TSLPatcher should be able to do that properly, AFAIK.
I personally love editing .git's, but true, I haven't really had to account for other mods at this point I think, rather than my own XD. Of course most mods do drop most stuff in the override, and .git cannot possibly EVER be there, so you need to insert them in the .rim (will be overwritten if TSLRCM) and/or .mod.
I'm pretty sure a repository of TSLRCM scripts' is impossible at this point, also slightly due to lack of organisation (our fault). But most files can be de-compiled with DeNCS, there are very few exclusions. And we had to work around stuff we couldn't decompile either (Handmaidens fight on Telos for example).
A TSLRCM respitory at this point would pretty much involve all scripts at this point, not much is excluded, so you might aswell take make it a respitory of all TSL files (using TSLRCM).
@ sELFiNDUCEDcOMA:
I'm not sure a tool exists to merge scripts automatically, so you still need to make enter scripts for all mods you want to be compatible with. And no, there's no way a file executing another file can "outcomment" something happening. That's simply not possible. As I stated before; I really think it's just adding another layer for incompatibility with the added effect of being less lenient on your options what to do. Nothing positive at all.
Also, why, if you can modify the onenter, would you want to execute another script rather than just doing it right there (unless of course engine crap demands it, as seen in the Telos Cantina for example IIRC). Adding more and more 'runs' just adds to being it more likely to have issues, not less.
Also the "I have to upload all my files with the next TSLRCM version" doesn't really hold much water after we're pretty much done, it's very unlikely that more is done and if so it's also unlikely to modify the onenter. They're really barely updated per version, big updates like 1.7,1.8 or 1.8.2 excluded.
1.8.3b it was just 207TEL (fixing issues with the Swoopstuff OE had set up) and 351NAR (fixing stuff we had set up inproperly).
Some of my own mods editing enter scripts (like My Dantooine Statue) has been as is since 29 janury 2012. Only the .dlg's got updated.
I personally see little harm in modmakers double checking if their mods work with the next TSLRCM rather than just "drop and forget" leading to potential issues later down the road. You can always ask me what's changed, and I happily cross-reference the changes to your modified files. And yes, I also do this every single of my own mods.
Rather safe than sorry after all.
And it's very likely for alternative onenters to cause issues, just try making one doing a cutscene on the EH, and then running the original onenter. It's going to work poorly.