SK suggested a change to the generation of the root-based index, which we implemented, but in order to test it I finally had to bite the bullet and go through the process of getting the dictionary build set up (config was lost during the hard-drive failure last year, and the subsequent transition to a new machine). I discovered a number of things:

• My XEP config had been lost because it was in ~/apps, which was not backed up. I've now reconstructed it; the config file xep.xml was partially reconstructed already based on the ScanCan server setup, but was missing the Aboriginal Sans fonts. I've now added those fonts to the font folder in the xep app folder and to xep.xml, and this stuff is in my backup script.
• I have three Java collations used in the form of jar files for sorting purposes. The source code for two of them is in svn, but the third, MosesOrthographyCollation, was missing both its jar file and source code, although the project framework was there. Not sure how that happened, but probably because it was developed in a different location on the dead drive and didn't get svn'ed or backed up for some reason. I had a built copy of the jar file in the eXist project, so I'm able to use that, but I'll actually need to reconstruct the source code (not complicated) so it can be tweaked if necessary. There's a hard-coded list of the orth symbols in order showing in the built dictionary PDF, so that won't be hard.
• The dictionary now builds OK, and the change to compound discovery, although it should not have retrieved any new compounds per SK for the moment (the particular cases in point are in a file that's not yet being used in the build), it does seem to have found some; I'm waiting for SK to look at those and determine whether they are actually correct, or whether our new criteria are too broad somehow.