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Fix ApacheThriftGen chroot normalization scope.

Previously, ApacheThriftGen attempted to normalize the gen chroot once
per file.  In a multi-file target with nested namespaces, this could
lead to move errors when a previous file generated shared namespace
directories.

A `test_nested_namespaces` test is added that fails without the fix and
passes with the fix.

Testing Done:
Paul provided an example repo here:
  https://github.com/pgroudas/issues-1918
The README describes steps that fail and reproduce the bug using pants
0.0.40, but with this fix, pants works against that sample repo.

CI went green here:
  https://travis-ci.org/pantsbuild/pants/builds/74287990

Bugs closed: 1918, 1919

Reviewed at https://rbcommons.com/s/twitter/r/2568/

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