feat: docs reference generates a human command reference under docs/reference/ from the command records, one page per group plus exit codes and gates; toc never lands inside another generated region (#188)

Files changed:
- CHANGES.md
- README.md
- VERSION
- docs/reference/README.md
- docs/reference/commands/README.md
- docs/reference/commands/catalog-and-log.md
- docs/reference/commands/content-migrations.md
- docs/reference/commands/distribution-and-versioning.md
- docs/reference/commands/finding-and-checking.md
- docs/reference/commands/git.md
- docs/reference/commands/guideline-export.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/links-and-citations.md
- docs/reference/commands/pages.md
- docs/reference/commands/provenance.md
- docs/reference/commands/raw-material-and-uploads.md
- docs/reference/commands/telemetry.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/commands/workshop-runs-and-session-budget.md
- docs/reference/exit-codes.md
- instructions/dev/doc-pull-through.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/test_reference_doc.py
- tools/chemenu/toc.py

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2

README.md

@@ -66,7 +66,8 @@ The human documentation lives under `docs/`, sorted by what you want from it:
 - [docs/how-to/](docs/how-to/README.md) - doing: one task per page, for the operator of an
   instance.
 - [docs/reference/](docs/reference/README.md) - looking up: commands, exit codes, skills, page
-  types. The command reference is [tools/CONTRACT.md](tools/CONTRACT.md).
+  types. The command reference is [docs/reference/commands/](docs/reference/commands/README.md);
+  agents use the same records in [tools/CONTRACT.md](tools/CONTRACT.md).
 - [docs/explanation/](docs/explanation/README.md) - understanding: why the stack is built the way
   it is.