Merge pull request #537 from melissalinkert/primitive-warnings

Consolidate OME-XML primitive type logging
Use charAt() instead of beginsWith().
Add ResourceNamer class.
Refactor FakeGenerator to use ResourceNamer.
merge develop -D org -I include -E exclude: PR 528 (Tile performance improvements for VMS and NDPI)
merge develop -D org -I include -E exclude: PR 529 (Still more bug fixes)
merge develop -D org -I include -E exclude: PR 534 (Revert "MetadataTools: Remove deprecated and unused methods")
merge develop -D org -I include -E exclude: PR 541 (Adjust logging of setId)
merge develop -D org -I include -E exclude: PR 544 (Zeiss ZVI: ignore invalid plane coordinates)
merge develop -D org -I include -E exclude: PR 548 (SEQ: do not automatically pick up files with the .seq suffix)
merge develop -D org -I include -E exclude: PR 550 (AFI: only initialize internal SVS readers once per file)
merge develop -D org -I include -E exclude: PR 555 (Adding 2013-06 versions of the samples)
merge develop -D org -I include -E exclude: PR 556 (Add ``mkfake`` tool)