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
Immediately return null lookup tables if initialization is not complete

This prevents throwing a FormatException in FileStitcher.
Prevent FileStitcher from overriding the .pattern file's pattern

This fixes reading a subset of the files in a directory.
Merge pull request #1123 from melissalinkert/pattern-reader

Add a reader that accepts a file containing a file pattern
Update auto-generated documentation

Repository: openmicroscopy/bioformats
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