Add branch-specific link for downloading the JAR file if unfound
Also modify link in bf.bat
IM3Reader for Perkin-Elmer Nuance
Added some more record types + parsing of spectral library (.csl) files
Reader for Amaris FlowSight .cif format

Conflicts:

	components/formats-api/src/loci/formats/readers.txt
Was not populating the pixel metadata - now it does.
One last tweak - turn off saveOriginalMetadata
Fix up indentation and remove tabs
FlowSight: fix a couple of minor issues with metadata population and the 'in' variable
Fix invalid channel IDs
Fix FlowSight format name
#1315 modifications as suggested by @melissalinkert + better parsing of some records
FlowSight: add a space to make mask channel names more readable
Merge pull request #1315 from LeeKamentsky/im3

IM3Reader for Perkin-Elmer Nuance
Merge pull request #1339 from melissalinkert/lee-kamentsky-amaris

Amaris FlowSight
Merge pull request #1302 from sbesson/rebased/develop/tools_download_link

Add branch-specific link for downloading the JAR file if unfound (rebased onto develop)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1353 seb-berger 'KodakReader: Bugfix and file info metadata' (user: seb-berger)
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter' (user: melissalinkert)
  # PR 1328 sbesson 'Use in-place caching by default in Memoizer' (user: sbesson)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 1352 rleigh-dundee 'C++ TIFF tiling support' (user: rleigh-dundee)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories' (user: melissalinkert)
  # PR 1356 sbesson 'Re-order plugin repositories in format-bsd/pom.xml' (user: sbesson)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1265 qidane 'New units' (status: error)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1351 melissalinkert 'ND2: reset series count before allocating offset array' (user: melissalinkert)
Updating a9cad62..a49ec02
Previously merged:
  # PR 1302 sbesson 'Add branch-specific link for downloading the JAR file if unfound (rebased onto develop)'
  # PR 1339 melissalinkert 'Amaris FlowSight'
  # PR 1315 LeeKamentsky 'IM3Reader for Perkin-Elmer Nuance'

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