MAINT: Remove no longer existing files from MANIFEST.in.
MAINT: Move doc/swig to tools/swig.

Also update MANIFEST.in and documentation to reflect the move. The
discussion of this change is at #2384.

Closes #2384. Closes #4374.
STY: Whitespace patrol on numpy.i.
DOC: Document doc/swig move in 1.9.0 release notes.
Merge pull request #4487 from charris/move-swig-to-tools-directory

Move swig to tools directory