Move all mutations into a specific place.
This makes coherency checks more consistent for DEPS vs .gclient. It's still not thread safe but the mutation code paths are easier to follow. R=dpranke@chromium.org BUG= TEST= Review URL: http://codereview.chromium.org/8135019 git-svn-id: svn://svn.chromium.org/chrome/trunk/tools/depot_tools@104772 0039d316-1c4b-4281-b951-d872f2087c98
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