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

docs/reference/README.md

@@ -5,6 +5,10 @@ reference page describes what is, not how to use it or why it is so - and wherev
 it exists in the code, it is generated from that source and checked against it rather than
 written by hand.
 
-Nothing is generated here yet. Until it is, the command reference is
-[tools/CONTRACT.md](../../tools/CONTRACT.md) (and `tools/wikitool <command> -h`), and a page
-type is described by `tools/wikitool types describe <type>`.
+- [Command reference](commands/README.md) - every `wikitool` command, one page per group,
+  generated from the same records as `tools/wikitool <command> -h`.
+- [Exit codes and gates](exit-codes.md) - which commands can stop and wait for a person, and
+  why.
+
+Page types are not generated here yet; until they are, a page type is described by
+`tools/wikitool types describe <type>`.