I've also been thinking about that automatic mod merger program PeredexisErrant gave up on a while ago. ("Gave up" is too strong a word, really - he was satisfied with a less full-featured version than I would have been, is all.)
What would you want that isn't implemented? As of PyLNP 0.9.2a (which I finished work on a few hours ago ), I've got almost everything working. Line-by-line merges of an uncapped number of mods, integration with graphics packs including changing graphics on modded saves, and so on.
Last I kept up with your mod merger you were still rejecting anything with extra/non-vanilla files?
I'll check out the newer version sometime & see what I can see.
On a different note, do you have that list of modified files? I'm particularly interested in knowing if any lines changed by Phoebus are further changed by Modest Mod (which affects merge compatibility), and more importantly how likely it is that updates will be save-compatible with older versions of Modest Mod.
2-3 lines changed by Phoebus are further changed by Modest Mod. They're in the Plump Helmet definition, and change the tile for the base plump helmet fungus "shrub". (Since the helmets need to be growths in order to be pickable in adventure mode, the shrub sticks around after harvesting in fortress mode, so I needed a different graphic to show "Hey you already picked this.")
Plant Fixes, if made into a Module, would do this a
lot.
I'm not aware of any older versions of Modest Mod for 0.40.x to be compatible with.
All of the files included in the zip are modified. I'd download it and list them out for you, but I'm on my work computer right now and corporate recently slapped me on the wrist for downloading files from the new DFFD.