Lab: doctor extensions repair: clean catalog-only orphans

Problem

`swamp extension rm ` short-circuits with `Extension is not installed` when no lockfile entry exists for that name (rm.ts:181 in the W2 lifecycle services branch). This is correct for the user-facing rm contract — "already gone" is a clean no-op.

But it leaves a gap: if the catalog has rows for an extension that no longer has a lockfile entry (e.g., from a half-applied install whose lockfile write rolled back, a hand-edited `upstream_extensions.json`, or a `W1b → W2` migration where stale rows were written before the lifecycle services landed), there's no CLI path to clean those rows. They'd accumulate as ghost catalog entries that `swamp doctor extensions` reports but cannot repair.

Proposed solution

Add a `swamp doctor extensions repair` (or extend the existing `doctor extensions` command with a `--repair` flag) that:

Identifies rows in the catalog whose `extension_name` has no corresponding lockfile entry AND whose `source_path` doesn't exist on disk.
Tombstones + DELETEs them via `ExtensionRepository.saveAll([tombstoneAll(...)])` so the same SQLite txn semantics that protect the lifecycle services apply here too.
Reports the count cleaned (and surfaces a clear message in `--json` mode).

Why W6, not W2/3/4/5

The lifecycle services (W2) explicitly target the user-facing install/rm/upgrade flows. The catalog-only orphan cleanup is a doctor-side repair surface — distinct from the lifecycle layer's contract. The architecture-agent review of W2 explicitly tagged this as W6 territory.

Context

Spotted in code review of feat/w2-extension-lifecycle-services (the W2 PR for swamp-club#231).
W2 closes swamp-club#201 (rm now prunes catalog rows during normal flow). This issue is the safety-net for state that bypasses the normal flow.
Implementation should reuse `ExtensionRepository.saveAll` + `tombstoneAll` so I-Repo-1 evaluation and SQLite ROLLBACK semantics carry over.

Acceptance criteria

`swamp doctor extensions --repair` (or equivalent) can prune catalog rows whose lockfile entry is gone and whose source files don't exist.
Idempotent: running twice on a clean catalog is a no-op.
Tested with a fixture catalog seeded with orphan rows; rows are gone after repair.
`--json` output reports the action taken.

extension unyank needs -y/--yes flag for non-interactive use

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Workflow-scope report artifacts unreachable via `swamp data get --workflow`

Add --stdin support to method run and workflow run for Unix pipe composition

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Fix invalidate-then-reconcile sequencing in doctor extensions; failure-mode RowStates unreachable in sourceDetails

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Extension failure recording has dual write paths (legacy buildIndex vs W3 reconcile)

Expose workflow run ID in CEL so resource keys can be run-scoped

Add `swamp doctor workflows` subcommand to surface workflow YAML parse errors during preflight

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Close #327 — fixed in 20260511.160514.0-sha.9d03b09a

Nested workflow task fails with 'Bad resource ID' when workflowIdOrName uses @collective/ prefix

Detect stale skill directories and prompt for repo upgrade

Improve skill trigger routing for cross-model edge cases

Add type search for driver, datastore, and report kinds

Surface ReconcileFromDisk dryRun transitions in swamp doctor extensions

Docs: update doctor extensions reference for W6 aggregate-state rendering + repair flags

swamp issue: check if reporter is on an outdated binary before opening

Implement W6: swamp doctor extensions aggregate-state rendering + repair surface (extension catalog rearchitecture)

extension pull fails referencing removed source after extension source rm

Investigate whether allExtensionMethodsAttached guard can be removed via registration-path consolidation

Trace context is lost: CLI ignores inbound TRACEPARENT and raw driver doesn't propagate active context into in-process methods

swamp model create --global-arg KEY=VALUE doesn't coerce strings to z.number() schemas

swamp model create --global-arg KEY=VALUE doesn't coerce strings to z.number() schemas

swamp issue get should rate-limit unauthenticated users instead of blocking

swamp issue get should not require authentication

telemetry: emit child entries for follow-up action method invocations

Publish release-candidate / unstable extension versions

extension source rm leaves stale @local/. rows in catalog, blocking later pulls of registry types

extension push drops binaries: field from re-emitted archive manifest.yaml

macOS launchd autoupdate (club.swamp.autoupdate) silently fails — binary stays stale

Clicking @hivemq/honeycomb extension card on /extensions shows 'Something went wrong'

Docs: Update model-definitions.md and workflows.md for direct type execution

Docs: document binaries manifest field in extension-manifest.md

Add an official @swamp/ssh extension for general-purpose SSH (brownfield-friendly)

Accept and display binaries field from extension push metadata

Direct type execution: collapse model create + method run into one command

Per-method telemetry events for workflow runs

Workflow run liveness: orphaned 'running' records when originating CLI process dies mid-run

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swamp extension push deadlocks when invoked from inside a swamp workflow step

Collective-scoped auth keys + OIDC federation for CI publishing

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swamp config set crashes with YAML serialization error

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Repo-level version gating: minSwampVersion high-water mark for team consistency

Docs: document self.* expressions in modelIdOrName during forEach

Docs: How-to guide for background autoupdating

Manifest version bumps silently ignored for existing local extension aggregates

materialiseExtensions misclassifies pulled rows when manifest name collides with a pulled extension

Local extension edits don't reliably trigger rebundle

Missing unique indexes on user.email and user.username allow duplicate users

Resolve self.* expressions in modelIdOrName during forEach expansion

discord-bot double-sends sign_up notifications

Discord bot sends duplicate signup notifications

Add 'swamp workflow list' as alias for 'swamp workflow search'

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Extension bundle cache does not invalidate on source edits

extension pull fails on @local/[email protected] phantom-claim collision when local repo has its own extension

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W3 sourceToRow writes empty source_mtime — should carry filesystem mtime through Source entity

Warm-start rebundleAndUpdateCatalog should respect terminal RowStates set by reconcile

Implement W4: KindAdapter + unified loader (extension catalog rearchitecture)

Docs: add vault read-secret command to reference manual

Extension layer garbage collection: prune catalog rows + evict orphaned bundles

Docs: document workflow concurrency limits in reference manual

Locally-sourced extension: source_mtime updates without regenerating stale bundle

Extension push: allow shipping executable host helpers (bin/mudroom blocker)

Vault expressions silently deliver __SWAMP_VSEC__ sentinels under the docker driver

First-class shell-shim support for extensions, with registry-level visibility

Local extension model bundles don't rebuild when source changes (no rebuild CLI; manual cache delete breaks the runner)

Configurable concurrency limits for workflow fan-out (forEach, parallel jobs/steps)

feat(security): redact sensitive method arg values from audit log

Workflow-level runtime expressions (env., vault.) not resolved in driverConfig — docker driver receives literal ${{ ... }} strings