Got it

Author: mtodd

app/assets/javascripts/task_list.coffee

@@ -125,10 +125,17 @@ itemPattern = ///
     #{escapePattern(complete)}|
     #{escapePattern(incomplete)}
   )
-  (?=\s)                  # is followed by whitespace
-  (?!                     # but not a link to this destination
-    \s*
-    \(.*?\)
+  \s+                     # is followed by whitespace
+  (                       # followed by anything unmistakable for a link,
+    ([^\[\(]|$)           # or end of line
+  |
+    (?!
+      \(.*?\)             # or, not immediately followed by a link URL
+    )
+    (                     # and not part of a link reference
+      (\[.*?\]\s*(\[.*?\]|\(.*?\))\s*)+
+      ([^\[]|$)
+    )
   )
 ///
 

test/unit/test_updates.coffee

@@ -466,18 +466,18 @@ asyncTest "update ignores items that look like Task List items but are links", -
 
   field = $ '<textarea>', class: 'js-task-list-field', text: """
     - [ ] (link)
-    # - [ ] [reference]
+    - [ ] [reference]
     - [ ] () collapsed
-    # - [ ] [] collapsed reference
+    - [ ] [] collapsed reference
     - [ ] \\(escaped item)
     - [ ] item
   """
 
   changes = """
     - [ ] (link)
-    # - [ ] [reference]
+    - [ ] [reference]
     - [ ] () collapsed
-    # - [ ] [] collapsed reference
+    - [ ] [] collapsed reference
     - [ ] \\(escaped item)
     - [x] item
   """