Last round of fixes for Maven build system

This should finish everything listed in https://trac.openmicroscopy.org.uk/ome/ticket/8797.  ```loci_tools.jar``` and ```ome_tools.jar``` are now roughly the same size regardless of which build system produced them (the Maven jars are still slightly bigger due to the xalan dependency, but they are much closer).  Artifacts are deployed to our own Artifactory, ```system```-scoped dependencies have been changed to ```runtime``` scoping, and unit tests should be the same between build systems.

Aside from verifying that what is in https://trac.openmicroscopy.org.uk/ome/ticket/8797 is fixed, it would be nice to verify that the Maven-generated ```loci_tools.jar``` can be dropped into ImageJ/Matlab/etc. and give the same results as the Ant-generated ```loci_tools.jar```.