Make FormatReader's RandomAccessInputStream transient

This prevents Kryo from throwing an IllegalAccessError on every memo file.
Previous versions of Kryo did not require this, but upgrading to 2.24.0 makes it necessary.
Add reopenFile() as an API method in IFormatReader

This allows any underlying file handles that are expected to be open when
setId returns to be reopened.  This handles the case when a reader is
initialized via memo file, or when close(true) was called.
Add a new test for determining memo file validity
Update readers to make RandomAccessInputStream fields transient

This should allow the new memo test to pass, as well as reopening
relevant streams after a reader is initialized from a memo file.
Store memo files in a unique tmp directory
Log the memo file size during testing
TIFF reader: reinitialize the input stream as well as the TiffParser
Fix several remaining memoization issues
FlowSight: override reopenFile to initialize the TiffParser
Zeiss TIFF: fix used file list when expected files are missing

The top-level .tif file in particular can be missing without causing any
other problems.  This prevents any files that do not exist from
appearing on the used file list, as that would cause import into OMERO
to fail.
TIFF: attempt to correct incorrectly stored StripByteCounts values

If an entry in the StripByteCounts array is negative, this logs the
original value and attempts to set it to the previous entry in the
array.

Fixes #12583.
Metamorph: fix description delimiter to account for XML sanitization

Fixes #12633.
Initial version of I2I reader

See #12426
Zeiss TIFF: fix one more bug when the master .tif file is missing

This prevents an exception from being thrown if the master .tif file is
missing when the recorded original name ends with .zvi.
Merge pull request #1422 from melissalinkert/zeiss-tiff-missing-file

Zeiss TIFF: fix used file list when expected files are missing
Merge pull request #1432 from melissalinkert/12633

Metamorph: fix description delimiter to account for XML sanitization
Merge pull request #1433 from melissalinkert/i2i

Initial version of I2I reader
Merge pull request #1423 from melissalinkert/12583

TIFF: attempt to correct incorrectly stored StripByteCounts values
Merge pull request #1362 from melissalinkert/memo-fix

Make FormatReader's RandomAccessInputStream transient
Update auto-generated documentation

Repository: openmicroscopy/bioformats
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