AutoModpack should work with all minecraft modifications (it would be a bit bad modpack updater if it didn't). However, there are some exceptions and limitations that you should be aware of:

- Majrusz's Mods: Requires a modified Majrusz Library to work with AutoModpack. [Github Issue](https://github.com/Skidamek/AutoModpack/issues/268). Or `forceCopyFilesToStandardLocation` in server config.
- [CITResewnNeoPatcher](https://modrinth.com/mod/cit-resewn-neopatcher): Requires to specify fabric version of CITResewn in `forceCopyFilesToStandardLocation` in server config, like (`/mods/citresewn-1.2.1+1.21.jar`).
- [ModSets](https://modrinth.com/mod/mod-sets): It's currently broken due to similarities in mod loading modification process.