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Fix (most) generated includes to have gen/ in their path.

This makes it easier to tell where files exist on disk.

Unfortunately I had to leave the old include path
in engine/BUILD.gn to support all the v8 includes
which were too many to deal with in this patch.

It's a little nasty to have the raw build directory
in our include path, but it produces nicer paths.

R=abarth@chromium.org