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 dev_5_0 -D org: PR 915 (Fix for single channel  meas_mode 13 data.)
merge dev_5_0 -D org: PR 941 (Fix the download URL for stable release jars)
merge dev_5_0 -D org: PR 946 (Read internal pyramids from CellSens .vsi data)
merge dev_5_0 -D org: PR 951 (Fix up Bio-Formats POMs)
merge dev_5_0 -D org: PR 952 (Memoization fixes)
merge dev_5_0 -D org: PR 957 (Correctly set Modulo annotations for multi-Image datasets (rebased onto dev_5_0))
merge dev_5_0 -D org: PR 958 (Flex: be more permissive in parsing IFDs and XML (rebased onto dev_5_0))
merge dev_5_0 -D org: PR 960 (Cache OME-XML between ImagePluses (rebased onto dev_5_0))
merge dev_5_0 -D org: PR 966 (Update logging jars)
merge dev_5_0 -D org: PR 968 (Cellomics: a few fixes for single-file datasets (rebased onto dev_5_0))