[build] Fix Makefile based (native) build.
This fixes the Python include path after the GYP files have been relocated into another directory. It only affects 'make native', other targets have been fixed in previous changes already. R=jkummerow@chromium.org Review-Url: https://codereview.chromium.org/2001053003 Cr-Commit-Position: refs/heads/master@{#36432}
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