Refactor codebase

todo

@@ -0,0 +1,19 @@
+[x] Merge .omp/APPEND_SYSTEM.md into AGENTS.md
+[x] Use git submodule for toolkit/ with URL git@git.sr.ht:~iacore/mpi-translation-toolkit
+    (push failed: remote may not exist or SSH key not configured; run `git push -u origin main` in toolkit/)
+[x] Rename terms-search/ -> terms-database/
+[x] Rename skill directories with mpi- prefix
+[x] Create toolkit/ and fold scripts/, references/, terms-database/, skills/ into it
+[x] Update all in-repo references
+[ ] Update external Hermes config:
+    ~/.hermes/config.yaml: skills.external_dirs -> $MPI_PROJECT_ROOT/toolkit/skills
+[x] Test
+    - toolkit/terms-database/search.py runs
+    - toolkit/scripts/gen-bilingual.py runs
+    - no stale references to scripts/, references/, terms-search/, or skills/
+[x] Delete .omp/APPEND_SYSTEM.md
+
+Next:
+- Replace the placeholder URL in .gitmodules with the real remote for toolkit/.
+- Push the toolkit/ submodule to its remote, then run `git submodule update --init`.
+- Update ~/.hermes/config.yaml as noted above.