Migrate all remaining pass-through call sites (social, skills, budget,
entityCrud, documents, knowledge, automation, wakeup, backup, threads,
settings, snapshot, connectors, workspaces, activity) to their owning
domain modules. `AppDatabase` now carries only three methods:
- createHireRequest (multi-module composite: agents + approvalsMod)
- rollbackConfigRevision (multi-module composite: documents + entityCrud)
- queryAll (raw-SQL escape hatch, @internal)
The vault/env-binding infrastructure previously passed argument-by-
argument into `entityCrud.saveSecret`/`resolveSecretEnv` now binds at
module construction, letting callers invoke `db.entityCrud.saveSecret({...})`
without carrying vault plumbing.
Structural types that narrowed AppDatabase to a bag of flat methods
(`ConnectorModelPolicyDeps` callers, `CapabilityMatchDb`, test mocks in
budget-enforcement / budget-incidents / task-quality-gates /
failure-escalation / task-quality-gates-sweep) are reshaped to the new
namespace. `connectorPolicyDepsFromDb` replaces the old pattern of
handing the whole AppDatabase to `validateConnectorModelSelection`.
A new ESLint rule in eslint.config.mjs blocks new top-level methods on
AppDatabase so the pass-through layer cannot silently grow back.
`AppDatabase.ts` dropped from 193 lines to 58; `AppDatabaseBase` lost
the 270-line trailing pass-through block.
Rewrite ~376 call sites for messages, runs, approvalsMod, and company
domains and delete the corresponding pass-through methods on
AppDatabase / AppDatabaseBase. Structural type references
(ReturnType<HandlerDeps["db"]["getRun"]>) and SweepStaleReviewsDeps-style
mocks are updated to route through the owning sub-module.
Rewrite ~525 call sites from `db.<method>()` to `db.<module>.<method>()`
for tasks and agents domains (including `getAgent`/`findAgent`/`getTask`
which live on the `entityCrud` field). Delete the corresponding
pass-through methods on AppDatabaseBase. Structural types that narrowed
`db` to a bag of flat methods (CapabilityMatchDb, EscalationDeps,
SweepStaleReviewsDeps) are reshaped to match the new namespace. Internal
callback references inside database.ts/database-base.ts now invoke the
owning module directly (e.g. `this.agents.saveAgent`) rather than the
deleted pass-through.
The codemod lives at scripts/codemod/remove-appdatabase-passthrough.mjs
and filters by owning module + optional explicit method list. It is
idempotent and does not re-rewrite already-namespaced calls.
Before running any pending migration, take a synchronous snapshot of the
profile to backups/pre-migration-v<target>-<ts>/ and write a
backup-manifest.json recording reason, schema version, app version, and
git SHA. A failed migration now has a well-labelled recovery point
instead of a half-upgraded profile.
- createAutomaticBackup(reason): synchronous snapshot via VACUUM INTO +
recursive cpSync of logs/artifacts, plus JSON manifest. No fallback —
failure throws so the caller refuses to touch the schema.
- runMigrations accepts createAutomaticBackup and invokes it when any
migration is pending. No optional chaining; callers must supply it.
- AppDatabase constructor takes appVersion so main-runtime stamps the
manifest with app.getVersion().
A DM addressed to one agent that @-mentions another was silently
dropping the second agent out of the conversation:
* `dispatchAgentMessage` added the mentioned agent to the wake set,
so CEO's heartbeat fired — but
* `listAgentInboxUnread` only surfaced messages where the current
agent was `to_agent_id` or sat in a matching channel/project/
department. Mentions were invisible, so CEO's next turn saw nothing
new and returned silently. From the operator's chair this looked
exactly like "CEO ignored me; 张工程师 answered instead".
* `findMentionedAgentIds` had a latent bug on top: its unique-alias
filter used `ids.length === 1`, but a single agent whose name
matched its role registered itself twice, tripped the filter, and
every `@CEO` in a scaffold with role === name was a no-op. Once
inbox visibility was fixed the bug became load-bearing.
Root-cause fixes:
* New migration v48 adds `agent_message_mentions(message_id, agent_id,
company_id, created_at)` so mention fan-out is a first-class join.
* `sendAgentMessage` now takes the resolved mention set and writes
the row + mentions in a single transaction — a crash between the
two writes can no longer leave a message visible to the recipient
but invisible to the mentioned agent.
* `dispatchAgentMessage` computes the mention set exactly once via
`resolveMentionedAgentIds` and hands the same list to both the DB
write and `resolveMessageWakeTargets`, so persistence and wake
stay in lockstep.
* `listAgentInboxUnread` and `listAgentMessages` gain an `id IN
(select message_id from agent_message_mentions …)` clause so the
mentioned agent's inbox actually contains the message that woke it.
* `findMentionedAgentIds` now stores per-alias agent IDs in a `Set`
and filters on `ids.size === 1`, dropping the self-duplication
bug while preserving the "refuse ambiguous aliases" semantics.
* Company teardown drops `agent_message_mentions` alongside the
existing `agent_message_reads` cleanup so deletes stay clean.
Tests pin the new behaviour: a DM with a `@CEO` mention reaches
CEO's inbox and both agents get woken, while a DM whose recipient
is `__board__` never attempts to wake the human sentinel.
The standup briefing knew about tasks, approvals, comments, and
report statuses but had no view of what the agent itself recently
produced. Without that view the model could narrate "I wrote the
PRD" in its assistant text without ever calling POST /documents,
and we'd have no automated way to catch the drift — the user just
saw an empty document page and a confused agent.
Standup now returns:
- `recentDocuments` — documents the agent authored (capped at 20),
with id / type / title / status / version / updatedAt;
- `recentWorkProducts` — filesystem artifacts produced on tasks
the agent owns (capped at 20), with title / externalId / url /
status / task title / updatedAt.
The CEO operating prompt was already updated in the previous
commit to reference these fields and re-do a missing POST when a
task claims completion but the persistence is absent. The trust-
but-verify loop is now closed: the agent can compare its own
narration against its own actual outputs every wake.
The inbox projection used to call `markAgentInboxDelivered` after
appending each message to the agent's session shadow. That helper
sets `agent_messages.read_at = now()` for direct messages and
inserts into `agent_message_reads` for channel messages — the SAME
flags `listAgentInboxUnread` and the public `?unreadOnly=true` API
use to define "unread". So the moment we put a message into the
recipient's transcript, the recipient's own API call returned
nothing pending. The IC prompt told the agent to "respond to ALL
unread messages"; the API said zero unread; the agent posted a
status comment instead of replying. Every silent-employee report
traces back here.
Replay safety lives entirely on `agent_message_projections`
(installed in v46) — that ledger is keyed by `(message_id,
session_id)` and `claimProjection` already short-circuits a re-run
without touching `read_at` at all. The two concepts are now
properly separated:
- "delivered" (we put it in front of the agent) — tracked by
the projection ledger, owned by the runtime bridge;
- "read" (the agent acknowledged it) — tracked by `read_at` and
`agent_message_reads`, only flipped by the explicit POST
/messages/{id}/read endpoint the agent calls itself.
`markAgentInboxDelivered` is removed because there is no remaining
caller and its semantics were the bug — keeping it around would
just invite the same mistake again.
`retireDeletedArtifacts` used to iterate `deleted.slice(0,
MAX_BASH_PROJECTED_FILES)` and emit no signal for paths past the cap
— a large `rm -r` would leave the 51st row onward visible in the
DocumentCenter with no indication anything was missed. The cap was
inherited from the registration path, where it bounds file-stat
round-trips; retirement is a pure metadata update with no filesystem
cost, so the cap was value-free safety theatre.
New DB surface `archiveWorkProductsByExternalPaths` runs a single
`UPDATE … SET status = 'archived' … WHERE external_id IN (…)
AND status <> 'archived' RETURNING id, external_id` per 500-path
chunk — one round-trip per chunk instead of one per path. The
projector feeds the full `deleted` list in, maps the returned ids
back to `retired` outcomes, and no deletion is left behind regardless
of the run's cleanup fan-out size.
The natural key used to be (companyId, provider, externalId), so two
workspaces with the same workspace-relative path collided onto one
row. Provenance was also frozen at the first write: `created_by_run_id`
never refreshed, so a run that edited a pre-existing file never
qualified as a deliverable and the DocumentCenter "open" link could
still jump into the first workspace after a repo move.
Migration v45 adds `workspace_id` + `last_touched_by_run_id`, backfills
`workspace_id` via the task/run join, seeds `last_touched_by_run_id =
created_by_run_id`, and installs a partial unique index on
`(company_id, workspace_id, provider, external_id)` scoped to rows
that have a workspace. The artifact projector now records
`workspace_id` on insert and refreshes `last_touched_by_run_id` on
every upsert. The deliverable signal query reads either provenance
column so a run that only edited a pre-existing file still counts.
`resolveWorkProductTarget` prefers the stored `workspace_id` and falls
back to the task/run join for legacy NULL rows.
Filesystem work products store `external_id` as a workspace-relative
path so artifacts survive a workspace-root move, but the renderer was
handing that relative fragment straight to `shell.openPath`, which
needs an absolute managed path. Clicks flickered into a failed open.
Add a dedicated `openWorkProduct({ companyId, id })` IPC backed by
`resolveWorkProductTarget` on the DB layer. The resolver joins the
work-product row back to its originating task → workspace (or run →
workspace for taskless runs), composes an absolute path, and rejects
any relative fragment that would escape the workspace root. The
renderer now passes the work product's id — path resolution stays on
the main process where the managed-path policy already lives.
The deliverable check used to compare a run against knowledge entries,
documents, and substantial task comments only, so a research or content
task that produced its output as a markdown file on disk (via
write/edit/bash) stayed pinned in_progress even though the deliverable
was already sitting in `work_products`.
Split the DB query into `collectRunDeliverableSignals`, which returns
the four surfaces (knowledge / document / work product / substantial
comment) explicitly, and push the per-task-type acceptance logic into
`automation-run-completion`. Each task type declares which signal set
counts as a valid deliverable: content tasks now require a document or
an on-disk artifact and will not advance on a knowledge entry alone;
research and general accept any of the four; code and management
preserve their broader surface. Tests updated to cover the new signal
and the content/knowledge rejection case.
`hasUnresolvedWaitStatesForAgent` only joined through tasks, so
approval-only threads and ad-hoc threads where the agent is the
requesting party or an explicit participant were invisible. Result:
the heartbeat scheduler silently resumed agents that the board had
asked to wait on, Co-Founder approval chains deadlocked on the
agent side, and any new gate that relies on the query inherits the
same hole.
Root-fix the query at the SQL layer. `hasUnresolvedWaitStateForAgent`
now returns true when any of the three ownership predicates hold:
- task thread whose task.assignee_agent_id = agent
- approval thread whose approval.requested_by_agent_id = agent
- any thread on which the agent is a recorded participant
Each branch is an EXISTS subquery so the query short-circuits on
first match. The thread-integration helper delegates here so the
heartbeat scheduler and the `beforeToolCall` gate share one source
of truth rather than reimplementing half-policies in parallel.
Sessions are already agent-scoped post-v34, but the code kept routing
rotation / accumulation / handoff through the task indirection. Heartbeat
runs (no task) silently skipped all three, letting taskless transcripts
grow past the model's context window — the 7M-token explosion.
- DB adds getSessionById(sessionId) — direct lookup bypassing
tasks.active_session_id
- session-management-service: generateHandoff(session) is now agent-scoped,
walking recent runs across tasks + heartbeats; getHandoffForAgent(agentId)
is the canonical lookup, getHandoffContext(taskId) is a thin shim for
callers that still hold a task id
- turn-context.ts::resolveSession drops the `if (!task)` early return:
rotation evaluation runs on the agent session unconditionally
- run-finished-helpers.ts::accumulateAndRotateSession drops the `!task`
gate: tokens accumulate and rotation fires for every run, keyed on the
agent session, not the task
- Rotation evaluator contract: evaluatePreRunSessionRotation(agentId,
connectorId) → { rotated, handoff, sessionId }; old (taskId, connectorId)
signature removed
IPC contract tightening: ipc-support::emitEvent becomes a best-effort
sink. "Render frame was disposed" during renderer reload is a lifecycle
signal, not a logic error; silently drop it instead of letting it abort
downstream event emissions.
Artifact projection: pi's write/edit tool results now upsert a
`work_products` row via a new agent-runtime/artifact-projector.ts. No
more agents writing 54 files into the workspace that the UI never sees.
Migration v40 relaxes work_products.task_id to nullable so heartbeat
artifacts can register too.
File size: split agent-event-projection.ts out of runtime-bridge.ts to
keep the bridge under the 400-line cap after adding the projector hook.
Tests: 604 unit + integration green; generateHandoff callsites updated
for the single-argument signature; artifact-projector has pure-function
coverage via the projector module's own shape.
`company_skills.markdown` stored the full SKILL.md body. The on-disk
file under `profile/skills/{companyId}/{slug}/SKILL.md` is what pi-
coding-agent actually reads via `loadSkills` at runtime. The DB column
was a duplicate — import wrote to both, renderer read from DB. Any
discrepancy between disk and DB was invisible until the agent behaved
differently from what the user saw in SkillDetail.
Disk becomes the single source of truth. DB keeps name / description /
metadata / source info / file inventory — the cheap lookup row. UI reads
SKILL.md content live via a new IPC channel.
## Migration v37 (rebuild company_skills without markdown)
Table-rebuild pattern matching v35/v36: `fn:` form, PRAGMA walk for
drift columns, row-count assertion before DROP, `defer_foreign_keys`
for the `agent_skill_assignments(skill_id)` reference. Indexes
recreated. Idempotent via `schema_migrations` ledger.
Existing DB rows' markdown content is discarded — but the on-disk
SKILL.md files are the authoritative copy, so no user-visible data
loss. Any agent using those skills keeps working; the UI just starts
reading from disk instead of the DB cache.
## Code changes
- `src/main/database/skills.ts`: drop `markdown` from read mapping,
upsert input type, INSERT column/bind list, ON CONFLICT DO UPDATE.
- `src/shared/types/records-core.ts`: `SkillRecord.markdown` removed.
- `src/main/skills/import.ts` + `import-github.ts`: drop `markdown:`
from 4 `saveCompanySkill` call sites. Disk-write via
`materializeSkillFiles` unchanged (it's what the file agent reads).
- `src/main/skills/index.ts`: expose `skillFilesDir` for the new IPC
handler to resolve `${profile}/skills/${companyId}/${slug}/SKILL.md`.
- `src/shared/contracts/channels.ts` + `schemas-execution.ts` +
`desktop-api/skills.ts`: new `getSkillMarkdown` channel
`{ companyId, slug } → DesktopResult<string>`.
- `src/preload/index.ts`: expose `getSkillMarkdown(companyId, slug)`.
- `src/main/ipc-skill-handlers.ts`: handler validates schema, ensures
company, resolves path, `readFile`, returns content. Fails closed
with `SKILL_NOT_FOUND` on ENOENT, `SKILL_READ_FAILED` on other
read errors.
- `src/renderer/components/skills/SkillDetail.tsx`: `useEffect` fetches
markdown via IPC when the skill detail loads; shows "Loading…" until
resolved, surfaces read errors. Preserves `stripFrontmatter`.
- Tests: drop `markdown:` from 2 fixture sites
(`skill-types.test.ts`, `skill-aware-assignment.spec.ts`).
## Verification
- typecheck / lint / 578 tests green
- `grep 'skill\.markdown' src/` → 0 DB-record reads
- `grep '\.markdown\b' src/main/database/skills.ts` → 0
- Remaining `.markdown` references are all `ghSkill.markdown` (GitHub
fetcher's intermediate struct feeding `materializeSkillFiles` to
disk) and parameter names in `stripFrontmatter(markdown: string)` /
fs-writer helpers — none read from a DB row.
Inter-agent messages previously entered the recipient's context as a
separate prompt block (recentMessages), rebuilt every turn. This double-
charged tokens and kept messages outside pi's native AgentMessage stream.
Now at prepareRun: pull the recipient's unread inbox, project each
AgentMessageRecord into a pi user-role AgentMessage, persist to
SqliteSessionStore, and mark delivered. The recipient reads messages
as natural conversation turns in the transcript.
- db: listAgentInboxUnread + markAgentInboxDelivered (transactional)
- agent-runtime/inbox-projection.ts: AgentMessageRecord -> pi AgentMessage
- runtime-bridge.prepareRun: inject + deliver before loadMessages
- prompt-builder: delete recentMessages context block + buildMessagesSection
- message-normalize: drop unused normalizeMessagesForPrompt
- delete prompt-builder/attachment-resolver.ts (orphan after section removal)
Send path (api-server/routes-messages, ipc, UI) unchanged — inbox table
remains the UI source. Transactional delivery marking prevents duplicate
injection across runs. Failed append -> no mark -> retry on next run.
Follow-up to P2-37: delegation wrapper for the knowledge module method
introduced in the previous commit was missed, leaving TS2339 at
automation-run-completion.
P2-23: 'lead' in system-prompt.ts matched 'cleaner' / 'leaderboard' via
substring .includes(). Hoist LEADERSHIP_ROLE_KEYWORDS into a shared
agent-role-helpers.ts module; tokenize input on non-alphanum to require
whole-word match.
P3-54: Same keyword list was duplicated in automation-skills with drift
(missing 'ceo', different members). Both sites now call through the
shared helper.
Replace six inline queryAll calls in routes-work-graph.ts with domain
methods. db.entityCrud gains listGoals, getGoalForUpdate, listProjects,
getProjectForUpdate. db.knowledge gains listSprints. db.company gains
getDashboardSnapshot, which returns the raw agent/task/activity rows
the dashboard handler aggregates. The route-level row shapes are
preserved in the new GoalListRow / ProjectListRow / SprintListRow
types so HTTP responses remain identical.
Replace inline queryAll calls in routes-meetings.ts with two new
domain methods on db.knowledge: listMeetings (powers
GET /api/companies/:companyId/meetings) and getMeeting (used by the
PATCH meeting handler). The MeetingListRow shape mirrors the historical
inline projection so HTTP responses stay byte-stable. Also adds
listKnowledgeEntries here for use by routes-misc.
Replace raw queryAll calls in routes-files.ts with two new domain
methods on db.documents: listDocuments (powers
GET /api/companies/:companyId/documents) and getDocumentForUpdate (used
by the PATCH document handler). The DocumentListRow / DocumentLookupRow
shapes preserve the historical inline-SQL projections so HTTP responses
remain identical.
Replace inline queryAll calls in routes-tasks.ts with two new domain
methods: tasks.listTasksByStatuses (used by GET /api/companies/:id/issues)
and documents.listImportantDocsForReview (used by the deliverable-review
gate). Routes now hold no SQL or column-mapping logic; the
TaskListByStatusesRow shape preserves the existing HTTP response fields
including requiresUserReview as a boolean.
- Add findReusableHeartbeatTask() to find most recent done/in_review heartbeat task per agent
- Add cleanupDuplicateHeartbeatTasks() to cancel old duplicates using ROW_NUMBER window function
- Add 12 unit tests covering coalescing behavior, cross-agent isolation, status filtering
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add scanWorkspaceSkills method to skill service that iterates all
workspace local paths for a company and imports SKILL.md files from
.agents/skills/ subdirectories. Uses path.join for cross-platform
compatibility (Windows/macOS/Linux). The scan runs automatically
when skills are listed via IPC, with graceful error handling per
workspace so one bad path does not block the entire listing.
Also adds listWorkspaceLocalPaths to database for retrieving workspace
paths by company.
- Add getActiveTaskSession, incrementSessionUsage, archiveSession, createNewSession,
getRecentRunsForTask, getRecentActivityForTask methods to AppDatabase
- Add nativeContextManagement optional boolean to ServerAdapterModule interface
- Set nativeContextManagement: true for claude_local and codex_local, false for gemini_local
- Add TaskSessionRecord interface to shared types
- Add unit tests for task_sessions CRUD and adapter exemption flags
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Migration 13 columns were skipped when ensureOptionalColumns added
checkout_run_id first, triggering 'duplicate column' catch that marked
the entire migration as applied without running remaining ALTERs.
- Add randomUUID import for pre-generated runId in CAS checkout flow
- Replace task-level hasActiveRun checks with db.checkoutTask CAS in startAgentHeartbeatRun and queueTaskRun
- Pass pre-generated runId to createRun (database.ts accepts optional id field)
- Log execution.checkout_rejected activity on CAS failure (D-04)
- Return fail("CHECKOUT_RACE_LOST") in queueTaskRun on CAS failure
- Rewrite wakeAgentIfPossible with proper lifecycle tracking via enqueueWakeupRequest
- Add stale lock recovery sweep at startup (resumeQueuedRuns) and each heartbeat tick
- Log execution.lock_recovered activity entries for recovered stale locks
- Fix SQLInputValue type in listWakeupRequests params
- Fix leftover pendingWakes reference in worker-service.ts
- Fix RunStatus 'completed' -> 'succeeded' in atomic-checkout test
- Update autonomous-chain.spec.ts to use new wakeup lifecycle API
- Rewrite checkoutTask to use runId-based CAS with checkout_run_id IS NULL guard
- Add releaseTaskLock and recoverStaleLocks methods
- Add lock release in finishRun and cancelRunForDeletion exit paths
- Add migration 16: pending_wakes to wakeup_requests cutover with DROP TABLE
- Replace all pending_wakes references with wakeup_requests
- Add wakeup lifecycle CRUD: enqueue, claim, complete, defer, promote, list
- Update api-server, orchestration-service, worker-service callers
- Update existing database.test.ts for new checkoutTask signature
- Add ManagedSkillRef type to adapter-utils for cross-package use
- Add createManagedSkillSymlinks() with Windows junction support (D-13)
- Add managedSkills field to worker RunJob and connector config
- Add listRuntimeSkillEntries dependency to orchestration service
- Wire SkillService lazy init in service-graph for runtime skill resolution
- Include prerequisite skill system files from plans 02-01/02-02
- Add deliverable review gate: pause workflow when agents produce important
documents (PRDs, design docs, etc.) for human review before continuing
- Add company-level reviewDeliverables setting with onboarding card selector
- Block agent heartbeats when deliverable review is pending (agent + CEO)
- Trigger review at document creation time in API server for reliability
- Fix autoApproveHires vs reviewDeliverables conflict in approval-policy
- Fix app quit: force-exit on all platforms (macOS Dock, Windows tray, Linux)
- Add multi-platform CI/CD pipeline (macOS arm64/x64, Windows x64/arm64,
Linux x64/arm64 with deb/AppImage/rpm/snap) with code signing support
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Add searchMessages method to AppDatabase with LIKE query, wildcard escaping, channel scoping, ORDER BY created_at DESC with limit
- Add searchMessages IPC channel and searchMessagesSchema to contracts.ts
- Register IPC handler in ipc-agent-coordination-handlers.ts with Zod validation
- Wire searchMessages through preload bridge
- Add 8 unit tests covering body/subject search, wildcard escaping, channel scoping, empty results, limit, and ordering
- Add consecutiveWakeMap with MAX_CONSECUTIVE_WAKES=5 circuit breaker in worker-service
- Circuit breaker resets on successful run completion, escalates to manager when tripped
- Add checkRunProducedDeliverable in automation-service to check for knowledge entries, documents, or substantial comments
- Non-code tasks (research/content) require deliverable artifact before auto-advancing to in_review
- Add public queryAll method to database for cross-service deliverable queries
ZacharyZhang-NY
