Ninja complains with:
expected depfile 'foo.d' to mention 'bar', got 'baz'

Running ninja twice now reports "no work to do" again.

This change required updating all calls to build_utils.WriteDepFile() so
that the output is passed in. While doing this, I also made the helper
add in GetPythonDependencies() by default.

build/android/gyp/ant.py I just deleted rather than updating since it's
GYP-only.

BUG=646165

Review-Url: https://codereview.chromium.org/2336173003
Cr-Commit-Position: refs/heads/master@{#418455}