Lab: Docs: multi-tool repo support

The swamp CLI now supports enrolling multiple AI agent tools per repo (e.g., swamp repo init --tool claude --tool kiro). The marker schema changed from a single tool field to a tools: AiTool[] array. Several manual pages still describe the old single-tool model.

Parent: swamp-club issue 172

Pages to update

Reference

content/manual/reference/repository-configuration.md: Document the new tools: AiTool[] field on .swamp.yaml. Note the lazy migration: legacy tool: <name> is auto-promoted to tools: [<name>] on the next marker write, so existing repos need no manual migration.

Explanation

content/manual/explanation/ai-agent-integration.md: Drop the one-tool-per-repo assumption. Describe enrolling multiple tools, the "primary tool" concept (marker.tools[0], used by audit recording / extension skills resolution), and the "replace semantics" of swamp repo upgrade --tool ....

How-to (one note per page)

content/manual/how-to/use-swamp-with-claude-code.md
content/manual/how-to/use-swamp-with-cursor.md
content/manual/how-to/use-swamp-with-kiro.md
content/manual/how-to/use-swamp-with-opencode.md
content/manual/how-to/use-swamp-with-codex.md
content/manual/how-to/use-swamp-with-copilot.md

Add a short "Use alongside another agent" paragraph to each: you can enroll multiple tools by repeating --tool on swamp repo init (e.g., swamp repo init --tool claude --tool kiro), and each tool's scaffolding (skills directory, instructions file, settings/hooks) is written independently.

Suggested key points

Primary tool: the first entry in marker.tools. Used by commands that still operate on one tool (audit recording, extension skills resolution, doctor checks). Order is preserved on upgrade; appending a tool keeps the existing primary stable.
Replace semantics on upgrade: swamp repo upgrade --tool <X> replaces the full enrolled list. To add kiro to a [claude] repo, run swamp repo upgrade --tool claude --tool kiro (list the full intended set). Plain swamp repo upgrade preserves the existing list and bumps the version.
No destructive deletes: dropping a tool from the list does not delete its on-disk scaffolding (.claude/, .kiro/, etc.). The renderer surfaces a note so the user can remove them by hand if desired.
--tool none: clears the enrolled list; cannot be combined with other --tool values.

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

Provide a CLI-shape primer for AI agents to reduce rediscovery overhead

quality rubric: don't penalize extensions whose upstream constrains them to a single platform

Extension update rejects multiple .ts files extending the same target type within one local extension (regression)

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

Collective-scoped auth keys + OIDC federation for CI publishing

forEach self.* in modelIdOrName not resolved in runtime execution path

Award leaderboard points for referrals and collective invites

Add agent harness detection and AiTool to telemetry

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

Implement W5: Per-fingerprint import URLs + subprocess test harness (extension catalog rearchitecture)

swamp config set crashes with YAML serialization error

datastore compact: VACUUM fails in compiled binary (SQLITE_LIMIT_ATTACHED=0)

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'

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