I apologize, but this is gonna sound a big frustrated I think by the end.
And now to dive in:
I'm curious as to how it assembles files outside of the entity and creature entries. These are handled spot on (for the most part see bit later about comment text). If you fix a typo -but you fixed it in the raw dir accidentally (and not the mod dir) you can run it through UltraCompare (or any line by line comparison tool) and quickly add it to the mod dir as well. "It was 4am and what not... mistakes happen" some might say.
With reactions and buildings... even Core reactions and buildings it seems to scramble the files completely. They're perfectly fine for Dwarf Fortress don't misread me here. However if you hunt down and fix a typo at 4am(or fix a line for the particular DF version), and then when you get up later try to populate that to the mod dir... you'd better remember the exact line you changed. I say this because your files (mod or core) are not what ends up in the save directory. Alphabetized (or even just [REACTION:MB_DESTROY_STONE_V01], [REACTION:MB_DESTROY_STONE_V02] sorting) reactions get tossed all over the place ([REACTION:MB_DESTROY_STONE_V11] is at the top of the file... a few entries later a reaction from the bottom of the file is next... the bit at the top might be in the middle of the file)
Also file comments... even Toady One's in the Core files get played with... For example a list of Contributors who helped sponsor a creature. The Comment block is fine up until the last line or so, where the last line is slid into the next entry right under first line:
Penguins were sponsored by the generous contributions of the Bay 12 community.
Alluvian Est-Endrati; Bearer of the White Flame
themel - Note to Urist: R M Laws, A Perspective on Antarctic Cookery
For my Penga
For Bs->PhiPhi penguin loop decays! - by Psieye
Sponsored by penguinofhonor!
Greenacre
[CREATURE:BIRD_PENGUIN]
Theq629
(based on Magellanic penguin like the ones in the local zoo, while we only have 3 kinds)
Instead of:
Penguins were sponsored by the generous contributions of the Bay 12 community.
Alluvian Est-Endrati; Bearer of the White Flame
themel - Note to Urist: R M Laws, A Perspective on Antarctic Cookery
For my Penga
For Bs->PhiPhi penguin loop decays! - by Psieye
Sponsored by penguinofhonor!
Greenacre
Theq629
[CREATURE:BIRD_PENGUIN] (based on Magellanic penguin like the ones in the local zoo, while we only have 3 kinds)
Thus I'm curious how it recreates files. I'd just grab the files from DFMM's perspective but I'm also worried that if a given file changes enough the resultant dir might end up changed again.
So does it recreate line by line or some such (my suspicion hence why it is first) rather than create a blank file with the right number of lines and then fix those lines as it comes across them?