Ignore namespaces when filling in an XMLAnnotation's Value

This prevents the xmlns on Value from being set to an empty string.
MRC: fix handling of mode 16 data

Mode 16 denotes 8-bit RGB data, not 16-bit data.  See
https://trello.com/c/guQdSW8V/235-follow-ups-with-joaquin
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
Add some trace-level logging

This is mostly to assist in debugging issues with very large files.
ImageInfo: add flag to enable trace-level logging
Zeiss CZI: fix value of Rectangle.Y

The stored Y coordinate is the actual Y coordinate; it doesn't need to
be subtracted from the image height.

Fixes ticket #11367.
Zeiss CZI: fix copying of prestitched tiles

This uses the stored tile row/column instead of assuming that tiles were
acquired in comb mode.  It also prevents tiles from being copied to the
wrong row when the image width is greater than the sum of the tile widths.

Fixes #11784.
Zeiss CZI: fix reading of RGB images

The channel count and interleaved values were previously set
incorrectly; openBytes also did not account for the fact that RGB images
are stored in BGR order.

Fixes #11233.
CZI: do not overwrite SizeT if SizeT is equal to the number of planes

Fixes #12003.
CZI: parse plane positions from an alternate location

Fixes #11784.
CZI: fix FilterSet/Dichroic/Channel linkages

Fixes #11166.
CZI: add support for known camera-dependent "compression" types

These are really just packed pixels; 12 bits are stored for 16-bit (12
valid bit) data.  Some transposing needs to occur type 504, though it's
not completely clear to me why.

Fixes #11204, fixes #9398.
CZI: update to correctly group files in multi-file datasets

Also updates the relevant test to check for the new behavior.

Fixes #12189.
Allow NIOFileHandle's buffer size to be passed through from RAIS

This lets us set a buffer size for a specific stream/handle, instead of
calling the static setDefaultBufferSize method in NIOFileHandle.
CZI: use a buffer size of 1024 in most places

We have to do a lot of seeking and opening new streams to read a small
number of bytes; the only place where large chunks of bytes are read is
when the pixel data is processed.  This should speed up setId times, as
we're not attempting to buffer 1MB every time a new stream is opened
(potentially millions of times for very large datasets).
Improve master file detection
Revert to accepting unknown compression types as raw data

...instead of throwing an exception.  Many of the camera-dependent
encoding types are just raw data, and were correctly handled previously.
Prevent an NPE when retrieving the DichroicRef