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
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.
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.
ScanR: fix exposure time units

See http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7554
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
CZI: prevent NumberFormatExceptions on missing/invalid position values

Fixes QA 9382.
Merge pull request #1194 from melissalinkert/rebased/develop/qa9382

CZI: prevent NumberFormatExceptions on missing/invalid position values (rebased onto develop)
Merge pull request #1187 from melissalinkert/scanr-exposure

ScanR: fix exposure time units
Merge pull request #1164 from melissalinkert/liflim-modulo

Add modulo support for LI-FLIM data