Fixes bug in path handling of analyzer

Was using os.getcwd when it needs to use options.toplevel_dir

R=mark@chromium.org
BUG=383609
TEST=none

Review URL: https://codereview.chromium.org/395483002

git-svn-id: http://gyp.googlecode.com/svn/trunk@1951 78cadc50-ecff-11dd-a971-7dbc132099af