Fix flag parsing after the configuration file

Fixes #52

cmd/step-ca/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"bytes"
+	"flag"
 	"fmt"
 	"io/ioutil"
 	"log"
@@ -143,6 +144,25 @@ intermediate private key.`,
 	}
 
 	app.Action = func(ctx *cli.Context) error {
+		// Hack to be able to run a the top action as a subcommand
+		cmd := cli.Command{Name: "start", Action: startAction, Flags: app.Flags}
+		set := flag.NewFlagSet(app.Name, flag.ContinueOnError)
+		set.Parse(os.Args)
+		ctx = cli.NewContext(app, set, nil)
+		return cmd.Run(ctx)
+	}
+
+	if err := app.Run(os.Args); err != nil {
+		if os.Getenv("STEPDEBUG") == "1" {
+			fmt.Fprintf(os.Stderr, "%+v\n", err)
+		} else {
+			fmt.Fprintln(os.Stderr, err)
+		}
+		os.Exit(1)
+	}
+}
+
+func startAction(ctx *cli.Context) error {
 	passFile := ctx.String("password-file")
 
 	// If zero cmd line args show help, if >1 cmd line args show error.
@@ -177,16 +197,6 @@ intermediate private key.`,
 		fatal(err)
 	}
 	return nil
-	}
-
-	if err := app.Run(os.Args); err != nil {
-		if os.Getenv("STEPDEBUG") == "1" {
-			fmt.Fprintf(os.Stderr, "%+v\n", err)
-		} else {
-			fmt.Fprintln(os.Stderr, err)
-		}
-		os.Exit(1)
-	}
 }
 
 // fatal writes the passed error on the standard error and exits with the exit