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

docs/reference/skills.md

@@ -0,0 +1,19 @@
+# Skill catalogue
+
+The skills the stack ships, as an agent's harness sees them once `tools/wikitool instructions sync`
+has published them: each one's name, what it does and the requests it answers, generated from its
+`instructions/<name>/SKILL.md`. Any skill also runs when you ask for it by name.
+
+This page describes the stack's shipped defaults. An instance may add instructions of its own;
+`tools/wikitool instructions list` shows what this instance has.
+
+<!-- wikitool:reference-skills -->
+| Skill | What it does | Use it when |
+|---|---|---|
+| `gtd-weekly-review` | Turns the findings from `wikitool review` into decisions and page updates - the GTD Weekly Review, with a machine that prepares the list instead of a human reconstructing it from memory. | the user asks for "the weekly review", "review my projects", "what's stalled", or after `wikitool review` has findings nobody has acted on yet. |
+| `wiki-ingest` | Processes a new source file into the LLM wiki - extracts entities and concepts, creates a source summary page, files a tracker item for any commitment the source also carries, cross-references, rebuilds indexes, and publishes. | the user drops a file or folder into incoming/ or raw/, names a URL to ingest, or says "ingest &lt;file&gt;", "ingest &lt;url&gt;", "process this source", "add this to the wiki" - or just "ingest" with nothing named, which takes the oldest entry waiting in incoming/ - or asks to "update the captured repositories" / "pull the repo docs", which takes the next bundle `raw status` reports as changed. |
+| `wiki-lint` | Checks the health of the LLM wiki - broken links, orphan pages, uncovered raw files, stale claims, duplicated rules, missing cross-references. | the user says "lint the wiki", "health-check the wiki", or periodically every 10 sources per the Maintenance Schedule. |
+| `wiki-manage` | Creates a new wiki page (entity, concept, source, comparison) or updates an existing page with new information, including cross-references, index/log, and publishing. | the user says "create a new entity/concept/comparison", "add a page for X", "update the X page", or new information needs integrating into an existing page. |
+| `wiki-query` | Answers a question using the LLM wiki's compiled knowledge - read-only, cites sources, can file a valuable answer back as a new page. | the user asks a question about entities, projects, concepts, or anything the wiki might know, or says "query the wiki", "what do we know about X", "search the wiki". |
+| `wiki-status` | Shows a quick read-only snapshot of the LLM wiki - page counts, orphan pages, uncovered raw files, recent activity. | the user says "wiki status", "show wiki statistics", "what's new", or wants a quick health snapshot without running a full lint. |
+<!-- /wikitool:reference-skills -->