Cellomics: a few fixes for single-file datasets

This allows the field to contain either 2 or 3 digits, and fixes the
image name setting so that field/well indices are not 0.
Cellomics: fix reading of directories with mixed o/d channels

The channel letter for the initial file is respected now, instead of
allowing any file with a matching name.
One more fix for channel file grouping
merge develop -D org: PR 528 (Tile performance improvements for VMS and NDPI)
merge develop -D org: PR 857 (Initial support for Zeiss .lms files)
merge develop -D org: PR 858 (Initial support for Veeco AFM data)
merge develop -D org: PR 859 (Assorted metadata/tile parsing fixes)
merge develop -D org: PR 945 (cpp: bioformats: Add MetadataMap class for original metadata)
merge develop -D org: PR 948 (Updating Aperio ImageScope weblink (rebased onto develop))
merge develop -D org: PR 949 (C++ fixes to work around clang++/libc++ bugs)
merge develop -D org: PR 950 (Cellomics: a few fixes for single-file datasets)