Add a reader that accepts a file containing a file pattern

This lets us take advantage of FileStitcher as needed without explicitly
including it in the stack of wrapped readers.  Files ending in .pattern
are accepted, and should only contain a single line with the absolute or
relative file pattern (in the same format accepted by FileStitcher).
Fix used files/companion file reporting

The pattern file should now be correctly included in the used file list.
Update used file tests for FilePatternReader
Merge remote-tracking branch 'origin/develop' into pattern-reader

Conflicts:
	components/test-suite/src/loci/tests/testng/FormatReaderTest.java
Merge pull request #981 from melissalinkert/originalmetadata-ns

Ignore namespaces when filling in an XMLAnnotation's Value
CZI: prevent AIOOB exception when populating position metadata

See gh-1148.
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 1164 (Add modulo support for LI-FLIM data)
merge develop -D org: PR 1170 (cmake: Enable CMP0042 @rpath usage for MacOSX)
merge develop -D org: PR 1174 (CZI: prevent AIOOB exception when populating position metadata (rebased onto develop))
merge develop -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1162 melissalinkert 'AFI: populate magnification and physical pixel size metadata' (status: failure)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1175 melissalinkert 'Fix channel count when exporting RGB images in ImageJ' (status: error)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
Updating 8b306aa..3c3e69c
Merged PRs (fast-forward):
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value'
  # PR 1138 melissalinkert 'Lots of Zeiss CZI fixes (rebased onto develop)'
  # PR 1169 melissalinkert 'ImportProcess: remove UI-level exception reporting'
  # PR 1168 melissalinkert 'Inveon: ignore the absolute path to the image file'
  # PR 1165 melissalinkert 'First round of Nikon ND2 fixes (rebased onto develop)'

Merged PRs:
  # 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 1164 melissalinkert 'Add modulo support for LI-FLIM data'
  # PR 1170 rleigh-dundee 'cmake: Enable CMP0042 @rpath usage for MacOSX'
  # PR 1174 melissalinkert 'CZI: prevent AIOOB exception when populating position metadata (rebased onto develop)'

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