Lab: Manifest version bumps silently ignored for existing local extension aggregates

Summary

Filed as follow-up from swamp-club#273 adversarial review (second pass, medium finding #2).

When ReconcileFromDiskService.reconcileLocalAndSourceMounted finds an existing aggregate by name match, it uses the existing aggregate as-is (ext = existing), preserving the OLD version. The manifest version (localVersion) is only used when creating a new aggregate from scratch (the fallback path when no existing aggregate is found).

If a user bumps the manifest version (e.g. 2026.04.21.1 to 2026.04.22.1), the reconciler keeps the stale version indefinitely. Subsequent loadAll() reads back the persisted old version, and no future reconcile fixes it because the name match always finds the old aggregate.

Impact

swamp doctor extensions and other version-displaying surfaces show the old version permanently. The only recovery is a full catalog wipe (invalidateAll + restart).

Steps to reproduce

Create a repo with extensions/manifest.yaml declaring name: @scope/foo, version: 2026.04.21.1
Run any swamp command (triggers reconcile, writes version 2026.04.21.1 to catalog)
Bump manifest version to 2026.04.22.1
Run any swamp command again
Observe: catalog still shows version 2026.04.21.1

Suggested fix

When existing is found but existing.version !== localVersion, treat it as an identity migration: tombstone the old-version aggregate and create a new one with localVersion, same as the name-migration path.

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

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

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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

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Resolve self.* expressions in modelIdOrName during forEach expansion

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Discord bot sends duplicate signup notifications

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

Add 'swamp auth status' as alias for 'swamp auth whoami'

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

Lab search by numeric issue ID returns no results

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

docs: document swamp datastore compact and GC WAL behaviour

UAT: swamp datastore compact reclaims WAL and catalog space

Plan v4 step 9 literal test untestable under current catalog PK semantics

Cross-process concurrency stress for W2 lifecycle services

UAT additions for W2 lifecycle services (Install/Remove/Upgrade)

Implement W3: ReconcileFromDisk + freshness-as-aggregate-query (extension catalog rearchitecture)

doctor extensions repair: clean catalog-only orphans

Extensions should be able to ship Claude Code skills

Pre-existing TOCTOU windows in YAML repo walkers (findAll directory level + findById)

`swamp datastore setup` migration is not resumable / leaves the repo in a partial state on failure

Built-in models must honor AbortSignal so --timeout works in practice

Reader-lock or lock-free read path for data list/get/search/query

data search: surface jobTag alongside workflowTag and stepTag (follow-up to #237)

global-arg silently strips unknown keys; should reject via strict Zod schema

redmine extension: adopt state machine patterns from @magistr for agent-driven workflows

performance degrades significantly with large SQLite catalog

summarise: timeout/hang on repos with many workflow runs

extension quality/fmt fail on pulled extensions (path mismatch)

vault: add read-secret CLI command for agent-driven secret retrieval

data query: stepName and jobName fields always empty in CEL results

Extension ecosystem: shared utility library, version sync tooling, and HTTP resilience patterns

Agentic CLI improvements: --json stdout isolation, array inputs, and --repo-dir consistency

data delete fails with "Directory not empty (os error 39)" when concurrent writes are active

Extract LockfileRepository (W2 prequel for swamp-club#231)

Extend DatastoreSyncService.markDirty() with optional relPath argument

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