkDAO(tx Transaction, logger util.Logger) *LinkDAO {
+	return &LinkDAO{
+		tx:     tx,
+		logger: logger,
+
+		// Add a new link.
+		addLinkStmt: tx.PrepareLazy(`
+			INSERT INTO links (source_id, target_id, title, href, type, external, rels, snippet, snippet_start, snippet_end)
+			VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+		`),
+
+		// Remove all the outbound links of a note.
+		removeLinksStmt: tx.PrepareLazy(`
+			DELETE FROM links
+			 WHERE source_id = ?
+		`),
+
+		updateTargetIDStmt: tx.PrepareLazy(`
+			UPDATE links
+			   SET target_id = ?
+			 WHERE id = ?
+		`),
+	}
+}
+
+// Add inserts all the outbound links of the given note.
+func (d *LinkDAO) Add(links []core.ResolvedLink) error {
+	for _, link := range links {
+		sourceID := noteIDToSQL(link.SourceID)
+		targetID := noteIDToSQL(link.TargetID)
+
+		_, err := d.addLinkStmt.Exec(sourceID, targetID, link.Title, link.Href, link.Type, link.IsExternal, joinLinkRels(link.Rels), link.Snippet, link.SnippetStart, link.SnippetEnd)
+		if err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+// RemoveAll removes all the outbound links of the given note.
+func (d *LinkDAO) RemoveAll(id core.NoteID) error {
+	_, err := d.removeLinksStmt.Exec(noteIDToSQL(id))
+	return err
+}
+
+// SetTargetID updates the target note of a link.
+func (d *LinkDAO) SetTargetID(id core.LinkID, targetID core.NoteID) error {
+	_, err := d.updateTargetIDStmt.Exec(noteIDToSQL(targetID), linkIDToSQL(id))
+	return err
+}
+
+// joinLinkRels will concatenate a list of rels into a SQLite ready string.
+// Each rel is delimited by \x01 for easy matching in queries.
+func joinLinkRels(rels []core.LinkRelation) string {
+	if len(rels) == 0 {
+		return ""
+	}
+	delimiter := "\x01"
+	res := delimiter
+	for _, rel := range rels {
+		res += string(rel) + delimiter
+	}
+	return res
+}
+
+// FindInternal returns all the links internal to the notebook.
+func (d *LinkDAO) FindInternal() ([]core.ResolvedLink, error) {
+	return d.findWhere("external = 0")
+}
+
+// FindBetweenNotes returns all the links existing between the given notes.
+func (d *LinkDAO) FindBetweenNotes(ids []core.NoteID) ([]core.ResolvedLink, error) {
+	idsString := joinNoteIDs(ids, ",")
+	return d.findWhere(fmt.Sprintf("source_id IN (%s) AND target_id IN (%s)", idsString, idsString))
+}
+
+// findWhere returns all the links, filtered by the given where query.
+func (d *LinkDAO) findWhere(where string) ([]core.ResolvedLink, error) {
+	links := make([]core.ResolvedLink, 0)
+
+	query := `
+		SELECT id, source_id, source_path, target_id, target_path, title, href, type, external, rels, snippet, snippet_start, snippet_end
+		  FROM resolved_links
+	`
+
+	if where != "" {
+		query += "\nWHERE " + where
+	}
+
+	rows, err := d.tx.Query(query)
+	if err != nil {
+		return links, err
+	}
+	defer rows.Close()
+
+	for rows.Next() {
+		link, err := d.scanLink(rows)
+		if err != nil {
+			d.logger.Err(err)
+			continue
+		}
+		if link != nil {
+			links = append(links, *link)
+		}
+	}
+
+	return links, nil
+}
+
+func (d *LinkDAO) scanLink(row RowScanner) (*core.ResolvedLink, error) {
+	var (
+		id, sourceID, snippetStart, snippetEnd     int
+		targetID                                   sql.NullInt64
+		sourcePath, title, href, linkType, snippet string
+		external                                   bool
+		targetPath, rels                           sql.NullString
+	)
+
+	err := row.Scan(
+		&id, &sourceID, &sourcePath, &targetID, &targetPath, &title, &href,
+		&linkType, &external, &rels, &snippet, &snippetStart, &snippetEnd,
+	)
+	switch {
+	case err == sql.ErrNoRows:
+		return nil, nil
+	case err != nil:
+		return nil, err
+	default:
+		return &core.ResolvedLink{
+			ID:         core.LinkID(id),
+			SourceID:   core.NoteID(sourceID),
+			SourcePath: sourcePath,
+			TargetID:   core.NoteID(targetID.Int64),
+			TargetPath: targetPath.String,
+			Link: core.Link{
+				Title:        title,
+				Href:         href,
+				Type:         core.LinkType(linkType),
+				IsExternal:   external,
+				Rels:         core.LinkRels(parseListFromNullString(rels)...),
+				Snippet:      snippet,
+				SnippetStart: snippetStart,
+				SnippetEnd:   snippetEnd,
+			},
+		}, nil
+	}
+}

internal/adapter/sqlite/link_dao_test.go

@@ -0,0 +1,53 @@
+package sqlite
+
+import (
+	"fmt"
+	"testing"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/test/assert"
+)
+
+func testLinkDAO(t *testing.T, callback func(tx Transaction, dao *LinkDAO)) {
+	testTransaction(t, func(tx Transaction) {
+		callback(tx, NewLinkDAO(tx, &util.NullLogger))
+	})
+}
+
+type linkRow struct {
+	SourceId                         core.NoteID
+	TargetId                         *core.NoteID
+	Href, Type, Title, Rels, Snippet string
+	SnippetStart, SnippetEnd         int
+	IsExternal                       bool
+}
+
+func queryLinkRows(t *testing.T, q RowQuerier, where string) []linkRow {
+	links := make([]linkRow, 0)
+
+	rows, err := q.Query(fmt.Sprintf(`
+		SELECT source_id, target_id, title, href, type, external, rels, snippet, snippet_start, snippet_end
+		  FROM links
+		 WHERE %v
+		 ORDER BY id
+	`, where))
+	assert.Nil(t, err)
+
+	for rows.Next() {
+		var row linkRow
+		var sourceId int64
+		var targetId *int64
+		err = rows.Scan(&sourceId, &targetId, &row.Title, &row.Href, &row.Type, &row.IsExternal, &row.Rels, &row.Snippet, &row.SnippetStart, &row.SnippetEnd)
+		assert.Nil(t, err)
+		row.SourceId = core.NoteID(sourceId)
+		if targetId != nil {
+			row.TargetId = idPointer(*targetId)
+		}
+		links = append(links, row)
+	}
+	rows.Close()
+	assert.Nil(t, rows.Err())
+
+	return links
+}

internal/adapter/sqlite/metadata_dao.go

@@ -3,7 +3,7 @@ package sqlite
 import (
 	"database/sql"
 
-	"github.com/mickael-menu/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/errors"
 )
 
 // Known metadata keys.

internal/adapter/sqlite/metadata_dao_test.go

@@ -3,7 +3,7 @@ package sqlite
 import (
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestMetadataDAOGetUnknown(t *testing.T) {

internal/adapter/sqlite/note_dao.go

@@ -5,18 +5,15 @@ import (
 	"encoding/json"
 	"fmt"
 	"regexp"
-	"strconv"
 	"strings"
 	"time"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/errors"
-	"github.com/mickael-menu/zk/internal/util/fts5"
-	"github.com/mickael-menu/zk/internal/util/icu"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	"github.com/mickael-menu/zk/internal/util/paths"
-	strutil "github.com/mickael-menu/zk/internal/util/strings"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/fts5"
+	"github.com/zk-org/zk/internal/util/paths"
+	strutil "github.com/zk-org/zk/internal/util/strings"
 )
 
 // NoteDAO persists notes in the SQLite database.
@@ -30,11 +27,8 @@ type NoteDAO struct {
 	updateStmt             *LazyStmt
 	removeStmt             *LazyStmt
 	findIdByPathStmt       *LazyStmt
-	findIdByPathPrefixStmt *LazyStmt
+	findIdsByPathRegexStmt *LazyStmt
 	findByIdStmt           *LazyStmt
-	addLinkStmt            *LazyStmt
-	setLinksTargetStmt     *LazyStmt
-	removeLinksStmt        *LazyStmt
 }
 
 // NewNoteDAO creates a new instance of a DAO working on the given database
@@ -75,10 +69,12 @@ func NewNoteDAO(tx Transaction, logger util.Logger) *NoteDAO {
 			 WHERE path = ?
 		`),
 
-		// Find a note ID from a prefix of its path.
-		findIdByPathPrefixStmt: tx.PrepareLazy(`
+		// Find note IDs from a regex matching their path.
+		findIdsByPathRegexStmt: tx.PrepareLazy(`
 			SELECT id FROM notes
-			 WHERE path LIKE ? || '%'
+			 WHERE path REGEXP ?
+				-- To find the best match possible, we sort by path length.
+				-- See https://github.com/zk-org/zk/issues/23
 			 ORDER BY LENGTH(path) ASC
 		`),
 
@@ -88,26 +84,6 @@ func NewNoteDAO(tx Transaction, logger util.Logger) *NoteDAO {
 			  FROM notes_with_metadata
 			 WHERE id = ?
 		`),
-
-		// Add a new link.
-		addLinkStmt: tx.PrepareLazy(`
-			INSERT INTO links (source_id, target_id, title, href, external, rels, snippet, snippet_start, snippet_end)
-			VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
-		`),
-
-		// Set links matching a given href and missing a target ID to the given
-		// target ID.
-		setLinksTargetStmt: tx.PrepareLazy(`
-			UPDATE links
-			   SET target_id = ?
-			 WHERE target_id IS NULL AND external = 0 AND ? LIKE href || '%'
-		`),
-
-		// Remove all the outbound links of a note.
-		removeLinksStmt: tx.PrepareLazy(`
-			DELETE FROM links
-			 WHERE source_id = ?
-		`),
 	}
 }
 
@@ -173,14 +149,12 @@ func (d *NoteDAO) Add(note core.Note) (core.NoteID, error) {
 		return 0, err
 	}
 
-	id := core.NoteID(lastId)
-	err = d.addLinks(id, note)
-	return id, err
+	return core.NoteID(lastId), err
 }
 
 // Update modifies an existing note.
 func (d *NoteDAO) Update(note core.Note) (core.NoteID, error) {
-	id, err := d.findIdByPath(note.Path)
+	id, err := d.FindIdByPath(note.Path)
 	if err != nil {
 		return 0, err
 	}
@@ -193,16 +167,6 @@ func (d *NoteDAO) Update(note core.Note) (core.NoteID, error) {
 		note.Title, note.Lead, note.Body, note.RawContent, note.WordCount,
 		metadata, note.Checksum, note.Modified, note.Path,
 	)
-	if err != nil {
-		return id, err
-	}
-
-	_, err = d.removeLinksStmt.Exec(d.idToSql(id))
-	if err != nil {
-		return id, err
-	}
-
-	err = d.addLinks(id, note)
 	return id, err
 }
 
@@ -217,41 +181,9 @@ func (d *NoteDAO) metadataToJSON(note core.Note) string {
 	return string(json)
 }
 
-// addLinks inserts all the outbound links of the given note.
-func (d *NoteDAO) addLinks(id core.NoteID, note core.Note) error {
-	for _, link := range note.Links {
-		targetId, err := d.findIdByPathPrefix(link.Href)
-		if err != nil {
-			return err
-		}
-
-		_, err = d.addLinkStmt.Exec(id, d.idToSql(targetId), link.Title, link.Href, link.IsExternal, joinLinkRels(link.Rels), link.Snippet, link.SnippetStart, link.SnippetEnd)
-		if err != nil {
-			return err
-		}
-	}
-
-	_, err := d.setLinksTargetStmt.Exec(int64(id), note.Path)
-	return err
-}
-
-// joinLinkRels will concatenate a list of rels into a SQLite ready string.
-// Each rel is delimited by \x01 for easy matching in queries.
-func joinLinkRels(rels []core.LinkRelation) string {
-	if len(rels) == 0 {
-		return ""
-	}
-	delimiter := "\x01"
-	res := delimiter
-	for _, rel := range rels {
-		res += string(rel) + delimiter
-	}
-	return res
-}
-
 // Remove deletes the note with the given path from the index.
 func (d *NoteDAO) Remove(path string) error {
-	id, err := d.findIdByPath(path)
+	id, err := d.FindIdByPath(path)
 	if err != nil {
 		return err
 	}
@@ -263,7 +195,7 @@ func (d *NoteDAO) Remove(path string) error {
 	return err
 }
 
-func (d *NoteDAO) findIdByPath(path string) (core.NoteID, error) {
+func (d *NoteDAO) FindIdByPath(path string) (core.NoteID, error) {
 	row, err := d.findIdByPathStmt.QueryRow(path)
 	if err != nil {
 		return core.NoteID(0), err
@@ -271,35 +203,49 @@ func (d *NoteDAO) findIdByPath(path string) (core.NoteID, error) {
 	return idForRow(row)
 }
 
-func (d *NoteDAO) findIdsByPathPrefixes(paths []string) ([]core.NoteID, error) {
-	ids := make([]core.NoteID, 0)
-	for _, path := range paths {
-		id, err := d.findIdByPathPrefix(path)
+func idForRow(row *sql.Row) (core.NoteID, error) {
+	var id sql.NullInt64
+	err := row.Scan(&id)
+
+	switch {
+	case err == sql.ErrNoRows:
+		return 0, nil
+	case err != nil:
+		return 0, err
+	default:
+		return core.NoteID(id.Int64), nil
+	}
+}
+
+func (d *NoteDAO) findIdsByPathRegex(regex string) ([]core.NoteID, error) {
+	ids := []core.NoteID{}
+	rows, err := d.findIdsByPathRegexStmt.Query(regex)
+	if err != nil {
+		return ids, err
+	}
+	defer rows.Close()
+
+	for rows.Next() {
+		var id sql.NullInt64
+		err := rows.Scan(&id)
 		if err != nil {
 			return ids, err
 		}
-		if id.IsValid() {
-			ids = append(ids, id)
-		}
-	}
 
-	if len(ids) == 0 {
-		return ids, fmt.Errorf("could not find notes at: " + strings.Join(paths, ", "))
+		ids = append(ids, core.NoteID(id.Int64))
 	}
+
 	return ids, nil
 }
 
-func (d *NoteDAO) findIdByPathPrefix(path string) (core.NoteID, error) {
-	row, err := d.findIdByPathPrefixStmt.QueryRow(path)
+func (d *NoteDAO) findIdWithStmt(stmt *LazyStmt, args ...interface{}) (core.NoteID, error) {
+	row, err := stmt.QueryRow(args...)
 	if err != nil {
-		return 0, err
+		return core.NoteID(0), err
 	}
-	return idForRow(row)
-}
 
-func idForRow(row *sql.Row) (core.NoteID, error) {
 	var id sql.NullInt64
-	err := row.Scan(&id)
+	err = row.Scan(&id)
 
 	switch {
 	case err == sql.ErrNoRows:
@@ -311,6 +257,54 @@ func idForRow(row *sql.Row) (core.NoteID, error) {
 	}
 }
 
+func (d *NoteDAO) FindIdByHref(href string, allowPartialHref bool) (core.NoteID, error) {
+	ids, err := d.FindIdsByHref(href, allowPartialHref)
+	if len(ids) == 0 || err != nil {
+		return 0, err
+	}
+	return ids[0], nil
+}
+
+func (d *NoteDAO) findIdsByHrefs(hrefs []string, allowPartialHrefs bool) ([]core.NoteID, error) {
+	ids := make([]core.NoteID, 0)
+	for _, href := range hrefs {
+		cids, err := d.FindIdsByHref(href, allowPartialHrefs)
+		if err != nil {
+			return ids, err
+		}
+		ids = append(ids, cids...)
+	}
+	return ids, nil
+}
+
+// FIXME: This logic is duplicated in NoteIndex.linkMatchesPath(). Maybe there's a way to share it using a custom SQLite function?
+func (d *NoteDAO) FindIdsByHref(href string, allowPartialHref bool) ([]core.NoteID, error) {
+	// Remove any anchor at the end of the HREF, since it's most likely
+	// matching a sub-section in the note.
+	href = strings.SplitN(href, "#", 2)[0]
+
+	href = regexp.QuoteMeta(href)
+
+	if allowPartialHref {
+		ids, err := d.findIdsByPathRegex("^(.*/)?[^/]*" + href + "[^/]*$")
+		if len(ids) > 0 || err != nil {
+			return ids, err
+		}
+
+		ids, err = d.findIdsByPathRegex(".*" + href + ".*")
+		if len(ids) > 0 || err != nil {
+			return ids, err
+		}
+	}
+
+	ids, err := d.findIdsByPathRegex("^(?:" + href + "[^/]*|" + href + "/.+)$")
+	if len(ids) > 0 || err != nil {
+		return ids, err
+	}
+
+	return []core.NoteID{}, nil
+}
+
 func (d *NoteDAO) FindMinimal(opts core.NoteFindOpts) ([]core.MinimalNote, error) {
 	notes := make([]core.MinimalNote, 0)
 
@@ -319,7 +313,7 @@ func (d *NoteDAO) FindMinimal(opts core.NoteFindOpts) ([]core.MinimalNote, error
 		return notes, err
 	}
 
-	rows, err := d.findRows(opts, true)
+	rows, err := d.findRows(opts, noteSelectionMinimal)
 	if err != nil {
 		return notes, err
 	}
@@ -339,27 +333,6 @@ func (d *NoteDAO) FindMinimal(opts core.NoteFindOpts) ([]core.MinimalNote, error
 	return notes, nil
 }
 
-func (d *NoteDAO) scanMinimalNote(row RowScanner) (*core.MinimalNote, error) {
-	var (
-		id          int
-		path, title string
-	)
-
-	err := row.Scan(&id, &path, &title)
-	switch {
-	case err == sql.ErrNoRows:
-		return nil, nil
-	case err != nil:
-		return nil, err
-	default:
-		return &core.MinimalNote{
-			ID:    core.NoteID(id),
-			Path:  path,
-			Title: title,
-		}, nil
-	}
-}
-
 // Find returns all the notes matching the given criteria.
 func (d *NoteDAO) Find(opts core.NoteFindOpts) ([]core.ContextualNote, error) {
 	notes := make([]core.ContextualNote, 0)
@@ -369,7 +342,7 @@ func (d *NoteDAO) Find(opts core.NoteFindOpts) ([]core.ContextualNote, error) {
 		return notes, err
 	}
 
-	rows, err := d.findRows(opts, false)
+	rows, err := d.findRows(opts, noteSelectionFull)
 	if err != nil {
 		return notes, err
 	}
@@ -389,57 +362,13 @@ func (d *NoteDAO) Find(opts core.NoteFindOpts) ([]core.ContextualNote, error) {
 	return notes, nil
 }
 
-func (d *NoteDAO) scanNote(row RowScanner) (*core.ContextualNote, error) {
-	var (
-		id, wordCount                 int
-		title, lead, body, rawContent string
-		snippets, tags                sql.NullString
-		path, metadataJSON, checksum  string
-		created, modified             time.Time
-	)
-
-	err := row.Scan(
-		&id, &path, &title, &lead, &body, &rawContent, &wordCount,
-		&created, &modified, &metadataJSON, &checksum, &tags, &snippets,
-	)
-	switch {
-	case err == sql.ErrNoRows:
-		return nil, nil
-	case err != nil:
-		return nil, err
-	default:
-		metadata, err := unmarshalMetadata(metadataJSON)
-		if err != nil {
-			d.logger.Err(errors.Wrap(err, path))
-		}
-
-		return &core.ContextualNote{
-			Snippets: parseListFromNullString(snippets),
-			Note: core.Note{
-				ID:         core.NoteID(id),
-				Path:       path,
-				Title:      title,
-				Lead:       lead,
-				Body:       body,
-				RawContent: rawContent,
-				WordCount:  wordCount,
-				Links:      []core.Link{},
-				Tags:       parseListFromNullString(tags),
-				Metadata:   metadata,
-				Created:    created,
-				Modified:   modified,
-				Checksum:   checksum,
-			},
-		}, nil
-	}
-}
-
 // parseListFromNullString splits a 0-separated string.
 func parseListFromNullString(str sql.NullString) []string {
 	list := []string{}
 	if str.Valid && str.String != "" {
 		list = strings.Split(str.String, "\x01")
 		list = strutil.RemoveDuplicates(list)
+		list = strutil.RemoveBlank(list)
 	}
 	return list
 }
@@ -450,23 +379,24 @@ func (d *NoteDAO) expandMentionsIntoMatch(opts core.NoteFindOpts) (core.NoteFind
 	if opts.Mention == nil {
 		return opts, nil
 	}
-	if opts.ExactMatch {
-		return opts, fmt.Errorf("--exact-match and --mention cannot be used together")
+	if opts.MatchStrategy != core.MatchStrategyFts {
+		return opts, fmt.Errorf("--mention can only be used with --match-strategy=fts")
 	}
 
 	// Find the IDs for the mentioned paths.
-	ids, err := d.findIdsByPathPrefixes(opts.Mention)
+	ids, err := d.findIdsByHrefs(opts.Mention, true /* allowPartialHrefs */)
 	if err != nil {
 		return opts, err
 	}
+	if len(ids) == 0 {
+		return opts, fmt.Errorf("could not find notes at: " + strings.Join(opts.Mention, ", "))
+	}
 
 	// Exclude the mentioned notes from the results.
-	for _, id := range ids {
-		opts = opts.ExcludingID(id)
-	}
+	opts = opts.ExcludingIDs(ids)
 
 	// Find their titles.
-	titlesQuery := "SELECT title, metadata FROM notes WHERE id IN (" + d.joinIds(ids, ",") + ")"
+	titlesQuery := "SELECT title, metadata FROM notes WHERE id IN (" + joinNoteIDs(ids, ",") + ")"
 	rows, err := d.tx.Query(titlesQuery)
 	if err != nil {
 		return opts, err
@@ -490,14 +420,21 @@ func (d *NoteDAO) expandMentionsIntoMatch(opts core.NoteFindOpts) (core.NoteFind
 	}
 
 	// Expand the mention queries in the match predicate.
-	match := opts.Match.String()
-	match += " " + strings.Join(mentionQueries, " OR ")
-	opts.Match = opt.NewString(match)
+	opts.Match = append(opts.Match, " ("+strings.Join(mentionQueries, " OR ")+") ")
 
 	return opts, nil
 }
 
-func (d *NoteDAO) findRows(opts core.NoteFindOpts, minimal bool) (*sql.Rows, error) {
+// noteSelection represents the amount of column selected with findRows.
+type noteSelection int
+
+const (
+	noteSelectionID noteSelection = iota + 1
+	noteSelectionMinimal
+	noteSelectionFull
+)
+
+func (d *NoteDAO) findRows(opts core.NoteFindOpts, selection noteSelection) (*sql.Rows, error) {
 	snippetCol := `n.lead`
 	joinClauses := []string{}
 	whereExprs := []string{}
@@ -508,42 +445,44 @@ func (d *NoteDAO) findRows(opts core.NoteFindOpts, minimal bool) (*sql.Rows, err
 	transitiveClosure := false
 	maxDistance := 0
 
-	setupLinkFilter := func(paths []string, direction int, negate, recursive bool) error {
-		ids, err := d.findIdsByPathPrefixes(paths)
+	setupLinkFilter := func(tableAlias string, hrefs []string, direction int, negate, recursive bool) error {
+		ids, err := d.findIdsByHrefs(hrefs, true /* allowPartialHrefs */)
 		if err != nil {
 			return err
 		}
 		if len(ids) == 0 {
-			return nil
+			return fmt.Errorf("could not find notes at: " + strings.Join(hrefs, ", "))
 		}
-		idsList := "(" + d.joinIds(ids, ",") + ")"
+		idsList := "(" + joinNoteIDs(ids, ",") + ")"
 
 		linksSrc := "links"
 
 		if recursive {
 			transitiveClosure = true
 			linksSrc = "transitive_closure"
+			additionalOrderTerms = append(additionalOrderTerms, tableAlias+".distance")
 		}
 
 		if !negate {
 			if direction != 0 {
-				snippetCol = "GROUP_CONCAT(REPLACE(l.snippet, l.title, '<zk:match>' || l.title || '</zk:match>'), '\x01')"
+				snippetCol = fmt.Sprintf("GROUP_CONCAT(REPLACE(%s.snippet, %[1]s.title, '<zk:match>' || %[1]s.title || '</zk:match>'), '\x01')", tableAlias)
 			}
 
 			joinOns := make([]string, 0)
 			if direction <= 0 {
 				joinOns = append(joinOns, fmt.Sprintf(
-					"(n.id = l.target_id AND l.source_id IN %s)", idsList,
+					"(n.id = %[1]s.target_id AND %[1]s.source_id IN %[2]s)", tableAlias, idsList,
 				))
 			}
 			if direction >= 0 {
 				joinOns = append(joinOns, fmt.Sprintf(
-					"(n.id = l.source_id AND l.target_id IN %s)", idsList,
+					"(n.id = %[1]s.source_id AND %[1]s.target_id IN %[2]s)", tableAlias, idsList,
 				))
 			}
 
 			joinClauses = append(joinClauses, fmt.Sprintf(
-				"LEFT JOIN %s l ON %s",
+				"LEFT JOIN %[2]s %[1]s ON %[3]s",
+				tableAlias,
 				linksSrc,
 				strings.Join(joinOns, " OR "),
 			))
@@ -577,35 +516,44 @@ func (d *NoteDAO) findRows(opts core.NoteFindOpts, minimal bool) (*sql.Rows, err
 		return nil
 	}
 
-	if !opts.Match.IsNull() {
-		if opts.ExactMatch {
-			whereExprs = append(whereExprs, `n.raw_content LIKE '%' || ? || '%' ESCAPE '\'`)
-			args = append(args, escapeLikeTerm(opts.Match.String(), '\\'))
-		} else {
+	if 0 < len(opts.Match) {
+		switch opts.MatchStrategy {
+		case core.MatchStrategyExact:
+			for _, match := range opts.Match {
+				whereExprs = append(whereExprs, `n.raw_content LIKE '%' || ? || '%' ESCAPE '\'`)
+				args = append(args, escapeLikeTerm(match, '\\'))
+			}
+		case core.MatchStrategyFts:
 			snippetCol = `snippet(fts_match.notes_fts, 2, '<zk:match>', '</zk:match>', '…', 20)`
 			joinClauses = append(joinClauses, "JOIN notes_fts fts_match ON n.id = fts_match.rowid")
 			additionalOrderTerms = append(additionalOrderTerms, `bm25(fts_match.notes_fts, 1000.0, 500.0, 1.0)`)
-			whereExprs = append(whereExprs, "fts_match.notes_fts MATCH ?")
-			args = append(args, fts5.ConvertQuery(opts.Match.String()))
+			for _, match := range opts.Match {
+				whereExprs = append(whereExprs, "fts_match.notes_fts MATCH ?")
+				args = append(args, fts5.ConvertQuery(match))
+			}
+		case core.MatchStrategyRe:
+			for _, match := range opts.Match {
+				whereExprs = append(whereExprs, "n.raw_content REGEXP ?")
+				args = append(args, match)
+			}
+			break
 		}
 	}
 
-	if opts.IncludePaths != nil {
-		regexes := make([]string, 0)
-		for _, path := range opts.IncludePaths {
-			regexes = append(regexes, "n.path REGEXP ?")
-			args = append(args, pathRegex(path))
+	if opts.IncludeHrefs != nil {
+		ids, err := d.findIdsByHrefs(opts.IncludeHrefs, opts.AllowPartialHrefs)
+		if err != nil {
+			return nil, err
 		}
-		whereExprs = append(whereExprs, strings.Join(regexes, " OR "))
+		opts = opts.IncludingIDs(ids)
 	}
 
-	if opts.ExcludePaths != nil {
-		regexes := make([]string, 0)
-		for _, path := range opts.ExcludePaths {
-			regexes = append(regexes, "n.path NOT REGEXP ?")
-			args = append(args, pathRegex(path))
+	if opts.ExcludeHrefs != nil {
+		ids, err := d.findIdsByHrefs(opts.ExcludeHrefs, opts.AllowPartialHrefs)
+		if err != nil {
+			return nil, err
 		}
-		whereExprs = append(whereExprs, strings.Join(regexes, " AND "))
+		opts = opts.ExcludingIDs(ids)
 	}
 
 	if opts.Tags != nil {
@@ -657,24 +605,25 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 	}
 
 	if opts.MentionedBy != nil {
-		ids, err := d.findIdsByPathPrefixes(opts.MentionedBy)
+		ids, err := d.findIdsByHrefs(opts.MentionedBy, true /* allowPartialHrefs */)
 		if err != nil {
 			return nil, err
 		}
+		if len(ids) == 0 {
+			return nil, fmt.Errorf("could not find notes at: " + strings.Join(opts.MentionedBy, ", "))
+		}
 
 		// Exclude the mentioning notes from the results.
-		for _, id := range ids {
-			opts = opts.ExcludingID(id)
-		}
+		opts = opts.ExcludingIDs(ids)
 
 		snippetCol = `snippet(nsrc.notes_fts, 2, '<zk:match>', '</zk:match>', '…', 20)`
-		joinClauses = append(joinClauses, "JOIN notes_fts nsrc ON nsrc.rowid IN ("+d.joinIds(ids, ",")+") AND nsrc.notes_fts MATCH mention_query(n.title, n.metadata)")
+		joinClauses = append(joinClauses, "JOIN notes_fts nsrc ON nsrc.rowid IN ("+joinNoteIDs(ids, ",")+") AND nsrc.notes_fts MATCH mention_query(n.title, n.metadata)")
 	}
 
 	if opts.LinkedBy != nil {
 		filter := opts.LinkedBy
 		maxDistance = filter.MaxDistance
-		err := setupLinkFilter(filter.Paths, -1, filter.Negate, filter.Recursive)
+		err := setupLinkFilter("l_by", filter.Hrefs, -1, filter.Negate, filter.Recursive)
 		if err != nil {
 			return nil, err
 		}
@@ -683,7 +632,7 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 	if opts.LinkTo != nil {
 		filter := opts.LinkTo
 		maxDistance = filter.MaxDistance
-		err := setupLinkFilter(filter.Paths, 1, filter.Negate, filter.Recursive)
+		err := setupLinkFilter("l_to", filter.Hrefs, 1, filter.Negate, filter.Recursive)
 		if err != nil {
 			return nil, err
 		}
@@ -691,11 +640,11 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 
 	if opts.Related != nil {
 		maxDistance = 2
-		err := setupLinkFilter(opts.Related, 0, false, true)
+		err := setupLinkFilter("l_rel", opts.Related, 0, false, true)
 		if err != nil {
 			return nil, err
 		}
-		groupBy += " HAVING MIN(l.distance) = 2"
+		groupBy += " HAVING MIN(l_rel.distance) = 2"
 	}
 
 	if opts.Orphan {
@@ -724,8 +673,12 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 		args = append(args, opts.ModifiedEnd)
 	}
 
+	if opts.IncludeIDs != nil {
+		whereExprs = append(whereExprs, "n.id IN ("+joinNoteIDs(opts.IncludeIDs, ",")+")")
+	}
+
 	if opts.ExcludeIDs != nil {
-		whereExprs = append(whereExprs, "n.id NOT IN ("+d.joinIds(opts.ExcludeIDs, ",")+")")
+		whereExprs = append(whereExprs, "n.id NOT IN ("+joinNoteIDs(opts.ExcludeIDs, ",")+")")
 	}
 
 	orderTerms := []string{}
@@ -739,8 +692,6 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 
 	// Credit to https://inviqa.com/blog/storing-graphs-database-sql-meets-social-network
 	if transitiveClosure {
-		orderTerms = append([]string{"l.distance"}, orderTerms...)
-
 		query += `WITH RECURSIVE transitive_closure(source_id, target_id, title, snippet, distance, path) AS (
     SELECT source_id, target_id, title, snippet,
            1 AS distance,
@@ -767,9 +718,12 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 		query += "\n)\n"
 	}
 
-	query += "SELECT n.id, n.path, n.title"
-	if !minimal {
-		query += fmt.Sprintf(", n.lead, n.body, n.raw_content, n.word_count, n.created, n.modified, n.metadata, n.checksum, n.tags, %s AS snippet", snippetCol)
+	query += "SELECT n.id"
+	if selection != noteSelectionID {
+		query += ", n.path, n.title, n.metadata"
+		if selection != noteSelectionMinimal {
+			query += fmt.Sprintf(", n.lead, n.body, n.raw_content, n.word_count, n.created, n.modified, n.checksum, n.tags, %s AS snippet", snippetCol)
+		}
 	}
 
 	query += "\nFROM notes_with_metadata n\n"
@@ -798,6 +752,91 @@ WHERE collection_id IN (SELECT id FROM collections t WHERE kind = '%s' AND (%s))
 	return d.tx.Query(query, args...)
 }
 
+func (d *NoteDAO) scanNoteID(row RowScanner) (core.NoteID, error) {
+	var id int
+	err := row.Scan(&id)
+	switch {
+	case err == sql.ErrNoRows:
+		return 0, nil
+	case err != nil:
+		return 0, err
+	default:
+		return core.NoteID(id), nil
+	}
+}
+
+func (d *NoteDAO) scanMinimalNote(row RowScanner) (*core.MinimalNote, error) {
+	var (
+		id                        int
+		path, title, metadataJSON string
+	)
+
+	err := row.Scan(&id, &path, &title, &metadataJSON)
+	switch {
+	case err == sql.ErrNoRows:
+		return nil, nil
+	case err != nil:
+		return nil, err
+	default:
+		metadata, err := unmarshalMetadata(metadataJSON)
+		if err != nil {
+			d.logger.Err(errors.Wrap(err, path))
+		}
+
+		return &core.MinimalNote{
+			ID:       core.NoteID(id),
+			Path:     path,
+			Title:    title,
+			Metadata: metadata,
+		}, nil
+	}
+}
+
+func (d *NoteDAO) scanNote(row RowScanner) (*core.ContextualNote, error) {
+	var (
+		id, wordCount                 int
+		title, lead, body, rawContent string
+		snippets, tags                sql.NullString
+		path, metadataJSON, checksum  string
+		created, modified             time.Time
+	)
+
+	err := row.Scan(
+		&id, &path, &title, &metadataJSON, &lead, &body, &rawContent,
+		&wordCount, &created, &modified, &checksum, &tags, &snippets,
+	)
+	switch {
+	case err == sql.ErrNoRows:
+		return nil, nil
+	case err != nil:
+		return nil, err
+	default:
+		metadata, err := unmarshalMetadata(metadataJSON)
+		if err != nil {
+			d.logger.Err(errors.Wrap(err, path))
+		}
+
+		return &core.ContextualNote{
+			Snippets: parseListFromNullString(snippets),
+			Note: core.Note{
+				ID:         core.NoteID(id),
+				Path:       path,
+				Title:      title,
+				Lead:       lead,
+				Body:       body,
+				RawContent: rawContent,
+				WordCount:  wordCount,
+				Links:      []core.Link{},
+				Tags:       parseListFromNullString(tags),
+				Metadata:   metadata,
+				Created:    created,
+				Modified:   modified,
+				Checksum:   checksum,
+			},
+		}, nil
+	}
+}
+
 func orderTerm(sorter core.NoteSorter) string {
 	order := " ASC"
 	if !sorter.Ascending {
@@ -817,42 +856,11 @@ func orderTerm(sorter core.NoteSorter) string {
 		return "n.title" + order
 	case core.NoteSortWordCount:
 		return "n.word_count" + order
-	case core.NoteSortPathLength:
-		return "LENGTH(path)" + order
 	default:
 		panic(fmt.Sprintf("%v: unknown core.NoteSortField", sorter.Field))
 	}
 }
 
-// pathRegex returns an ICU regex to match the files in the folder at given
-// `path`, or any file having `path` for prefix.
-func pathRegex(path string) string {
-	path = icu.EscapePattern(path)
-	return path + "[^/]*|" + path + "/.+"
-}
-
-func (d *NoteDAO) idToSql(id core.NoteID) sql.NullInt64 {
-	if id.IsValid() {
-		return sql.NullInt64{Int64: int64(id), Valid: true}
-	} else {
-		return sql.NullInt64{}
-	}
-}
-
-func (d *NoteDAO) joinIds(ids []core.NoteID, delimiter string) string {
-	strs := make([]string, 0)
-	for _, i := range ids {
-		strs = append(strs, strconv.FormatInt(int64(i), 10))
-	}
-	return strings.Join(strs, delimiter)
-}
-
-func unmarshalMetadata(metadataJSON string) (metadata map[string]interface{}, err error) {
-	err = json.Unmarshal([]byte(metadataJSON), &metadata)
-	err = errors.Wrapf(err, "cannot parse note metadata from JSON: %s", metadataJSON)
-	return
-}
-
 // buildMentionQuery creates an FTS5 predicate to match the given note's title
 // (or aliases from the metadata) in the content of another note.
 //
@@ -894,7 +902,3 @@ func buildMentionQuery(title, metadataJSON string) string {
 
 	return "(" + strings.Join(titles, " OR ") + ")"
 }
-
-type RowScanner interface {
-	Scan(dest ...interface{}) error
-}

internal/adapter/sqlite/note_dao_test.go

@@ -6,11 +6,11 @@ import (
 	"testing"
 	"time"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/opt"
-	"github.com/mickael-menu/zk/internal/util/paths"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/opt"
+	"github.com/zk-org/zk/internal/util/paths"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 func TestNoteDAOIndexed(t *testing.T) {
@@ -135,108 +135,6 @@ func TestNoteDAOAdd(t *testing.T) {
 	})
 }
 
-func TestNoteDAOAddWithLinks(t *testing.T) {
-	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
-		id, err := dao.Add(core.Note{
-			Path: "log/added.md",
-			Links: []core.Link{
-				{
-					Title: "Same dir",
-					Href:  "log/2021-01-04",
-					Rels:  core.LinkRels("rel-1", "rel-2"),
-				},
-				{
-					Title:        "Relative",
-					Href:         "f39c8",
-					Snippet:      "[Relative](f39c8) link",
-					SnippetStart: 50,
-					SnippetEnd:   100,
-				},
-				{
-					Title: "Second is added",
-					Href:  "f39c8",
-					Rels:  core.LinkRels("second"),
-				},
-				{
-					Title: "Unknown",
-					Href:  "unknown",
-				},
-				{
-					Title:      "URL",
-					Href:       "http://example.com",
-					IsExternal: true,
-					Snippet:    "External [URL](http://example.com)",
-				},
-			},
-		})
-		assert.Nil(t, err)
-
-		rows := queryLinkRows(t, tx, fmt.Sprintf("source_id = %d", id))
-		assert.Equal(t, rows, []linkRow{
-			{
-				SourceId: id,
-				TargetId: idPointer(2),
-				Title:    "Same dir",
-				Href:     "log/2021-01-04",
-				Rels:     "\x01rel-1\x01rel-2\x01",
-			},
-			{
-				SourceId:     id,
-				TargetId:     idPointer(4),
-				Title:        "Relative",
-				Href:         "f39c8",
-				Rels:         "",
-				Snippet:      "[Relative](f39c8) link",
-				SnippetStart: 50,
-				SnippetEnd:   100,
-			},
-			{
-				SourceId: id,
-				TargetId: idPointer(4),
-				Title:    "Second is added",
-				Href:     "f39c8",
-				Rels:     "\x01second\x01",
-			},
-			{
-				SourceId: id,
-				TargetId: nil,
-				Title:    "Unknown",
-				Href:     "unknown",
-				Rels:     "",
-			},
-			{
-				SourceId:   id,
-				TargetId:   nil,
-				Title:      "URL",
-				Href:       "http://example.com",
-				IsExternal: true,
-				Rels:       "",
-				Snippet:    "External [URL](http://example.com)",
-			},
-		})
-	})
-}
-
-func TestNoteDAOAddFillsLinksMissingTargetId(t *testing.T) {
-	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
-		id, err := dao.Add(core.Note{
-			Path: "missing_target.md",
-		})
-		assert.Nil(t, err)
-
-		rows := queryLinkRows(t, tx, fmt.Sprintf("target_id = %d", id))
-		assert.Equal(t, rows, []linkRow{
-			{
-				SourceId: 3,
-				TargetId: &id,
-				Title:    "Missing target",
-				Href:     "missing",
-				Snippet:  "There's a Missing target",
-			},
-		})
-	})
-}
-
 // Check that we can't add a duplicate note with an existing path.
 func TestNoteDAOAddExistingNote(t *testing.T) {
 	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
@@ -288,69 +186,6 @@ func TestNoteDAOUpdateUnknown(t *testing.T) {
 	})
 }
 
-func TestNoteDAOUpdateWithLinks(t *testing.T) {
-	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
-		links := queryLinkRows(t, tx, "source_id = 1")
-		assert.Equal(t, links, []linkRow{
-			{
-				SourceId: 1,
-				TargetId: idPointer(2),
-				Title:    "An internal link",
-				Href:     "log/2021-01-04.md",
-				Snippet:  "[[An internal link]]",
-			},
-			{
-				SourceId:   1,
-				TargetId:   nil,
-				Title:      "An external link",
-				Href:       "https://domain.com",
-				IsExternal: true,
-				Snippet:    "[[An external link]]",
-			},
-		})
-
-		_, err := dao.Update(core.Note{
-			Path: "log/2021-01-03.md",
-			Links: []core.Link{
-				{
-					Title:      "A new link",
-					Href:       "index",
-					IsExternal: false,
-					Rels:       core.LinkRels("rel"),
-					Snippet:    "[[A new link]]",
-				},
-				{
-					Title:      "An external link",
-					Href:       "https://domain.com",
-					IsExternal: true,
-					Snippet:    "[[An external link]]",
-				},
-			},
-		})
-		assert.Nil(t, err)
-
-		links = queryLinkRows(t, tx, "source_id = 1")
-		assert.Equal(t, links, []linkRow{
-			{
-				SourceId: 1,
-				TargetId: idPointer(3),
-				Title:    "A new link",
-				Href:     "index",
-				Rels:     "\x01rel\x01",
-				Snippet:  "[[A new link]]",
-			},
-			{
-				SourceId:   1,
-				TargetId:   nil,
-				Title:      "An external link",
-				Href:       "https://domain.com",
-				IsExternal: true,
-				Snippet:    "[[An external link]]",
-			},
-		})
-	})
-}
-
 func TestNoteDAORemove(t *testing.T) {
 	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
 		_, err := queryNoteRow(tx, `path = "ref/test/a.md"`)
@@ -391,19 +226,85 @@ func TestNoteDAORemoveCascadeLinks(t *testing.T) {
 	})
 }
 
+func TestNoteDAOFindIdsByHref(t *testing.T) {
+	test := func(href string, allowPartialHref bool, expected []core.NoteID) {
+		testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+			actual, err := dao.FindIdsByHref(href, allowPartialHref)
+			assert.Nil(t, err)
+			assert.Equal(t, actual, expected)
+		})
+	}
+
+	test("test", false, []core.NoteID{})
+	test("test", true, []core.NoteID{6, 5, 8})
+
+	// Filename takes precedence over the rest of the path.
+	// See https://github.com/zk-org/zk/issues/111
+	test("ref", true, []core.NoteID{8})
+}
+
+func TestNoteDAOFindIncludingHrefs(t *testing.T) {
+	test := func(href string, allowPartialHref bool, expected []string) {
+		testNoteDAOFindPaths(t,
+			core.NoteFindOpts{
+				IncludeHrefs:      []string{href},
+				AllowPartialHrefs: allowPartialHref,
+			},
+			expected,
+		)
+	}
+
+	test("test", false, []string{})
+	test("test", true, []string{"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md"})
+
+	// Filename takes precedence over the rest of the path.
+	// See https://github.com/zk-org/zk/issues/111
+	test("ref", true, []string{"ref/test/ref.md"})
+}
+
+func TestNoteDAOFindExcludingHrefs(t *testing.T) {
+	test := func(href string, allowPartialHref bool, expected []string) {
+		testNoteDAOFindPaths(t,
+			core.NoteFindOpts{
+				ExcludeHrefs:      []string{href},
+				AllowPartialHrefs: allowPartialHref,
+			},
+			expected,
+		)
+	}
+
+	test("test", false, []string{"ref/test/ref.md", "ref/test/b.md",
+		"f39c8.md", "ref/test/a.md", "log/2021-01-03.md", "log/2021-02-04.md",
+		"index.md", "log/2021-01-04.md"})
+	test("test", true, []string{"f39c8.md", "log/2021-01-03.md",
+		"log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
+
+	// Filename takes precedence over the rest of the path.
+	// See https://github.com/zk-org/zk/issues/111
+	test("ref", true, []string{"ref/test/b.md", "f39c8.md", "ref/test/a.md",
+		"log/2021-01-03.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
+}
+
 func TestNoteDAOFindMinimalAll(t *testing.T) {
 	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
 		notes, err := dao.FindMinimal(core.NoteFindOpts{})
 		assert.Nil(t, err)
 
 		assert.Equal(t, notes, []core.MinimalNote{
-			{ID: 5, Path: "ref/test/b.md", Title: "A nested note"},
-			{ID: 4, Path: "f39c8.md", Title: "An interesting note"},
-			{ID: 6, Path: "ref/test/a.md", Title: "Another nested note"},
-			{ID: 1, Path: "log/2021-01-03.md", Title: "Daily note"},
-			{ID: 7, Path: "log/2021-02-04.md", Title: "February 4, 2021"},
-			{ID: 3, Path: "index.md", Title: "Index"},
-			{ID: 2, Path: "log/2021-01-04.md", Title: "January 4, 2021"},
+			{ID: 8, Path: "ref/test/ref.md", Title: "", Metadata: map[string]interface{}{}},
+			{ID: 5, Path: "ref/test/b.md", Title: "A nested note", Metadata: map[string]interface{}{}},
+			{ID: 4, Path: "f39c8.md", Title: "An interesting note", Metadata: map[string]interface{}{}},
+			{ID: 6, Path: "ref/test/a.md", Title: "Another nested note", Metadata: map[string]interface{}{
+				"alias": "a.md",
+			}},
+			{ID: 1, Path: "log/2021-01-03.md", Title: "Daily note", Metadata: map[string]interface{}{
+				"author": "Dom",
+			}},
+			{ID: 7, Path: "log/2021-02-04.md", Title: "February 4, 2021", Metadata: map[string]interface{}{}},
+			{ID: 3, Path: "index.md", Title: "Index", Metadata: map[string]interface{}{
+				"aliases": []interface{}{"First page"},
+			}},
+			{ID: 2, Path: "log/2021-01-04.md", Title: "January 4, 2021", Metadata: map[string]interface{}{}},
 		})
 	})
 }
@@ -411,29 +312,35 @@ func TestNoteDAOFindMinimalAll(t *testing.T) {
 func TestNoteDAOFindMinimalWithFilter(t *testing.T) {
 	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
 		notes, err := dao.FindMinimal(core.NoteFindOpts{
-			Match:   opt.NewString("daily | index"),
-			Sorters: []core.NoteSorter{{Field: core.NoteSortWordCount, Ascending: true}},
-			Limit:   3,
+			Match:         []string{"daily | index"},
+			MatchStrategy: core.MatchStrategyFts,
+			Sorters:       []core.NoteSorter{{Field: core.NoteSortWordCount, Ascending: true}},
+			Limit:         3,
 		})
 		assert.Nil(t, err)
 
 		assert.Equal(t, notes, []core.MinimalNote{
-			{ID: 1, Path: "log/2021-01-03.md", Title: "Daily note"},
-			{ID: 3, Path: "index.md", Title: "Index"},
-			{ID: 7, Path: "log/2021-02-04.md", Title: "February 4, 2021"},
+			{ID: 1, Path: "log/2021-01-03.md", Title: "Daily note", Metadata: map[string]interface{}{
+				"author": "Dom",
+			}},
+			{ID: 3, Path: "index.md", Title: "Index", Metadata: map[string]interface{}{
+				"aliases": []interface{}{"First page"},
+			}},
+			{ID: 7, Path: "log/2021-02-04.md", Title: "February 4, 2021", Metadata: map[string]interface{}{}},
 		})
 	})
 }
 
 func TestNoteDAOFindAll(t *testing.T) {
 	testNoteDAOFindPaths(t, core.NoteFindOpts{}, []string{
-		"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-01-03.md",
+		"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-01-03.md",
 		"log/2021-02-04.md", "index.md", "log/2021-01-04.md",
 	})
 }
 
 func TestNoteDAOFindLimit(t *testing.T) {
-	testNoteDAOFindPaths(t, core.NoteFindOpts{Limit: 2}, []string{
+	testNoteDAOFindPaths(t, core.NoteFindOpts{Limit: 3}, []string{
+		"ref/test/ref.md",
 		"ref/test/b.md",
 		"f39c8.md",
 	})
@@ -453,14 +360,17 @@ func TestNoteDAOFindTag(t *testing.T) {
 	test([]string{"fiction | adventure | fantasy"}, []string{"ref/test/b.md", "f39c8.md", "log/2021-01-03.md"})
 	test([]string{"fiction | history", "adventure"}, []string{"ref/test/b.md", "log/2021-01-03.md"})
 	test([]string{"fiction", "unknown"}, []string{})
-	test([]string{"-fiction"}, []string{"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
-	test([]string{"NOT   fiction"}, []string{"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
-	test([]string{"NOTfiction"}, []string{"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
+	test([]string{"-fiction"}, []string{"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
+	test([]string{"NOT   fiction"}, []string{"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
+	test([]string{"NOTfiction"}, []string{"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"})
 }
 
 func TestNoteDAOFindMatch(t *testing.T) {
 	testNoteDAOFind(t,
-		core.NoteFindOpts{Match: opt.NewString("daily | index")},
+		core.NoteFindOpts{
+			Match:         []string{"daily | index"},
+			MatchStrategy: core.MatchStrategyFts,
+		},
 		[]core.ContextualNote{
 			{
 				Note: core.Note{
@@ -542,10 +452,26 @@ func TestNoteDAOFindMatch(t *testing.T) {
 	)
 }
 
+func TestNoteDAOFindMatchWithMultiMatch(t *testing.T) {
+	testNoteDAOFindPaths(t,
+		core.NoteFindOpts{
+			Match:         []string{"daily | index", "second"},
+			MatchStrategy: core.MatchStrategyFts,
+			Sorters: []core.NoteSorter{
+				{Field: core.NoteSortPath, Ascending: false},
+			},
+		},
+		[]string{
+			"log/2021-01-04.md",
+		},
+	)
+}
+
 func TestNoteDAOFindMatchWithSort(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			Match: opt.NewString("daily | index"),
+			Match:         []string{"daily | index"},
+			MatchStrategy: core.MatchStrategyFts,
 			Sorters: []core.NoteSorter{
 				{Field: core.NoteSortPath, Ascending: false},
 			},
@@ -563,8 +489,8 @@ func TestNoteDAOFindExactMatch(t *testing.T) {
 	test := func(match string, expected []string) {
 		testNoteDAOFindPaths(t,
 			core.NoteFindOpts{
-				Match:      opt.NewString(match),
-				ExactMatch: true,
+				Match:         []string{match},
+				MatchStrategy: core.MatchStrategyExact,
 			},
 			expected,
 		)
@@ -576,20 +502,34 @@ func TestNoteDAOFindExactMatch(t *testing.T) {
 	test(`[exact% ch\ar_acters]`, []string{"ref/test/a.md"})
 }
 
-func TestNoteDAOFindExactMatchCannotBeUsedWithMention(t *testing.T) {
+func TestNoteDAOFindMentionRequiresFtsMatchStrategy(t *testing.T) {
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		_, err := dao.Find(core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyExact,
+			Mention:       []string{"mention"},
+		})
+		assert.Err(t, err, "--mention can only be used with --match-strategy=fts")
+	})
 	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
 		_, err := dao.Find(core.NoteFindOpts{
-			ExactMatch: true,
-			Mention:    []string{"mention"},
+			MatchStrategy: core.MatchStrategyRe,
+			Mention:       []string{"mention"},
 		})
-		assert.Err(t, err, "--exact-match and --mention cannot be used together")
+		assert.Err(t, err, "--mention can only be used with --match-strategy=fts")
+	})
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		_, err := dao.Find(core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyFts,
+			Mention:       []string{"mention"},
+		})
+		assert.Err(t, err, "could not find notes at: mention")
 	})
 }
 
 func TestNoteDAOFindInPathAbsoluteFile(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			IncludePaths: []string{"log/2021-01-03.md"},
+			IncludeHrefs: []string{"log/2021-01-03.md"},
 		},
 		[]string{"log/2021-01-03.md"},
 	)
@@ -599,7 +539,7 @@ func TestNoteDAOFindInPathAbsoluteFile(t *testing.T) {
 func TestNoteDAOFindInPathWithFilePrefix(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			IncludePaths: []string{"log/2021-01"},
+			IncludeHrefs: []string{"log/2021-01"},
 		},
 		[]string{"log/2021-01-03.md", "log/2021-01-04.md"},
 	)
@@ -609,13 +549,15 @@ func TestNoteDAOFindInPathWithFilePrefix(t *testing.T) {
 func TestNoteDAOFindInPathRequiresCompleteDirName(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			IncludePaths: []string{"lo"},
+			IncludeHrefs:      []string{"lo"},
+			AllowPartialHrefs: false,
 		},
 		[]string{},
 	)
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			IncludePaths: []string{"log"},
+			IncludeHrefs:      []string{"log"},
+			AllowPartialHrefs: false,
 		},
 		[]string{"log/2021-01-03.md", "log/2021-02-04.md", "log/2021-01-04.md"},
 	)
@@ -625,25 +567,25 @@ func TestNoteDAOFindInPathRequiresCompleteDirName(t *testing.T) {
 func TestNoteDAOFindInMultiplePaths(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			IncludePaths: []string{"ref", "index.md"},
+			IncludeHrefs: []string{"ref", "index.md"},
 		},
-		[]string{"ref/test/b.md", "ref/test/a.md", "index.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "index.md"},
 	)
 }
 
 func TestNoteDAOFindExcludingPath(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			ExcludePaths: []string{"log"},
+			ExcludeHrefs: []string{"log"},
 		},
-		[]string{"ref/test/b.md", "f39c8.md", "ref/test/a.md", "index.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "index.md"},
 	)
 }
 
 func TestNoteDAOFindExcludingMultiplePaths(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			ExcludePaths: []string{"ref", "log/2021-01"},
+			ExcludeHrefs: []string{"ref", "log/2021-01"},
 		},
 		[]string{"f39c8.md", "log/2021-02-04.md", "index.md"},
 	)
@@ -651,7 +593,10 @@ func TestNoteDAOFindExcludingMultiplePaths(t *testing.T) {
 
 func TestNoteDAOFindMentions(t *testing.T) {
 	testNoteDAOFind(t,
-		core.NoteFindOpts{Mention: []string{"log/2021-01-03.md", "index.md"}},
+		core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyFts,
+			Mention:       []string{"log/2021-01-03.md", "index.md"},
+		},
 		[]core.ContextualNote{
 			{
 				Note: core.Note{
@@ -663,7 +608,7 @@ func TestNoteDAOFindMentions(t *testing.T) {
 					RawContent: "# A nested note\nThis one is in a sub sub directory",
 					WordCount:  8,
 					Links:      []core.Link{},
-					Tags:       []string{"adventure", "history"},
+					Tags:       []string{"adventure", "history", "science"},
 					Metadata:   map[string]interface{}{},
 					Created:    time.Date(2019, 11, 20, 20, 32, 56, 0, time.UTC),
 					Modified:   time.Date(2019, 11, 20, 20, 34, 6, 0, time.UTC),
@@ -715,9 +660,10 @@ func TestNoteDAOFindMentions(t *testing.T) {
 func TestNoteDAOFindUnlinkedMentions(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			Mention: []string{"log/2021-01-03.md", "index.md"},
+			MatchStrategy: core.MatchStrategyFts,
+			Mention:       []string{"log/2021-01-03.md", "index.md"},
 			LinkTo: &core.LinkFilter{
-				Paths:  []string{"log/2021-01-03.md", "index.md"},
+				Hrefs:  []string{"log/2021-01-03.md", "index.md"},
 				Negate: true,
 			},
 		},
@@ -725,9 +671,23 @@ func TestNoteDAOFindUnlinkedMentions(t *testing.T) {
 	)
 }
 
+func TestNoteDAOFindMentionUnknown(t *testing.T) {
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		opts := core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyFts,
+			Mention:       []string{"will-not-be-found"},
+		}
+		_, err := dao.Find(opts)
+		assert.Err(t, err, "could not find notes at: will-not-be-found")
+	})
+}
+
 func TestNoteDAOFindMentionedBy(t *testing.T) {
 	testNoteDAOFind(t,
-		core.NoteFindOpts{MentionedBy: []string{"ref/test/b.md", "log/2021-01-04.md"}},
+		core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyFts,
+			MentionedBy:   []string{"ref/test/b.md", "log/2021-01-04.md"},
+		},
 		[]core.ContextualNote{
 			{
 				Note: core.Note{
@@ -779,9 +739,10 @@ func TestNoteDAOFindMentionedBy(t *testing.T) {
 func TestNoteDAOFindUnlinkedMentionedBy(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			MentionedBy: []string{"ref/test/b.md", "log/2021-01-04.md"},
+			MatchStrategy: core.MatchStrategyFts,
+			MentionedBy:   []string{"ref/test/b.md", "log/2021-01-04.md"},
 			LinkedBy: &core.LinkFilter{
-				Paths:  []string{"ref/test/b.md", "log/2021-01-04.md"},
+				Hrefs:  []string{"ref/test/b.md", "log/2021-01-04.md"},
 				Negate: true,
 			},
 		},
@@ -789,11 +750,22 @@ func TestNoteDAOFindUnlinkedMentionedBy(t *testing.T) {
 	)
 }
 
+func TestNoteDAOFindMentionedByUnknown(t *testing.T) {
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		opts := core.NoteFindOpts{
+			MatchStrategy: core.MatchStrategyFts,
+			MentionedBy:   []string{"will-not-be-found"},
+		}
+		_, err := dao.Find(opts)
+		assert.Err(t, err, "could not find notes at: will-not-be-found")
+	})
+}
+
 func TestNoteDAOFindLinkedBy(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkedBy: &core.LinkFilter{
-				Paths:     []string{"f39c8.md", "log/2021-01-03"},
+				Hrefs:     []string{"f39c8.md", "log/2021-01-03"},
 				Negate:    false,
 				Recursive: false,
 			},
@@ -806,7 +778,7 @@ func TestNoteDAOFindLinkedByRecursive(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkedBy: &core.LinkFilter{
-				Paths:     []string{"log/2021-01-04.md"},
+				Hrefs:     []string{"log/2021-01-04.md"},
 				Negate:    false,
 				Recursive: true,
 			},
@@ -819,7 +791,7 @@ func TestNoteDAOFindLinkedByRecursiveWithMaxDistance(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkedBy: &core.LinkFilter{
-				Paths:       []string{"log/2021-01-04.md"},
+				Hrefs:       []string{"log/2021-01-04.md"},
 				Negate:      false,
 				Recursive:   true,
 				MaxDistance: 2,
@@ -832,7 +804,7 @@ func TestNoteDAOFindLinkedByRecursiveWithMaxDistance(t *testing.T) {
 func TestNoteDAOFindLinkedByWithSnippets(t *testing.T) {
 	testNoteDAOFind(t,
 		core.NoteFindOpts{
-			LinkedBy: &core.LinkFilter{Paths: []string{"f39c8.md"}},
+			LinkedBy: &core.LinkFilter{Hrefs: []string{"f39c8.md"}},
 		},
 		[]core.ContextualNote{
 			{
@@ -884,16 +856,28 @@ func TestNoteDAOFindLinkedByWithSnippets(t *testing.T) {
 	)
 }
 
+func TestNoteDAOFindLinkedByUnknown(t *testing.T) {
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		opts := core.NoteFindOpts{
+			LinkedBy: &core.LinkFilter{
+				Hrefs: []string{"will-not-be-found"},
+			},
+		}
+		_, err := dao.Find(opts)
+		assert.Err(t, err, "could not find notes at: will-not-be-found")
+	})
+}
+
 func TestNoteDAOFindNotLinkedBy(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkedBy: &core.LinkFilter{
-				Paths:     []string{"f39c8.md", "log/2021-01-03"},
+				Hrefs:     []string{"f39c8.md", "log/2021-01-03"},
 				Negate:    true,
 				Recursive: false,
 			},
 		},
-		[]string{"ref/test/b.md", "f39c8.md", "log/2021-02-04.md", "index.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "log/2021-02-04.md", "index.md"},
 	)
 }
 
@@ -901,7 +885,7 @@ func TestNoteDAOFindLinkTo(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkTo: &core.LinkFilter{
-				Paths:     []string{"log/2021-01-04", "ref/test/a.md"},
+				Hrefs:     []string{"log/2021-01-04", "ref/test/a.md"},
 				Negate:    false,
 				Recursive: false,
 			},
@@ -914,7 +898,7 @@ func TestNoteDAOFindLinkToRecursive(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkTo: &core.LinkFilter{
-				Paths:     []string{"log/2021-01-04.md"},
+				Hrefs:     []string{"log/2021-01-04.md"},
 				Negate:    false,
 				Recursive: true,
 			},
@@ -927,7 +911,7 @@ func TestNoteDAOFindLinkToRecursiveWithMaxDistance(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
 			LinkTo: &core.LinkFilter{
-				Paths:       []string{"log/2021-01-04.md"},
+				Hrefs:       []string{"log/2021-01-04.md"},
 				Negate:      false,
 				Recursive:   true,
 				MaxDistance: 2,
@@ -940,12 +924,24 @@ func TestNoteDAOFindLinkToRecursiveWithMaxDistance(t *testing.T) {
 func TestNoteDAOFindNotLinkTo(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
-			LinkTo: &core.LinkFilter{Paths: []string{"log/2021-01-04", "ref/test/a.md"}, Negate: true},
+			LinkTo: &core.LinkFilter{Hrefs: []string{"log/2021-01-04", "ref/test/a.md"}, Negate: true},
 		},
-		[]string{"ref/test/b.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "log/2021-02-04.md", "index.md", "log/2021-01-04.md"},
 	)
 }
 
+func TestNoteDAOFindLinkToUnknown(t *testing.T) {
+	testNoteDAO(t, func(tx Transaction, dao *NoteDAO) {
+		opts := core.NoteFindOpts{
+			LinkTo: &core.LinkFilter{
+				Hrefs: []string{"will-not-be-found"},
+			},
+		}
+		_, err := dao.Find(opts)
+		assert.Err(t, err, "could not find notes at: will-not-be-found")
+	})
+}
+
 func TestNoteDAOFindRelated(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{
@@ -965,7 +961,7 @@ func TestNoteDAOFindRelated(t *testing.T) {
 func TestNoteDAOFindOrphan(t *testing.T) {
 	testNoteDAOFindPaths(t,
 		core.NoteFindOpts{Orphan: true},
-		[]string{"ref/test/b.md", "log/2021-02-04.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "log/2021-02-04.md"},
 	)
 }
 
@@ -987,7 +983,7 @@ func TestNoteDAOFindCreatedBefore(t *testing.T) {
 		core.NoteFindOpts{
 			CreatedEnd: &end,
 		},
-		[]string{"ref/test/b.md", "ref/test/a.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md"},
 	)
 }
 
@@ -1019,7 +1015,7 @@ func TestNoteDAOFindModifiedBefore(t *testing.T) {
 		core.NoteFindOpts{
 			ModifiedEnd: &end,
 		},
-		[]string{"ref/test/b.md", "ref/test/a.md", "index.md"},
+		[]string{"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "index.md"},
 	)
 }
 
@@ -1035,55 +1031,55 @@ func TestNoteDAOFindModifiedAfter(t *testing.T) {
 
 func TestNoteDAOFindSortCreated(t *testing.T) {
 	testNoteDAOFindSort(t, core.NoteSortCreated, true, []string{
-		"ref/test/b.md", "ref/test/a.md", "index.md", "f39c8.md",
+		"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "index.md", "f39c8.md",
 		"log/2021-01-03.md", "log/2021-02-04.md", "log/2021-01-04.md",
 	})
 	testNoteDAOFindSort(t, core.NoteSortCreated, false, []string{
 		"log/2021-02-04.md", "log/2021-01-04.md", "log/2021-01-03.md",
-		"f39c8.md", "index.md", "ref/test/b.md", "ref/test/a.md",
+		"f39c8.md", "index.md", "ref/test/ref.md", "ref/test/b.md", "ref/test/a.md",
 	})
 }
 
 func TestNoteDAOFindSortModified(t *testing.T) {
 	testNoteDAOFindSort(t, core.NoteSortModified, true, []string{
-		"ref/test/b.md", "ref/test/a.md", "index.md", "f39c8.md",
+		"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "index.md", "f39c8.md",
 		"log/2021-02-04.md", "log/2021-01-03.md", "log/2021-01-04.md",
 	})
 	testNoteDAOFindSort(t, core.NoteSortModified, false, []string{
 		"log/2021-01-04.md", "log/2021-01-03.md", "log/2021-02-04.md",
-		"f39c8.md", "index.md", "ref/test/b.md", "ref/test/a.md",
+		"f39c8.md", "index.md", "ref/test/ref.md", "ref/test/b.md", "ref/test/a.md",
 	})
 }
 
 func TestNoteDAOFindSortPath(t *testing.T) {
 	testNoteDAOFindSort(t, core.NoteSortPath, true, []string{
 		"f39c8.md", "index.md", "log/2021-01-03.md", "log/2021-01-04.md",
-		"log/2021-02-04.md", "ref/test/a.md", "ref/test/b.md",
+		"log/2021-02-04.md", "ref/test/a.md", "ref/test/b.md", "ref/test/ref.md",
 	})
 	testNoteDAOFindSort(t, core.NoteSortPath, false, []string{
-		"ref/test/b.md", "ref/test/a.md", "log/2021-02-04.md",
+		"ref/test/ref.md", "ref/test/b.md", "ref/test/a.md", "log/2021-02-04.md",
 		"log/2021-01-04.md", "log/2021-01-03.md", "index.md", "f39c8.md",
 	})
 }
 
 func TestNoteDAOFindSortTitle(t *testing.T) {
 	testNoteDAOFindSort(t, core.NoteSortTitle, true, []string{
-		"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-01-03.md",
+		"ref/test/ref.md", "ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-01-03.md",
 		"log/2021-02-04.md", "index.md", "log/2021-01-04.md",
 	})
 	testNoteDAOFindSort(t, core.NoteSortTitle, false, []string{
 		"log/2021-01-04.md", "index.md", "log/2021-02-04.md",
-		"log/2021-01-03.md", "ref/test/a.md", "f39c8.md", "ref/test/b.md",
+		"log/2021-01-03.md", "ref/test/a.md", "f39c8.md", "ref/test/b.md", "ref/test/ref.md",
 	})
 }
 
 func TestNoteDAOFindSortWordCount(t *testing.T) {
 	testNoteDAOFindSort(t, core.NoteSortWordCount, true, []string{
 		"log/2021-01-03.md", "log/2021-02-04.md", "index.md",
-		"log/2021-01-04.md", "f39c8.md", "ref/test/a.md", "ref/test/b.md",
+		"log/2021-01-04.md", "ref/test/ref.md", "f39c8.md", "ref/test/a.md", "ref/test/b.md",
 	})
 	testNoteDAOFindSort(t, core.NoteSortWordCount, false, []string{
-		"ref/test/b.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md",
+		"ref/test/b.md", "ref/test/ref.md", "f39c8.md", "ref/test/a.md", "log/2021-02-04.md",
 		"index.md", "log/2021-01-04.md", "log/2021-01-03.md",
 	})
 }
@@ -1146,43 +1142,6 @@ func queryNoteRow(tx Transaction, where string) (noteRow, error) {
 	return row, err
 }
 
-type linkRow struct {
-	SourceId                   core.NoteID
-	TargetId                   *core.NoteID
-	Href, Title, Rels, Snippet string
-	SnippetStart, SnippetEnd   int
-	IsExternal                 bool
-}
-
-func queryLinkRows(t *testing.T, tx Transaction, where string) []linkRow {
-	links := make([]linkRow, 0)
-
-	rows, err := tx.Query(fmt.Sprintf(`
-		SELECT source_id, target_id, title, href, external, rels, snippet, snippet_start, snippet_end
-		  FROM links
-		 WHERE %v
-		 ORDER BY id
-	`, where))
-	assert.Nil(t, err)
-
-	for rows.Next() {
-		var row linkRow
-		var sourceId int64
-		var targetId *int64
-		err = rows.Scan(&sourceId, &targetId, &row.Title, &row.Href, &row.IsExternal, &row.Rels, &row.Snippet, &row.SnippetStart, &row.SnippetEnd)
-		assert.Nil(t, err)
-		row.SourceId = core.NoteID(sourceId)
-		if targetId != nil {
-			row.TargetId = idPointer(*targetId)
-		}
-		links = append(links, row)
-	}
-	rows.Close()
-	assert.Nil(t, rows.Err())
-
-	return links
-}
-
 func idPointer(i int64) *core.NoteID {
 	id := core.NoteID(i)
 	return &id

internal/adapter/sqlite/note_index.go

@@ -1,30 +1,38 @@
 package sqlite
 
 import (
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/errors"
-	"github.com/mickael-menu/zk/internal/util/paths"
+	"path/filepath"
+	"regexp"
+	"strings"
+
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/paths"
+	strutil "github.com/zk-org/zk/internal/util/strings"
 )
 
 // NoteIndex persists note indexing results in the SQLite database.
 // It implements the port core.NoteIndex and acts as a facade to the DAOs.
 type NoteIndex struct {
-	db     *DB
-	dao    *dao
-	logger util.Logger
+	notebookPath string
+	db           *DB
+	dao          *dao
+	logger       util.Logger
 }
 
 type dao struct {
 	notes       *NoteDAO
+	links       *LinkDAO
 	collections *CollectionDAO
 	metadata    *MetadataDAO
 }
 
-func NewNoteIndex(db *DB, logger util.Logger) *NoteIndex {
+func NewNoteIndex(notebookPath string, db *DB, logger util.Logger) *NoteIndex {
 	return &NoteIndex{
-		db:     db,
-		logger: logger,
+		notebookPath: notebookPath,
+		db:           db,
+		logger:       logger,
 	}
 }
 
@@ -46,10 +54,50 @@ func (ni *NoteIndex) FindMinimal(opts core.NoteFindOpts) (notes []core.MinimalNo
 	return
 }
 
+// FindLinkMatch implements core.NoteIndex.
+func (ni *NoteIndex) FindLinkMatch(baseDir string, href string, linkType core.LinkType) (id core.NoteID, err error) {
+	err = ni.commit(func(dao *dao) error {
+		id, err = ni.findLinkMatch(dao, baseDir, href, linkType)
+		return err
+	})
+	return
+}
+
+func (ni *NoteIndex) findLinkMatch(dao *dao, baseDir string, href string, linkType core.LinkType) (core.NoteID, error) {
+	if strutil.IsURL(href) {
+		return 0, nil
+	}
+
+	id, _ := ni.findPathMatch(dao, baseDir, href)
+	if id.IsValid() {
+		return id, nil
+	}
+
+	allowPartialMatch := (linkType == core.LinkTypeWikiLink)
+	return dao.notes.FindIdByHref(href, allowPartialMatch)
+}
+
+func (ni *NoteIndex) findPathMatch(dao *dao, baseDir string, href string) (core.NoteID, error) {
+	href, err := ni.relNotebookPath(baseDir, href)
+	if err != nil {
+		return 0, err
+	}
+	return dao.notes.FindIdByHref(href, false)
+}
+
+// FindLinksBetweenNotes implements core.NoteIndex.
+func (ni *NoteIndex) FindLinksBetweenNotes(ids []core.NoteID) (links []core.ResolvedLink, err error) {
+	err = ni.commit(func(dao *dao) error {
+		links, err = dao.links.FindBetweenNotes(ids)
+		return err
+	})
+	return
+}
+
 // FindCollections implements core.NoteIndex.
-func (ni *NoteIndex) FindCollections(kind core.CollectionKind) (collections []core.Collection, err error) {
+func (ni *NoteIndex) FindCollections(kind core.CollectionKind, sorters []core.CollectionSorter) (collections []core.Collection, err error) {
 	err = ni.commit(func(dao *dao) error {
-		collections, err = dao.collections.FindAll(kind)
+		collections, err = dao.collections.FindAll(kind, sorters)
 		return err
 	})
 	return
@@ -72,6 +120,17 @@ func (ni *NoteIndex) Add(note core.Note) (id core.NoteID, err error) {
 		if err != nil {
 			return err
 		}
+		note.ID = id
+
+		err = ni.addLinks(dao, id, note.Links)
+		if err != nil {
+			return err
+		}
+
+		err = ni.fixExistingLinks(dao, note.ID, note.Path)
+		if err != nil {
+			return err
+		}
 
 		return ni.associateTags(dao.collections, id, note.Tags)
 	})
@@ -80,20 +139,108 @@ func (ni *NoteIndex) Add(note core.Note) (id core.NoteID, err error) {
 	return
 }
 
+// fixExistingLinks will go over all indexed links and update their target to
+// the given id if they match the given path better than their current
+// targetPath.
+func (ni *NoteIndex) fixExistingLinks(dao *dao, id core.NoteID, path string) error {
+	links, err := dao.links.FindInternal()
+	if err != nil {
+		return err
+	}
+
+	for _, link := range links {
+		// To find the best match possible, shortest paths take precedence.
+		// See https://github.com/zk-org/zk/issues/23
+		if link.TargetPath != "" && len(link.TargetPath) < len(path) {
+			continue
+		}
+
+		if matches, err := ni.linkMatchesPath(link, path); matches && err == nil {
+			err = dao.links.SetTargetID(link.ID, id)
+		}
+		if err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+// linkMatchesPath returns whether the given link can be used to reach the
+// given note path.
+func (ni *NoteIndex) linkMatchesPath(link core.ResolvedLink, path string) (bool, error) {
+	// Remove any anchor at the end of the HREF, since it's most likely
+	// matching a sub-section in the note.
+	href := strings.SplitN(link.Href, "#", 2)[0]
+
+	matchString := func(pattern string, s string) bool {
+		reg := regexp.MustCompile(pattern)
+		return reg.MatchString(s)
+	}
+
+	matches := func(href string, allowPartialHref bool) bool {
+		if href == "" {
+			return false
+		}
+		href = regexp.QuoteMeta(href)
+
+		if allowPartialHref {
+			if matchString("^(.*/)?[^/]*"+href+"[^/]*$", path) {
+				return true
+			}
+			if matchString(".*"+href+".*", path) {
+				return true
+			}
+		}
+
+		return matchString("^(?:"+href+"[^/]*|"+href+"/.+)$", path)
+	}
+
+	baseDir := filepath.Join(ni.notebookPath, filepath.Dir(link.SourcePath))
+	if relHref, err := ni.relNotebookPath(baseDir, href); err != nil {
+		if matches(relHref, false) {
+			return true, nil
+		}
+	}
+
+	allowPartialMatch := (link.Type == core.LinkTypeWikiLink)
+	return matches(href, allowPartialMatch), nil
+}
+
+// relNotebookHref makes the given href (which is relative to baseDir) relative
+// to the notebook root instead.
+func (ni *NoteIndex) relNotebookPath(baseDir string, href string) (string, error) {
+	path := filepath.Clean(filepath.Join(baseDir, href))
+	path, err := filepath.Rel(ni.notebookPath, path)
+
+	return path,
+		errors.Wrapf(err, "failed to make href relative to the notebook: %s", href)
+}
+
 // Update implements core.NoteIndex.
 func (ni *NoteIndex) Update(note core.Note) error {
 	err := ni.commit(func(dao *dao) error {
-		noteId, err := dao.notes.Update(note)
+		id, err := dao.notes.Update(note)
 		if err != nil {
 			return err
 		}
 
-		err = dao.collections.RemoveAssociations(noteId)
+		// Reset links
+		err = dao.links.RemoveAll(id)
+		if err != nil {
+			return err
+		}
+		err = ni.addLinks(dao, id, note.Links)
 		if err != nil {
 			return err
 		}
 
-		return ni.associateTags(dao.collections, noteId, note.Tags)
+		// Reset tags
+		err = dao.collections.RemoveAssociations(id)
+		if err != nil {
+			return err
+		}
+		return ni.associateTags(dao.collections, id, note.Tags)
 	})
 
 	return errors.Wrapf(err, "%v: failed to update note index", note.Path)
@@ -114,6 +261,33 @@ func (ni *NoteIndex) associateTags(collections *CollectionDAO, noteId core.NoteI
 	return nil
 }
 
+func (ni *NoteIndex) addLinks(dao *dao, id core.NoteID, links []core.Link) error {
+	resolvedLinks, err := ni.resolveLinkNoteIDs(dao, id, links)
+	if err != nil {
+		return err
+	}
+	return dao.links.Add(resolvedLinks)
+}
+
+func (ni *NoteIndex) resolveLinkNoteIDs(dao *dao, sourceID core.NoteID, links []core.Link) ([]core.ResolvedLink, error) {
+	resolvedLinks := []core.ResolvedLink{}
+
+	for _, link := range links {
+		targetID, err := ni.findLinkMatch(dao, "" /* base dir */, link.Href, link.Type)
+		if err != nil {
+			return resolvedLinks, err
+		}
+
+		resolvedLinks = append(resolvedLinks, core.ResolvedLink{
+			Link:     link,
+			SourceID: sourceID,
+			TargetID: targetID,
+		})
+	}
+
+	return resolvedLinks, nil
+}
+
 // Remove implements core.NoteIndex
 func (ni *NoteIndex) Remove(path string) error {
 	err := ni.commit(func(dao *dao) error {
@@ -162,6 +336,7 @@ func (ni *NoteIndex) commit(transaction func(dao *dao) error) error {
 		return ni.db.WithTransaction(func(tx Transaction) error {
 			dao := dao{
 				notes:       NewNoteDAO(tx, ni.logger),
+				links:       NewLinkDAO(tx, ni.logger),
 				collections: NewCollectionDAO(tx, ni.logger),
 				metadata:    NewMetadataDAO(tx),
 			}

internal/adapter/sqlite/note_index_test.go

@@ -1,15 +1,185 @@
 package sqlite
 
 import (
+	"fmt"
 	"testing"
 
-	"github.com/mickael-menu/zk/internal/core"
-	"github.com/mickael-menu/zk/internal/util"
-	"github.com/mickael-menu/zk/internal/util/test/assert"
+	"github.com/zk-org/zk/internal/core"
+	"github.com/zk-org/zk/internal/util"
+	"github.com/zk-org/zk/internal/util/test/assert"
 )
 
 // FIXME: Missing tests
 
+func TestNoteIndexAddWithLinks(t *testing.T) {
+	db, index := testNoteIndex(t)
+
+	id, err := index.Add(core.Note{
+		Path: "log/added.md",
+		Links: []core.Link{
+			{
+				Title: "Same dir",
+				Href:  "log/2021-01-04",
+				Rels:  core.LinkRels("rel-1", "rel-2"),
+			},
+			{
+				Title:        "Relative",
+				Href:         "f39c8",
+				Snippet:      "[Relative](f39c8) link",
+				SnippetStart: 50,
+				SnippetEnd:   100,
+			},
+			{
+				Title: "Second is added",
+				Href:  "f39c8#anchor",
+				Rels:  core.LinkRels("second"),
+			},
+			{
+				Title: "Unknown",
+				Href:  "unknown",
+			},
+			{
+				Title:      "URL",
+				Href:       "http://example.com",
+				IsExternal: true,
+				Snippet:    "External [URL](http://example.com)",
+			},
+		},
+	})
+	assert.Nil(t, err)
+
+	rows := queryLinkRows(t, db.db, fmt.Sprintf("source_id = %d", id))
+	assert.Equal(t, rows, []linkRow{
+		{
+			SourceId: id,
+			TargetId: idPointer(2),
+			Title:    "Same dir",
+			Href:     "log/2021-01-04",
+			Rels:     "\x01rel-1\x01rel-2\x01",
+		},
+		{
+			SourceId:     id,
+			TargetId:     idPointer(4),
+			Title:        "Relative",
+			Href:         "f39c8",
+			Rels:         "",
+			Snippet:      "[Relative](f39c8) link",
+			SnippetStart: 50,
+			SnippetEnd:   100,
+		},
+		{
+			SourceId: id,
+			TargetId: idPointer(4),
+			Title:    "Second is added",
+			Href:     "f39c8#anchor",
+			Rels:     "\x01second\x01",
+		},
+		{
+			SourceId: id,
+			TargetId: nil,
+			Title:    "Unknown",
+			Href:     "unknown",
+			Rels:     "",
+		},
+		{
+			SourceId:   id,
+			TargetId:   nil,
+			Title:      "URL",
+			Href:       "http://example.com",
+			IsExternal: true,
+			Rels:       "",
+			Snippet:    "External [URL](http://example.com)",
+		},
+	})
+}
+
+func TestNoteIndexAddFillsLinksMissingTargetId(t *testing.T) {
+	db, index := testNoteIndex(t)
+
+	id, err := index.Add(core.Note{
+		Path: "missing_target.md",
+	})
+	assert.Nil(t, err)
+
+	rows := queryLinkRows(t, db.db, fmt.Sprintf("target_id = %d", id))
+	assert.Equal(t, rows, []linkRow{
+		{
+			SourceId: 3,
+			TargetId: &id,
+			Title:    "Missing target",
+			Href:     "missing",
+			Snippet:  "There's a Missing target",
+		},
+	})
+}
+
+func TestNoteIndexUpdateWithLinks(t *testing.T) {
+	db, index := testNoteIndex(t)
+
+	links := queryLinkRows(t, db.db, "source_id = 1")
+	assert.Equal(t, links, []linkRow{
+		{
+			SourceId: 1,
+			TargetId: idPointer(2),
+			Title:    "An internal link",
+			Href:     "log/2021-01-04.md",
+			Snippet:  "[[An internal link]]",
+		},
+		{
+			SourceId:   1,
+			TargetId:   nil,
+			Title:      "An external link",
+			Href:       "https://domain.com",
+			IsExternal: true,
+			Snippet:    "[[An external link]]",
+		},
+	})
+
+	err := index.Update(core.Note{
+		Path: "log/2021-01-03.md",
+		Links: []core.Link{
+			{
+				Title:      "A new link",
+				Href:       "index",
+				Type:       core.LinkTypeWikiLink,
+				IsExternal: false,
+				Rels:       core.LinkRels("rel"),
+				Snippet:    "[[A new link]]",
+			},
+			{
+				Title:      "An external link",
+				Href:       "https://domain.com",
+				Type:       core.LinkTypeMarkdown,
+				IsExternal: true,
+				Snippet:    "[[An external link]]",
+			},
+		},
+	})
+	assert.Nil(t, err)
+
+	links = queryLinkRows(t, db.db, "source_id = 1")
+	assert.Equal(t, links, []linkRow{
+		{
+			SourceId: 1,
+			TargetId: idPointer(3),
+			Title:    "A new link",
+			Href:     "index",
+			Type:     "wiki-link",
+			Rels:     "\x01rel\x01",
+			Snippet:  "[[A new link]]",
+		},
+		{
+			SourceId:   1,
+			TargetId:   nil,
+			Title:      "An external link",
+			Href:       "https://domain.com",
+			Type:       "markdown",
+			IsExternal: true,
+			Snippet:    "[[An external link]]",
+		},
+	})
+}
+
 func TestNoteIndexAddWithTags(t *testing.T) {
 	db, index := testNoteIndex(t)
 
@@ -50,7 +220,7 @@ func TestNoteIndexUpdateWithTags(t *testing.T) {
 
 func testNoteIndex(t *testing.T) (*DB, *NoteIndex) {
 	db := testDB(t)
-	return db, NewNoteIndex(db, &util.NullLogger)
+	return db, NewNoteIndex("", db, &util.NullLogger)
 }
 
 func assertTagExistsOrNot(t *testing.T, db *DB, shouldExist bool, tag string) {

internal/adapter/sqlite/stmt.go

@@ -4,7 +4,7 @@ import (
 	"database/sql"
 	"sync"
 
-	"github.com/mickael-menu/zk/internal/util/errors"
+	"github.com/zk-org/zk/internal/util/errors"
 )
 
 // LazyStmt is a wrapper around a sql.Stmt which will be evaluated on first use.

internal/adapter/sqlite/testdata/default/collections.yml

@@ -16,3 +16,6 @@
 - id: 6
   kind: "tag"
   name: "empty"
+- id: 7
+  kind: "tag"
+  name: "science"

internal/adapter/sqlite/testdata/default/notes.yml

@@ -88,3 +88,16 @@
   created: "2020-11-29T08:20:18Z"
   modified: "2020-11-10T08:20:18Z"
   metadata: "{}"
+
+- id: 8
+  path: "ref/test/ref.md"
+  sortable_path: "ref/ref.md"
+  title: ""
+  lead: ""
+  body: ""
+  raw_content: ""
+  word_count: 5
+  checksum: "ientrs"
+  created: "2019-11-20T20:32:56Z"
+  modified: "2019-11-20T20:34:06Z"
+  metadata: '{}'

internal/adapter/sqlite/testdata/default/notes_collections.yml

@@ -16,3 +16,12 @@
 - id: 6
   note_id: 5        # ref/test/b.md
   collection_id: 5  # tag:adventure
+- id: 7
+  note_id: 5        # ref/test/b.md
+  collection_id: 7  # tag:science
+- id: 8
+  note_id: 4        # f39c8.md
+  collection_id: 7  # tag:science
+- id: 9
+  note_id: 5        # ref/test/b.md
+  collection_id: 7  # tag:science

internal/adapter/sqlite/testdata/issue23/notes.yml

@@ -1,4 +1,4 @@
-# See https://github.com/mickael-menu/zk/issues/23
+# See https://github.com/zk-org/zk/issues/23
 - id: 1
   path: "prefix-longest.md"
   sortable_path: "prefix-longest.md"