used lookupInScope(name) to find the qualified names in comments.

pkg/docgen/lib/docgen.dart

 // Copyright (c) 2013, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 /**
  * **docgen** is a tool for creating machine readable representations of Dart 
  * code metadata, including: classes, members, comments and annotations.
  * 
  * docgen is run on a `.dart` file or a directory containing `.dart` files. 
  * 
@@ skipping 257 matching lines @@
   commentText = commentText == null ? '' : 
       markdown.markdownToHtml(commentText.trim(), linkResolver: linkResolver)
       .replaceAll('\n', ' ');
   return commentText;
 }
 
 /**
  * Converts all [_] references in comments to <code>_</code>.
  */
 // TODO(tmandel): Create proper links for [_] style markdown based
 // on scope once layout of viewer is finished.

[Tate Mandel, 2013/07/09 16:43:26]

Remove this TODO.

[janicejl, 2013/07/09 19:49:21]

Done.

 markdown.Node fixReference(String name, LibraryMirror currentLibrary, 
     ClassMirror currentClass, MemberMirror currentMember) {
-  return new markdown.Element.text('code', name);
+  
+  var reference;
+  var libraryScope = currentLibrary.lookupInScope(name);

[Tate Mandel, 2013/07/09 16:43:26]

I feel as though it should go the other way around. Don't you want to check
against the most specific member first and then check in a larger scope if it
returns null? 

[janicejl, 2013/07/09 19:49:21]

Done.

+  if (libraryScope != null) reference = libraryScope.qualifiedName;
+  else {
+    var classScope = currentClass == null ?
+        null : currentClass.lookupInScope(name);
+    if (classScope != null) reference = classScope.qualifiedName;
+    else {
+      var memberScope = currentMember == null ? 
+          null : currentMember.lookupInScope(name);
+      reference = memberScope != null ? memberScope.qualifiedname : name;
+    }
+  }
+  return new markdown.Element.text('code', reference);

[Tate Mandel, 2013/07/09 16:43:26]

We probably don't want this as a <code> tag anymore. Maybe make it an <a> for
now since that's what all links are in the viewer at the moment. 

[janicejl, 2013/07/09 19:49:21]

Done.

 }
 
 /**
  * Returns a map of [Variable] objects constructed from inputted mirrors.
  */
 Map<String, Variable> _getVariables(Map<String, VariableMirror> mirrorMap, 
     bool includePrivate) {
   var data = {};
   // TODO(janicejl): When map to map feature is created, replace the below with 
   // a filter. Issue(#9590).
@@ skipping 278 matching lines @@
     parameterMap['qualifiedname'] = qualifiedName;
     parameterMap['optional'] = isOptional.toString();
     parameterMap['named'] = isNamed.toString();
     parameterMap['default'] = hasDefaultValue.toString();
     parameterMap['type'] = type;
     parameterMap['value'] = defaultValue;
     parameterMap['annotations'] = new List.from(annotations);
     return parameterMap;
   } 
 }