GN bootstrap fixes:

- add missing file to compile
- fix final build directory (and make --output work)

BUG=none
R=dpranke@chromium.org,tfarina@chromium.org

Review URL: https://codereview.chromium.org/1411303008

Cr-Commit-Position: refs/heads/master@{#356999}

tools/gn/bootstrap/bootstrap.py

@@ -65,7 +65,7 @@ def run_build(tempdir, options):
     shutil.copy2(temp_gn, out_gn)
   else:
     print 'Building gn using itself to %s...' % build_rel
-    build_gn_with_gn(temp_gn, build_rel, options)
+    build_gn_with_gn(temp_gn, build_root, options)
 
   if options.output:
     # Preserve the executable permission bit.
@@ -156,6 +156,7 @@ def write_ninja(path, options):
       'base/third_party/superfasthash/superfasthash.c',
   ])
   static_libraries['base']['sources'].extend([
+      'base/allocator/allocator_extension_thunks.cc',
       'base/at_exit.cc',
       'base/base_paths.cc',
       'base/base_switches.cc',