Clean up logging uses

pkg/analyzer/lib/src/generated/source_io.dart

 // Copyright (c) 2014, 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.
 
 // This code was auto-generated, is not intended to be edited, and is subject to
 // significant change. Please see the README file for more information.
 
 library engine.source.io;
 
 import 'source.dart';
@@ skipping 413 matching lines @@
    * @param packagesDirectory the "packages" directory (not `null`)
    * @param pkgName the package name (not `null`, not empty)
    * @param relPath the path relative to the package directory (not `null`, no leading slash,
    *          but may be empty string)
    * @return the file (not `null`)
    */
   JavaFile getCanonicalFile(JavaFile packagesDirectory, String pkgName, String relPath) {
     JavaFile pkgDir = new JavaFile.relative(packagesDirectory, pkgName);
     try {
       pkgDir = pkgDir.getCanonicalFile();
-    } on JavaIOException catch (e) {
-      if (!e.toString().contains("Required key not available")) {
-        AnalysisEngine.instance.logger.logError2("Canonical failed: $pkgDir", e);
+    } on JavaIOException catch (exception, stackTrace) {
+      if (!exception.toString().contains("Required key not available")) {
+        AnalysisEngine.instance.logger.logError(
+            "Canonical failed: $pkgDir",
+            new CaughtException(exception, stackTrace));
       } else if (_CanLogRequiredKeyIoException) {
         _CanLogRequiredKeyIoException = false;
-        AnalysisEngine.instance.logger.logError2("Canonical failed: $pkgDir", e);
+        AnalysisEngine.instance.logger.logError(
+            "Canonical failed: $pkgDir",
+            new CaughtException(exception, stackTrace));
       }
     }
     return new JavaFile.relative(pkgDir, relPath.replaceAll('/', new String.fromCharCode(JavaFile.separatorChar)));
   }
 
   /**
    * @return `true` if "file" was found in "packagesDir", and it is part of the "lib" folder
    *         of the application that contains in this "packagesDir".
    */
   bool _isSelfReference(JavaFile packagesDir, JavaFile file) {
@@ skipping 49 matching lines @@
       for (JavaFile dir in _relativeDirectories) {
         JavaFile file = new JavaFile.relative(dir, filePath);
         if (file.exists()) {
           return new FileBasedSource.con2(uri, file);
         }
       }
     }
     return null;
   }
 }