melib: link threads with empty intermediates

A thread's chain link would get broken when empty intermediate
ThreadNodes exist. The pruning of the empty node did not properly chain
the empty node's parent with the empty node's children.

Old behaviour:

- [A]
/* [B] is missing */
- [C]
/* [D] is missing */
- [E]

New behaviour (`x` represents deleted links)

- [A]
  |
  |xxx> [empty node of B]
  |        x
  |        x
  |        \/
  |_______>[C]
	    |
	    |xxx> [empty node of D]
	    |        x
	    |        x
	    |        \/
	    |_______>[E]

melib/src/mailbox/thread.rs

@@ -499,17 +499,17 @@ impl Threads {
                 return true;
             }
 
-            if !thread_nodes[idx].has_message() {
+            if !thread_nodes[idx].has_message() && !thread_nodes[idx].has_parent() {
                 if thread_nodes[idx].children.len() == 1 {
                     /* "Do not promote the children if doing so would promote them to the root set
                      * -- unless there is only one child, in which case, do." */
                     let child = thread_nodes[idx].children[0];
                     root_set.push(child);
-                    thread_nodes[idx].children.clear();
-                    remove_from_parent!(thread_nodes, idx);
                     remove_from_parent!(thread_nodes, child);
                     return true; // Pruned
-                } else if let Some(p) = thread_nodes[idx].parent {
+                }
+            } else if let Some(p) = thread_nodes[idx].parent {
+                if !thread_nodes[idx].has_message() {
                     let orphans = thread_nodes[idx].children.clone();
                     for c in orphans {
                         make!((p) parent of (c), thread_nodes);
@@ -574,25 +574,38 @@ impl Threads {
 
         t.create_root_set(collection);
         t.build_collection(collection);
-        // for (i, _t) in t.thread_nodes.iter().enumerate() {
-        //     debug!("Thread #{}, children {}", i, _t.children.len());
-        //     if !_t.children.is_empty() {
-        //         debug!("{:?}", _t.children);
-        //     }
-        //     if let Some(m) = _t.message {
-        //         debug!("\tmessage: {}", collection[&m].subject());
-        //     } else {
-        //         debug!("\tNo message");
-        //     }
-        // }
-        // for (i, _t) in t.tree.borrow().iter().enumerate() {
-        //     debug!("Tree #{} id {}, children {}", i, _t.id, _t.children.len());
-        //     if let Some(m) = t.thread_nodes[_t.id].message {
-        //         debug!("\tmessage: {}", collection[&m].subject());
-        //     } else {
-        //         debug!("\tNo message");
-        //     }
-        // }
+        //for (i, _t) in t.thread_nodes.iter().enumerate() {
+        //    if !_t.has_parent() && _t.children.is_empty() && !_t.has_message() {
+        //        continue;
+        //    }
+        //    debug!("--------------------------");
+        //    if let Some(m) = _t.message {
+        //        debug!(
+        //            "\tmessage: {}\t{}",
+        //            collection[&m].subject(),
+        //            collection[&m].message_id()
+        //        );
+        //    } else {
+        //        debug!("\tNo message");
+        //    }
+        //    debug!(
+        //        "Thread #{}, children {}:\n\t{:#?}",
+        //        i,
+        //        _t.children.len(),
+        //        _t
+        //    );
+        //    if !_t.children.is_empty() {
+        //        debug!("{:?}", _t.children);
+        //    }
+        //}
+        //for (i, _t) in t.tree.borrow().iter().enumerate() {
+        //    debug!("Tree #{} id {}, children {}", i, _t.id, _t.children.len());
+        //    if let Some(m) = t.thread_nodes[_t.id].message {
+        //        debug!("\tmessage: {}", collection[&m].subject());
+        //    } else {
+        //        debug!("\tNo message");
+        //    }
+        //}
         t
     }
 
@@ -1215,9 +1228,6 @@ impl Threads {
 
         /* The index of the reference we are currently examining, start from current message */
         let mut ref_ptr = t_idx;
-        if self.thread_nodes[t_idx].has_parent() {
-            remove_from_parent!(&mut self.thread_nodes, t_idx);
-        }
 
         for &refn in envelope.references().iter().rev() {
             let r_id = refn.raw();
@@ -1234,7 +1244,9 @@ impl Threads {
                 new_id
             };
             /* If they are already linked, don't change the existing links. */
-            if self.thread_nodes[ref_ptr].has_parent() {
+            if self.thread_nodes[ref_ptr].has_parent()
+                && self.thread_nodes[ref_ptr].parent.unwrap() != parent_id
+            {
                 ref_ptr = parent_id;
                 continue;
             }
@@ -1248,6 +1260,7 @@ impl Threads {
                 self.union(ref_ptr, parent_id);
                 make!((parent_id) parent of (ref_ptr), &mut self.thread_nodes);
             }
+            ref_ptr = parent_id;
         }
     }