Those tools have no documentation and were created by various people at multiple years interval, some of them really are trial-and-error.

"accents patch.txt" - Documentation on the accents patch.

However from what I remember:
- 4BPP to OAM: Add a padding to any file you give to it for it to work with the RhythmHeavenOAMEditor.
- nmap: Texture extractor(?)
- RhythmHeavenOAMEditor: It's in the name.
- crystaltile2: GFX editor.
- R-IQ Tile Fixer: Reassemble BG from their tile arrangement and vice-versa.

The IPS adds probably some obscure binhacks for some emulator (vba?) to log the location of the sprite.
And the Lua script probably is the thing that works with it.