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

tools/README.md

@@ -164,7 +164,12 @@ bound at import time - `KB_DIR` and friends follow whatever `ROOT` currently is.
    a comment next to the code). `docs verify` fails in both directions - a command with
    no record and a `GROUPS` entry naming no real command are equally reported -
    and also checks that every non-hidden flag appears in the record's SYNOPSIS.
-   Then regenerate the copy: `wikitool docs contract --apply`. Write the
+   Then regenerate both copies: `wikitool docs contract --apply` for
+   CONTRACT.md and `wikitool docs reference --apply` for the human reference
+   under `docs/reference/commands/`. A new group needs its page there first -
+   `docs/reference/commands/<group>.md` with a title, a one-sentence head and
+   the `<!-- wikitool:reference-commands -->` marker pair; the command never
+   creates one. Write the
    record's prose without citing an issue number: `docs verify` also refuses
    one in a command's rendered `--help` text (a docstring above its `\f`
    marker, or an option's `help=`) and in any `.md`/`.template` `dist export`