Define the POM version number only once
Remove pom-scijava dependency
Use filtering tokens that can be used with both Ant and Maven

This required using the 'replace' target in Ant instead of 'filter'.
Finish fixing up version token replacement

Version tokens are now defined exclusively in a version.properties file
that is accessed by FormatTools.  Maven and Ant can now both replace the
tokens in version.properties.  This is a lot more straightforward than
trying to convince Maven to copy source files to target/, replace tokens
in the copied source files, and then compile from the updated copies.
Use the jgit-buildnumber and gmaven plugins to set version information
Use token replacement to set the versions in cppwrap/*.cpp

Ant does not currently do the replacement for these files, since they
are outside of the src/ directory.  I'm not worrying about that for the
moment, though, since Ant can't build the *.cpp files anyway.
UpgradeChecker: catch NFE when parsing the current version
Change POM groupIds to 'ome'

See #9639.
Final fixes to Maven version number population

This removes the jgit-buildnumber dependency in favor of just using
Groovy to do all of the hard work.  As with Ant, the exact tag name is
tried first, followed by a snapshot version based upon the last known
tag.  If the version number cannot be determined (e.g. 'git' is not in
the path), then "UNKNOWN" is used.
Merge remote-tracking branch 'origin/develop' into maven-build-numbers

Conflicts:
	components/loci-plugins/src/loci/plugins/config/ConfigWindow.java
Hard-code version number just once in the POM

This should work with Maven 2 and Maven 3.
Add some missing configuration to the top-level POM

This should allow third-party dependency resolution.
Multi-plane flex file with factor and no compression only reads first plane
Fix resource filtering so that files end up in the correct place

*.properties files were previously copied under target/classes/src/
instead of target/classes/, which meant that the tests could not locate
them.
Redo POM version number hardcoding

Using variable version numbers is very much unsupported in Maven 3.
Probably we'll need to write a script for release jobs to use that
manually replaces the hardcoded version numbers.
Merge remote-tracking branch 'origin/develop' into maven-build-numbers
Force top-level Maven build to run as part of cppwrap
Make sure that filtering happens correctly in cppwrap build
One more resource copying fix for the scifio component build
cpp: Add doxygen API reference