Fix various pub issues.

lib/src/log.dart

 // Copyright (c) 2012, 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.
 
 /// Message logging.
 library pub.log;
 
 import 'dart:async';
 import 'dart:convert';
 import 'dart:io';
@@ skipping 510 matching lines @@
   void error(error, [stackTrace]) {
     var errorJson = {"error": error.toString()};
 
     if (stackTrace == null && error is Error) stackTrace = error.stackTrace;
     if (stackTrace != null) {
       errorJson["stackTrace"] = new Chain.forTrace(stackTrace).toString();
     }
 
     // If the error came from a file, include the path.
     if (error is SourceSpanException && error.span.sourceUrl != null) {
-      errorJson["path"] = p.fromUri(error.span.sourceUrl);
+      // Normalize paths and make them absolute for backwards compatibility with
+      // the protocol used by the analyzer.
+      errorJson["path"] = p.normalize(p.absolute(
+          p.fromUri(error.span.sourceUrl)));
     }
 
     if (error is FileException) {
-      errorJson["path"] = error.path;
+      errorJson["path"] = p.normalize(p.absolute(error.path));
     }
 
     this.message(errorJson);
   }
 
   /// Encodes [message] to JSON and prints it if JSON output is enabled.
   void message(message) {
     if (!enabled) return;
 
     print(JSON.encode(message));
   }
 }