Micromanager: use full channel name in file names when necessary

If the trimmed name (everything before the first '-') is not sufficient
for picking up TIFF files, then use the full channel name.  I suspect
this is only an issue for datasets produced with older versions of
Micromanager, but that may not be correct.
MM: trim the timepoint count if all files are missing beyond a certain point

Fixes ticket #11972.
Update version numbers to 5.0.1
Flex: fix whitespace annoyances
Flex: fix the case where one field is stored in each file

See #11382 and
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-March/002721.html
Revert "CZI: restrict dimension adjustment"

This reverts commit f8ce7b1e749fe7d85d7fac1d2d547861166d3d43.
Add missing '>' to one of the URLs
Sort reader list, so that the template document ordering is consistent
Update POM version numbers to 5.0.2-SNAPSHOT
Merge pull request #1021 from melissalinkert/template-fix

Minor docs autogen fixes
Merge pull request #1023 from melissalinkert/version-history

Update version history for 5.0.1
DICOM: fix file grouping so that path names are normalized

On Windows in particular, the list of pattern files often has extra path separator escaping, which prevents the
pattern files from being matched with the files from the directory listing.
Merge pull request #1013 from melissalinkert/5.0.1-version

Update version numbers to 5.0.1
Add the series index to the default image name

This prevents confusion when importing multi-series datasets that do not
override the image name.
Remove note about Fiji shipping BF 4.4.x
Merge pull request #1025 from melissalinkert/5.0.2-snapshot

Update POM version numbers to 5.0.2-SNAPSHOT
Only add a MetadataOnly element if no TiffData elements are present

This prevents validation errors for most OME-TIFF files; noticed by @qidane.
Merge pull request #1034 from hflynn/fiji-5

Remove note about Fiji shipping BF 4.4.x
Fix link to bitplane release notes
Merge pull request #1037 from hflynn/bitplane-link

Fix link to bitplane release notes