Merge pull request #534 from melissalinkert/metadatatools-revert

Revert "MetadataTools: Remove deprecated and unused methods"
Merge pull request #541 from melissalinkert/setid-logging

Adjust logging of setId
Merge pull request #544 from melissalinkert/zvi-coordinates

Zeiss ZVI: ignore invalid plane coordinates
Merge pull request #550 from melissalinkert/afi-performance

AFI: only initialize internal SVS readers once per file
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 548 (SEQ: do not automatically pick up files with the .seq suffix)
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)