feat: docs reference generates a skill catalogue and a page-type reference under docs/reference/ from the shipped defaults, checked and written in the origin repo only (#189)

Files changed:
- CHANGES.md
- README.md
- VERSION
- docs/reference/README.md
- docs/reference/commands/README.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/page-types.md
- docs/reference/skills.md
- instructions/dev/doc-pull-through.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/test_reference_doc.py

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

tools/CONTRACT.md

@@ -145,7 +145,7 @@ docs verify           read  idempotent     budget:counted              exit:0,1
 docs toc              write idempotent     budget:counted              exit:0      Create, refresh or remove the generated table-of-contents region.
 docs prerequisites    write idempotent     budget:counted              exit:0,1    Regenerate `INSTALL.md`'s prerequisites lists from `tools/prerequisites.txt`.
 docs contract         write idempotent     budget:counted              exit:0,1    Regenerate `tools/CONTRACT.md`'s `<!-- wikitool:commands -->` region.
-docs reference        write idempotent     budget:counted              exit:0,1    Regenerate the human command reference under `docs/reference/`.
+docs reference        write idempotent     budget:counted              exit:0,1    Regenerate the human reference under `docs/reference/`.
 eval sessions         read  idempotent     budget:exempt               exit:0      List the sessions that have a trace under `reports/telemetry/`.
 eval score            read  idempotent     budget:exempt               exit:0,1    Score one traced session.
 dist export           write idempotent     budget:counted              exit:0,1    Write a contentless, distributable copy of this repo's machinery.
@@ -2516,8 +2516,8 @@ Check the docs that mirror the code.
 - 1    A type-spec's own frontmatter fails its schema
 - 1    A subtype template `types/<type>.<value>.md` has no type-spec with a `subtype_field:` beside it, names a value outside that field's enum, or carries frontmatter
 - 1    A shipped `.md`/`.template` cites an issue number
-- 1    A region of the human command reference under `docs/reference/` is stale
-- 1    A page of the human command reference is missing or lacks its marker pair, or a page under `docs/reference/commands/` belongs to no group
+- 1    A region of the human reference under `docs/reference/` is stale
+- 1    A page of the human reference is missing or lacks its marker pair, or a page under `docs/reference/commands/` belongs to no group
 - 1    A reference file's table-of-contents region is missing or stale
 - 1    A file sits directly in `docs/`, or in a directory there that is not one of its five areas
 - 1    A reference file's relative markdown link does not resolve to an existing file
@@ -2534,8 +2534,8 @@ Check the docs that mirror the code.
 - A type-spec's own frontmatter fails its schema -> Fix the field, or add a matching line to `types/type-spec.schema.yaml` if the field is legitimately new
 - A subtype template `types/<type>.<value>.md` has no type-spec with a `subtype_field:` beside it, names a value outside that field's enum, or carries frontmatter -> Rename the file to the type and value it was meant for, delete it, or remove its frontmatter block
 - A shipped `.md`/`.template` cites an issue number -> Say what was decided instead of pointing at where, or move the pointer behind a `<!-- dist:strip-start/end -->` block
-- A region of the human command reference under `docs/reference/` is stale -> Run `docs reference --apply`, then re-run
-- A page of the human command reference is missing or lacks its marker pair, or a page under `docs/reference/commands/` belongs to no group -> Create the page with a title, a one-sentence head and the marker pair the message names (or add the pair), then run `docs reference --apply`; `git mv` or `git rm` a page left over from a renamed or removed group
+- A region of the human reference under `docs/reference/` is stale -> Run `docs reference --apply`, then re-run
+- A page of the human reference is missing or lacks its marker pair, or a page under `docs/reference/commands/` belongs to no group -> Create the page with a title, a one-sentence head and the marker pair the message names (or add the pair), then run `docs reference --apply`; `git mv` or `git rm` a page left over from a renamed or removed group
 - A reference file's table-of-contents region is missing or stale -> Run `docs toc --apply`, then re-run
 - A file sits directly in `docs/`, or in a directory there that is not one of its five areas -> Move it (`git mv`) into the area its kind of documentation belongs to, and fix the links that pointed at the old path
 - A reference file's relative markdown link does not resolve to an existing file -> Fix the `../` count or the target's name
@@ -2559,7 +2559,7 @@ Check the docs that mirror the code.
 - Every reference file `docs toc` covers carries the current table-of-contents region for its own headings - missing and stale are one check.
 - Every relative markdown link in one of those reference files resolves to an existing file. A target's `#anchor` suffix is stripped first, and code fences and inline code spans are masked before scanning, so link syntax shown as an example is not mistaken for a real reference.
 - Every file under `docs/` sits in one of its areas - `tutorials/`, `how-to/`, `reference/`, `explanation/` or `dev/` - never directly in `docs/` or in another directory.
-- If `docs/` exists: every generated region of the human command reference under `docs/reference/` matches what `docs reference` would write, every `cli_contract.GROUPS` entry has its page under `docs/reference/commands/`, and no page there belongs to no group.
+- If `docs/` exists: every generated region of the human reference under `docs/reference/` matches what `docs reference` would write, every `cli_contract.GROUPS` entry has its page under `docs/reference/commands/`, and no page there belongs to no group. The skill catalogue and the page types are checked only in the origin repo (no `.wikitool-release.json`): they describe the stack's shipped defaults, which an instance's own type-specs and instructions may differ from.
 - `INSTALL.md` carries one generated `<!-- wikitool:prerequisites -->` region per platform value of `tools/prerequisites.txt` (`prerequisites-<platform>` for a platform-specific one), each current; and the `<!-- setup-question: <key> -->` markers in `instructions/setup-instance.md` and `INSTALL.md` name the same set of keys, so a question the agent asks is never one the human guide leaves out, nor the reverse.
 - `VERSION` parses and the newest versioned `CHANGES.md` entry names it. An entry that crosses the compatibility boundary from the last release carries `**Breaking Change:**`, has a migration document or `**Migration:** none required`, and its `**Migration:**` line names every required migration document targeting it.
 - The newest versioned `CHANGES.md` entry is at most 32 000 bytes (UTF-8) as `version notes` prints it, and each of its `###` sections is exactly one paragraph of at most 1 000 bytes, heading line excluded. Older entries and a changelog with no versioned entry are not checked.
@@ -2569,7 +2569,7 @@ Check the docs that mirror the code.
 
 - `wikitool docs toc` - regenerates tables of contents
 - `wikitool docs contract` - regenerates the commands region
-- `wikitool docs reference` - regenerates the human command reference
+- `wikitool docs reference` - regenerates the human reference
 - `wikitool docs prerequisites` - regenerates `INSTALL.md`'s prerequisites lists
 - `wikitool instructions verify` - the same kind of check for `instructions/`
 
@@ -2708,7 +2708,7 @@ Regenerate `tools/CONTRACT.md`'s `<!-- wikitool:commands -->` region.
 
 #### `docs reference`
 
-Regenerate the human command reference under `docs/reference/`.
+Regenerate the human reference under `docs/reference/`.
 
 **SYNOPSIS**
 
@@ -2743,6 +2743,7 @@ Regenerate the human command reference under `docs/reference/`.
 **NOTES**
 
 - Rewrites the generated region of every page of the human command reference from the `cli_contract` records: one `docs/reference/commands/<group>.md` per `cli_contract.GROUPS` entry (`<!-- wikitool:reference-commands -->`), the overview in `docs/reference/commands/README.md` (`<!-- wikitool:reference-commands-index -->`), and the gates and exit-42 causes in `docs/reference/exit-codes.md` (`<!-- wikitool:reference-exit-codes -->`).
+- Also, in the origin repo only, the skill catalogue `docs/reference/skills.md` (`<!-- wikitool:reference-skills -->`: one row per shipped `instructions/<name>/SKILL.md`, its description split at the sentence starting "Use when") and the page types `docs/reference/page-types.md` (`<!-- wikitool:reference-page-types -->`: one section per `root: kb` type-spec, from what `types describe` reads). Both describe the stack's shipped defaults. In an instance - a tree with `.wikitool-release.json` - they are left alone and the output says so: an instance's adopted type-specs and own instructions may differ, and rewriting a shipped page there would block the next `dist upgrade`.
 - Renders each command's summary, synopsis, options, examples, notes, properties in words, exit codes with their causes and see-also - but not the ON FAILURE reactions or NEVER, which address an agent; `tools/CONTRACT.md` keeps those.
 - Refreshes the table of contents of each page it writes in the same step.
 - Never creates a page or places a region: a page's title and one-sentence head are written by hand. A group's page is named after the group - lower case, every run of other characters one hyphen.