Disable "Plugins > LOCI > Update LOCI Plugins" in Fiji
Make the options in the file pattern dialog a little more clear

Now, the user must explicitly choose which of the three pattern
specification methods they wish to use.

Closes #6374.
Don't use a FileStitcher if "Group files..." was unchecked

Fixes #9778.
Do not recommend using "Plugins > LOCI > Update LOCI Plugins" in Fiji
Update screenshot of file grouping window
ND2: check the array size before allocating an array

See
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-December/003484.html
ImageInfo: do not allow the ImageViewer to close the reader

Fixes #10076.
FV1000: better handling of renamed files

Fixes #9851.
Only use a MinMaxCalculator if we need the min/max values

MinMaxCalculator imposes a substantial overhead on calls to openBytes,
so avoiding it when possible means that non-autoscaled images (e.g.
virtual stacks) will open more quickly.
Minor cleanup of loci-plugins tests

Includes removal of commented-out code, proper logging usage, and a few
speed improvements.
Prevent int overflow in sample count calculation

Fixes #10050.
ND2: catch potential long overflow

d79a091 should have included this.
Add utility methods to deal with lists of metadata values

See #9928.
Use add*MetaList methods to ensure that metadata keys are sorted correctly

Fixes #9928.
Remove obsolete format notes

All of these pages are severely outdated, and if updated would not
contain any information that is not already present in source code
comments and the existing format pages.

See #9835.
Final updates to the reader implementation guide

Closes #4534.
Recommend Homebrew instead of MacPorts

See #9835 and
https://github.com/openmicroscopy/bioformats/pull/243#commitcomment-2219859
Remove outdated paragraph
Add Javadoc links to the reader guide
Put metadata support documentation into Sphinx

The summary table still needs a little work.

See #9835.