Fix documentation gaps across day11
- layer.mld: add Layer module, update description for new core type
- batch.mld: add Profile and Snapshot modules
- doc.mld: add Doc_build module
- generate.mli: add doc comment for run function
- patches.mli: new interface file for Patches module
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>