Drop Obsidian vault (root domain) from default audit scope

wiki-vault/wiki-context are an MCP-owned, managed surface — a second scanner
risks interfering with how the vault MCP maintains its context. Remove the
'root' domain from DEFAULT_DOMAINS so a plain run no longer touches the vault;
the --scan/--repo escape hatch still allows manual one-offs. Updated SKILL.md,
check-catalog, findings-format, README, CLAUDE.md with the rationale.

Default run: 3 domains, 37 repos, 54 findings (was 61); clears the vault-only
false positives (herbygitea doc-mention, wiki-context uv-init stub).

CLAUDE.md

@@ -6,7 +6,7 @@ lives in `README.md` — this file is the concise, gotcha-focused guide.
 ## What this is
 
 A Claude skill that runs a repeatable, **read-only** hygiene audit across the
-homelab / pbs / docker / root project domains. Phase 7 of the
+homelab / pbs / docker project domains. Phase 7 of the
 repo-hygiene-remediation project: the durable version of the one-time audit.
 
 ## Architecture
@@ -26,9 +26,13 @@ repo-hygiene-remediation project: the durable version of the one-time audit.
 - **Read-only is the contract.** The script must never write to the trees it
   scans — only to `--output`. All git invocations use read subcommands. Don't
   add a check that mutates a repo.
-- **Each repo = an immediate child of a domain root.** The `root` domain is the
+- **Each repo = an immediate child of a domain root.** Domains can also name
-  exception: it names explicit repo paths (wiki-vault, wiki-context), not a
+  explicit repo paths via `repos` (vs `scan`) if a one-off is ever needed.
-  scan root.
+- **The Obsidian vault is intentionally NOT a default domain.** wiki-vault /
+  wiki-context are MCP-owned, managed surfaces — a second scanner risks
+  interfering with the vault MCP's context. Don't "helpfully" re-add a `root`
+  domain to `DEFAULT_DOMAINS`; the `--scan`/`--repo` escape hatch covers manual
+  one-offs.
 - **`docker` domain repos are compose stacks** — README expected, CLAUDE.md
   intentionally NOT expected (`COMPOSE_STACK_DOMAINS`). Don't "fix" the missing
   CLAUDE.md flag suppression there.

README.md

@@ -1,7 +1,7 @@
 # repo-hygiene-audit
 
 A Claude Code / Cowork skill that runs a **repeatable, read-only hygiene audit**
-across the `homelab`, `pbs`, `docker`, and `root` project domains and reports
+across the `homelab`, `pbs`, and `docker` project domains and reports
 the findings, grouped by remediation phase.
 
 It is the durable, repeatable version of the one-time 2026-05-19/20

repo-hygiene-audit/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: repo-hygiene-audit
 description: >
-  Repeatable hygiene audit across the homelab / pbs / docker / root project
+  Repeatable hygiene audit across the homelab / pbs / docker project
   domains. Runs scripted, read-only checks for git auditability and .git
   ownership drift, .env file permissions, inline secrets in compose files,
   non-git directories, uv-init leftover stubs, docker-compose.yml -> compose.yml
@@ -39,18 +39,24 @@ wrong doc is worse than a missing one). That semantic scoring is the human part.
 This skill automates the **mechanical enumeration** underneath it: sweep every
 repo in every domain and flag the objective signals that drift produces.
 
-Domains (the four the audit covered):
+Default domains scanned:
 
 | Domain | Roots scanned |
 |--------|---------------|
 | `homelab` | `/opt/projects/homelab/*` |
 | `pbs` | `/opt/projects/pbs/*` |
 | `docker` | `/opt/projects/docker/*`, `~/projects/docker/*` (compose stacks) |
-| `root` | `/opt/projects/wiki-vault`, `/opt/projects/wiki-context` |
 
 `docker` repos are treated as compose stacks: README expected, **no per-stack
 CLAUDE.md** (per the locked doc-role convention).
 
+**The Obsidian vault (`wiki-vault`, `wiki-context`) is intentionally out of
+scope.** It's an MCP-owned, managed surface — the vault MCP maintains its own
+context — so a second scanner poking at it risks interference. The original
+audit covered it as a "root" domain; this recurring skill deliberately does
+not. The `--scan` / `--repo` escape hatch can still point at it manually if
+ever truly needed; don't re-add it to the defaults.
+
 ## Workflow
 
 ### Step 1 — Run the scripted sweep

repo-hygiene-audit/references/check-catalog.md

@@ -12,6 +12,14 @@ CLAUDE.md = concise agent guide (not a README clone); docker compose stacks get
 README only; prefer `main` over `master`; GitHub-destined repos are pushed
 manually.
 
+## Scope
+
+Default domains: `homelab`, `pbs`, `docker`. The Obsidian vault (`wiki-vault`,
+`wiki-context`) is **intentionally excluded** — it's an MCP-owned, managed
+surface, so a second scanner risks interfering with how the vault MCP maintains
+its context. Use `--scan` / `--repo` to point at it manually if ever needed;
+don't re-add it to the defaults.
+
 ## AUDITABILITY (maps to Phase 3 — unblock un-auditable repos)
 
 | check id | Looks for | Severity | Why |

repo-hygiene-audit/scripts/audit.py

@@ -43,11 +43,15 @@ from pathlib import Path
 
 # A domain either scans the immediate children of one or more roots ("scan"),
 # or names explicit repo paths ("repos"), or both. Override with --config.
+#
+# The Obsidian vault (wiki-vault, wiki-context) is deliberately NOT a default
+# domain: it's an MCP-owned, managed surface (the vault MCP maintains its
+# context), so a second scanner poking at it risks interference. Point --scan
+# or --repo at it manually if you ever truly need to.
 DEFAULT_DOMAINS: dict[str, dict[str, list[str]]] = {
     "homelab": {"scan": ["/opt/projects/homelab"]},
     "pbs": {"scan": ["/opt/projects/pbs"]},
     "docker": {"scan": ["/opt/projects/docker", "/home/herbyadmin/projects/docker"]},
-    "root": {"repos": ["/opt/projects/wiki-vault", "/opt/projects/wiki-context"]},
 }
 
 # Conventions from the repo-hygiene-remediation plan (Locked Decisions).