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 pull request #1108 from melissalinkert/rebased/develop/mrc-pixel-type

MRC: fix handling of mode 16 data (rebased onto develop)
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

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (label: exclude)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
Updating 1c1996d..18bd912
Merged PRs (fast-forward):
  # PR 1108 melissalinkert 'MRC: fix handling of mode 16 data (rebased onto develop)'

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)'
Conflicting PRs (not included):
  # PR 1138 melissalinkert 'Lots of Zeiss CZI fixes (rebased onto develop)'

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