docs(tooling): T-1253 — sweep the live references to retired tool paths

A script scanned every tracked doc, rule, skill, agent, hook and source file
for tooling/ paths that no longer exist, skipping historical records (sprints,
discussions, workshops, governance, generated wiki pages). It found 62. The
ones that tell a reader what to RUN now name the reach verb:

- The atlas skill still sent agents to tooling/atlas, atlas-verify,
  atlas-update-field and atlas-commit-and-sync — about forty lines, all
  retired in T-1285. They now name the `reach atlas` verbs, and the skill
  records that commit-and-sync STAGES by default (--commit to commit) and
  takes --corridor as an option.
- The clerk agent named tooling/clerk-review (now `reach dev clerk`). The Si
  and clerk briefings sent those agents to the retired tooling/db/decision
  and sqlite-query CLIs and to decisions/*.md paths that moved to
  governance/ in the pql migration. They now name pql.
- The ticket-cli rule documented `pql decisions read`, which does not exist;
  `show` already includes the body.
- The culture authoring guide and the RON sources name
  `reach validate ron`, with the same arguments as before.
- The 41 Blender payloads' usage lines ran the retired tooling/blender
  wrapper, and the docstrings still cited pre-carve-out paths. They now read
  `reach blender run <payload>`.
- Doc comments in server/, client/, wiki TOMLs and the domain modules.

What is left is deliberate: "Formerly …" provenance, dated plans and findings
docs, the retired-pipeline doc, and a build-artefact path.

project.yaml 0.4.14 (mirrored to the client). Comment-only, but four touched
files are in the canvas-version registry (trait_catalog_reader.rs, since
T-1289, canvas_sources.py itself, and two client files). The gate is
path-based and has no override. The previous push was rejected on exactly
this.

Three of the edits are stamped ledger sources, so systems.db is regenerated
and the stamp is fresh.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

docs/briefings/clerk.md

@@ -23,13 +23,15 @@ Review branch changes before push to catch institutional drift: decision contrad
 
 ## Where to Find Decisions
 
-- **Decision index:** `decisions/README.md` — master index of all domain files
-- **Domain files:** `decisions/architecture.md`, `decisions/perception.md`, `decisions/content.md`, `decisions/scope.md`, `decisions/economics.md`, `decisions/process.md`
-- **Open questions:** `decisions/questions.md`, `decisions/questions-process.md`
-- **Rejected proposals:** `decisions/rejected.md`
-- **Decision DB table:**
+- **Decision index:** `governance/README.md` — the domain guide and the pql-maintained record index
+- **Confirmed decisions:** `governance/decisions/<domain>.md` — architecture, perception, content, scope, economics, process
+- **Open questions:** `governance/questions/<domain>.md`
+- **Rejected proposals:** `governance/rejected/<domain>.md`
+- **Queries** (pql; never the `sqlite3` CLI, which crashes in Claude Code):
   ```bash
-  tooling/db/sqlite-query "SELECT id, title, status, domain FROM decisions WHERE domain = '<domain>'"
+  pql decisions list --domain <domain>
+  pql decisions list --type question
+  pql decisions refs D-NNN                 # what cites a record
   ```
 
 ## Output

docs/briefings/si.md

@@ -26,14 +26,15 @@ If any of these conditions fail, the ticket is not ready. Flag what is missing a
 
 ## Where to Find Decisions
 
-- **Decision index:** `decisions/README.md` — lists all domain files and how to query them
-- **Domain files:** `decisions/architecture.md`, `decisions/perception.md`, `decisions/content.md`, `decisions/scope.md`, `decisions/economics.md`, `decisions/process.md`
-- **Open questions:** `decisions/questions.md` (Q-NNN), `decisions/questions-process.md` (Q-NNN process)
-- **Rejected proposals:** `decisions/rejected.md` (R-NNN)
-- **Decision DB queries:**
+- **Decision index:** `governance/README.md` — the domain guide and the pql-maintained record index
+- **Confirmed decisions (D-NNN):** `governance/decisions/<domain>.md` — architecture, perception, content, scope, economics, process
+- **Open questions (Q-NNN):** `governance/questions/<domain>.md`
+- **Rejected proposals (R-NNN):** `governance/rejected/<domain>.md`
+- **Queries** (pql — the old `tooling/db/decision` CLI was retired in the pql migration):
   ```bash
-  tooling/db/decision show D-NNN        # Show a specific decision
-  tooling/db/decision check-dupes "title"  # Check for duplicates before creating
+  pql decisions show D-NNN                 # one record, with its markdown body
+  pql decisions list --type question       # open questions
+  pql decisions claim D <domain> "title"   # next free id, before writing a new one
   ```
 
 ## Where to Find Workshop Outcomes

docs/diagrams/data-flow/wiki-generator-flow.d2

@@ -13,7 +13,7 @@
 #        red   = the trap (output that is read back as input)
 #
 # Every path here was read in the tool's own source, not inferred.
-# tooling/check-dataflow-graph asserts the paths still exist; it CANNOT verify
+# `reach check dataflow-graph` asserts the paths still exist; it CANNOT verify
 # that an edge's MEANING is still true — see D-262.
 #
 # View it:  clide draw --file docs/diagrams/data-flow/wiki-generator-flow.d2