LI-FLIM: add modulo support for phase and frequency data

Phases are added to ModuloT; frequencies are added to ModuloZ.  This is
consistent with how phases/frequencies are handled in other formats.

Fixes #12290.
Tidy up a few lingering series population issuse

The series count is now at most 2, so extra bookkeeping to divide
primary images from background images is not necessary.
ND2: fix XML trimming to prevent too much from being removed

Fixes #11998.
Fix loop state parsing

Each loop has a separate valid state flag, so rather than using a global
flag we now set and query each individual loop's flag.
Additional 0-size checking

Fixes #10939
ND2: one more adjustment to loop state parsing

Fixes #10939.
Remove loop state check from FramesBefore/FramesAfter logic
One more fix to position dimension detection

If no stage positions are recorded, assume position count is 1.
Fix stage position check to include non-XML metadata
Prevent NumberFormatException that caused TextInfo dimensions to be ignored
Correct for off-by-ones in SizeZ reporting
merge develop -D org: PR 981 (Ignore namespaces when filling in an XMLAnnotation's Value)
merge develop -D org: PR 983 (Woolz: make sure the service is initialized when calling openBytes (rebased onto develop))
merge develop -D org: PR 1123 (Add a reader that accepts a file containing a file pattern)
merge develop -D org: PR 1154 (Leica: prevent exception when linking EmissionFilter)
merge develop -D org: PR 1155 (Memoizer errs (rebased onto develop))
merge develop -D org: PR 1163 (Fix for BH .Sdt meas mode 0 & 1 single pixel files & (unrelated) problem with dividing by increment count. (rebased onto develop))
merge develop -D org: PR 1164 (Add modulo support for LI-FLIM data)
merge develop -D org: PR 1165 (First round of Nikon ND2 fixes (rebased onto develop))
merge develop -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1162 melissalinkert 'AFI: populate magnification and physical pixel size metadata' (status: failure)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1138 melissalinkert 'Lots of Zeiss CZI fixes (rebased onto develop)' (label: exclude)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1166 mtbc 'assist #12385: use ArrayList instead of Vector' (status: failure)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (label: exclude)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
Already up-to-date.

Merged PRs:
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value'
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)'
  # PR 1123 melissalinkert 'Add a reader that accepts a file containing a file pattern'
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1155 joshmoore 'Memoizer errs (rebased onto develop)'
  # PR 1163 melissalinkert 'Fix for BH .Sdt meas mode 0 & 1 single pixel files & (unrelated) problem with dividing by increment count. (rebased onto develop)'
  # PR 1164 melissalinkert 'Add modulo support for LI-FLIM data'
  # PR 1165 melissalinkert 'First round of Nikon ND2 fixes (rebased onto develop)'

Generated by OMERO-5.1-merge-push#285 (http://ci.openmicroscopy.org/job/OMERO-5.1-merge-push/285/)