Revert "MetadataTools: Remove deprecated and unused methods"

This reverts commit 6b31a4ff9ac4bfc1ccf356804add10dc637366f5.
Adjust logging of setId

ImageReader now logs setId at INFO, while FormatReader logs setId at
DEBUG.  This means that the top-level call to setId should show up by
default, but setId on any constituent files (e.g. TIFFs in a plate) will
only show up if the log level is changed to DEBUG or TRACE.

This should substantially clean up the INFO-level logs for multi-file datasets.
Zeiss ZVI: ignore invalid plane coordinates

If the parsed coordinates do not account for all of the images, then we
need to ignore them.  Otherwise, openBytes with different values of 'no'
may open the same image.

See http://www.openmicroscopy.org/community/posting.php?f=13&t=5130#pr10246
AFI: only initialize internal SVS readers once per file

This prevents us from having to re-initialize the internal reader on
every call to openBytes.
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