There is not really much documentation. The only thing that even comes close, to my knowledge, is the "Advanced mode" section of the Updater page which reads:
The details for each component can be edited by writing below the respective entry.
This means that you can literally edit that list of dependencies using that big text field in the graphical updater's Advanced mode.
However, this is not how I fixed the formats-bsd.jar's dependency on the old batik.jar. To do that, I edited the Bio-Formats update site's db.xml.gz file directly to purge the dependencies. This is honestly easier, but of course: 1) requires admin access to the sites.imagej.net box, and 2) must be done extremely carefully to avoid ending up with invalid XML.
It would be nice to have A) better documentation for the Updater; and B) more powerful Updater-related CLI tools. But no one has time/energy/expertise/funding/etc. to work on this at the moment.
In general, yes. But it's most important that the BOM list compatible versions. So if, e.g., a new version of ome-xml is released which breaks backward compatibility, and some Bio-Formats artifacts have not yet been updated to work correctly with it, we would of course hold off on updating the ome-xml version in pom-scijava until such time as all components in the dependency tree are realigned.
