Codemod db pass-through calls: messages + runs + approvals + company (C1 part 2/3)

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.

tests/integration/agent-model-switching.spec.ts

@@ -58,7 +58,7 @@ function createHarness(db: AppDatabase) {
     runDispatch.resolveWorkspace,
     runDispatch.getRunEligibilityFailure,
     runDispatch.dispatchRunToWorker,
-    (filter) => db.hasActiveRun(filter),
+    (filter) => db.runs.hasActiveRun(filter),
   );
 
   return { enqueueWorkerRun, taskRunner };
@@ -78,7 +78,7 @@ describe("agent model switching", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Model Switch Co",
       description: "Tests post-hire model switching",
       status: "active",
@@ -126,7 +126,7 @@ describe("agent model switching", () => {
       throw new Error("Expected first run to queue successfully.");
     }
 
-    db.finishRun({
+    db.runs.finishRun({
       runId: firstRun.data,
       status: "succeeded",
       summary: "Done",

tests/integration/api-recursive-org-execution.spec.ts

@@ -32,7 +32,7 @@ async function createHarness() {
     lastError: null,
   });
 
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Recursive Org Co",
     description: "Tests manager-driven recursive hires",
     status: "active",
@@ -81,7 +81,7 @@ async function createHarness() {
     priority: "high",
     status: "in_progress",
   });
-  const run = db.createRun({ companyId, taskId, agentId: ctoId, workspaceId, connectorId: "openai-codex" });
+  const run = db.runs.createRun({ companyId, taskId, agentId: ctoId, workspaceId, connectorId: "openai-codex" });
   const token = createAgentToken(ctoId, companyId, run.id);
   const server = createApiServer(db, () => {}, () => null);
   const port = await server.start();
@@ -130,12 +130,12 @@ describe("recursive org execution", () => {
       expect(pendingHire.status).toBe("pending_approval");
       expect(pendingHire.reportsTo).toBe(harness.ctoId);
 
-      const approval = harness.db.getApprovalRecord(body.approvalId);
+      const approval = harness.db.approvalsMod.getApprovalRecord(body.approvalId);
       expect(approval.type).toBe("hire_agent");
       expect(approval.requestedByAgentId).toBe(harness.ctoId);
       expect(approval.relatedAgentId).toBe(body.agentId);
 
-      harness.db.decideApproval({
+      harness.db.approvalsMod.decideApproval({
         approvalId: body.approvalId,
         state: "approved",
         decisionNote: "Approved by board",
@@ -192,7 +192,7 @@ describe("recursive org execution", () => {
         priority: "high",
         status: "in_progress",
       });
-      const hrRun = harness.db.createRun({
+      const hrRun = harness.db.runs.createRun({
         companyId: harness.companyId,
         taskId: hrTaskId,
         agentId: hrId,

tests/integration/api-run-events.spec.ts

@@ -24,7 +24,7 @@ async function createHarness() {
   const db = new AppDatabase(profileDir);
   db.init();
 
-  const companyId = db.saveCompany({ name: "Orbit Foundry", description: "API test", status: "active" });
+  const companyId = db.company.saveCompany({ name: "Orbit Foundry", description: "API test", status: "active" });
   const workspaceId = db.saveWorkspace({
     companyId,
     name: "Primary",
@@ -55,7 +55,7 @@ async function createHarness() {
     priority: "high",
     status: "todo",
   });
-  const run = db.createRun({ companyId, taskId, agentId, workspaceId, connectorId: "openai-codex" });
+  const run = db.runs.createRun({ companyId, taskId, agentId, workspaceId, connectorId: "openai-codex" });
   const token = createAgentToken(agentId, companyId, run.id);
   const server = createApiServer(db, () => {}, () => null);
   const port = await server.start();
@@ -95,7 +95,7 @@ describe("run event API", () => {
   it("returns persisted run events for the active run token", async () => {
     const harness = await createHarness();
     try {
-      harness.db.appendRunEvent({
+      harness.db.runs.appendRunEvent({
         companyId: harness.companyId,
         runId: harness.runId,
         agentId: harness.agentId,
@@ -141,7 +141,7 @@ describe("run event API", () => {
       expect(reader).toBeDefined();
 
       setTimeout(() => {
-        harness.db.appendRunEvent({
+        harness.db.runs.appendRunEvent({
           companyId: harness.companyId,
           runId: harness.runId,
           agentId: harness.agentId,

tests/integration/autonomous-chain/approval-decisions.spec.ts

@@ -14,7 +14,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
     const ceoId = createAgent({ name: "CEO", role: "CEO" });
     const hireId = createAgent({ name: "CTO", role: "CTO", reportsTo: ceoId, status: "pending_approval" as "idle" });
 
-    const approvalId = shared.db.requestApproval({
+    const approvalId = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "hire_agent",
@@ -23,7 +23,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
       payloadJson: JSON.stringify({ agentId: hireId }),
     });
 
-    shared.db.decideApproval({
+    shared.db.approvalsMod.decideApproval({
       approvalId,
       state: "approved",
       decisionNote: "Approved by board",
@@ -37,7 +37,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
     const ceoId = createAgent({ name: "CEO", role: "CEO" });
     const hireId = createAgent({ name: "CTO", role: "CTO", reportsTo: ceoId, status: "pending_approval" as "idle" });
 
-    const approvalId = shared.db.requestApproval({
+    const approvalId = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "hire_agent",
@@ -46,7 +46,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
       payloadJson: JSON.stringify({ agentId: hireId }),
     });
 
-    shared.db.decideApproval({
+    shared.db.approvalsMod.decideApproval({
       approvalId,
       state: "rejected",
       decisionNote: "Not needed",
@@ -59,7 +59,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
   it("getApprovalRecord includes payloadJson", () => {
     const ceoId = createAgent({ name: "CEO", role: "CEO" });
     const hireId = createAgent({ name: "CTO", role: "CTO", reportsTo: ceoId, status: "pending_approval" as "idle" });
-    const approvalId = shared.db.requestApproval({
+    const approvalId = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "hire_agent",
@@ -68,7 +68,7 @@ describe("Step 4: Hire approval + decideApproval", () => {
       payloadJson: JSON.stringify({ agentId: hireId, config: { connector: "openai-codex" } }),
     });
 
-    const approval = shared.db.getApprovalRecord(approvalId);
+    const approval = shared.db.approvalsMod.getApprovalRecord(approvalId);
     expect(approval.payloadJson).toBeTruthy();
     const payload = JSON.parse(approval.payloadJson!);
     expect(payload.agentId).toBe(hireId);

tests/integration/autonomous-chain/automation-messages.spec.ts

@@ -104,7 +104,7 @@ describe("Agent Messages", () => {
   });
 
   it("sends and retrieves direct messages", () => {
-    const msgId = shared.db.sendAgentMessage({
+    const msgId = shared.db.messages.sendAgentMessage({
       companyId: shared.companyId,
       fromAgentId: agentAId,
       toAgentId: agentBId,
@@ -116,7 +116,7 @@ describe("Agent Messages", () => {
 
     expect(msgId).toBeTruthy();
 
-    const messages = shared.db.listAgentMessages(shared.companyId);
+    const messages = shared.db.messages.listAgentMessages(shared.companyId);
     expect(messages).toHaveLength(1);
     expect(messages[0].subject).toBe("Need design review");
     expect(messages[0].fromAgentId).toBe(agentAId);
@@ -125,7 +125,7 @@ describe("Agent Messages", () => {
   });
 
   it("marks messages as read", () => {
-    const msgId = shared.db.sendAgentMessage({
+    const msgId = shared.db.messages.sendAgentMessage({
       companyId: shared.companyId,
       fromAgentId: agentAId,
       toAgentId: agentBId,
@@ -133,14 +133,14 @@ describe("Agent Messages", () => {
       body: "Hello",
     });
 
-    shared.db.markMessageReadForReader(msgId, shared.companyId);
-    const messages = shared.db.listAgentMessages(shared.companyId);
+    shared.db.messages.markMessageReadForReader(msgId, shared.companyId);
+    const messages = shared.db.messages.listAgentMessages(shared.companyId);
     const updatedMessage = messages.find((message) => message.id === msgId);
     expect(updatedMessage?.readAt).toBeTruthy();
   });
 
   it("tracks read state per agent without marking the sender unread", () => {
-    const msgId = shared.db.sendAgentMessage({
+    const msgId = shared.db.messages.sendAgentMessage({
       companyId: shared.companyId,
       fromAgentId: agentAId,
       toAgentId: agentBId,
@@ -148,22 +148,22 @@ describe("Agent Messages", () => {
       body: "Hello",
     });
 
-    const senderView = shared.db.listAgentMessages(shared.companyId, { agentId: agentAId });
+    const senderView = shared.db.messages.listAgentMessages(shared.companyId, { agentId: agentAId });
     expect(senderView).toHaveLength(1);
     expect(senderView[0].id).toBe(msgId);
     expect(senderView[0].readAt).toBeTruthy();
 
-    const recipientViewBefore = shared.db.listAgentMessages(shared.companyId, { agentId: agentBId, unreadOnly: true });
+    const recipientViewBefore = shared.db.messages.listAgentMessages(shared.companyId, { agentId: agentBId, unreadOnly: true });
     expect(recipientViewBefore).toHaveLength(1);
     expect(recipientViewBefore[0].id).toBe(msgId);
 
-    shared.db.markMessageReadForReader(msgId, shared.companyId, agentBId);
+    shared.db.messages.markMessageReadForReader(msgId, shared.companyId, agentBId);
 
-    const recipientViewAfter = shared.db.listAgentMessages(shared.companyId, { agentId: agentBId, unreadOnly: true });
+    const recipientViewAfter = shared.db.messages.listAgentMessages(shared.companyId, { agentId: agentBId, unreadOnly: true });
     expect(recipientViewAfter).toHaveLength(0);
 
     const thirdAgentId = createAgent({ name: "Agent C" });
-    const thirdView = shared.db.listAgentMessages(shared.companyId, { agentId: thirdAgentId });
+    const thirdView = shared.db.messages.listAgentMessages(shared.companyId, { agentId: thirdAgentId });
     expect(thirdView).toHaveLength(0);
   });
 
@@ -188,7 +188,7 @@ describe("Agent Messages", () => {
       priority: "medium",
     });
 
-    const deptMessageId = shared.db.sendAgentMessage({
+    const deptMessageId = shared.db.messages.sendAgentMessage({
       companyId: shared.companyId,
       fromAgentId: engineeringLeadId,
       channel: "department",
@@ -196,7 +196,7 @@ describe("Agent Messages", () => {
       subject: "Engineering update",
       body: "Only engineering should see this",
     });
-    const projectMessageId = shared.db.sendAgentMessage({
+    const projectMessageId = shared.db.messages.sendAgentMessage({
       companyId: shared.companyId,
       fromAgentId: engineeringLeadId,
       channel: "project",
@@ -205,30 +205,30 @@ describe("Agent Messages", () => {
       body: "Only project members should see this",
     });
 
-    const engineeringView = shared.db.listAgentMessages(shared.companyId, { agentId: engineeringLeadId });
+    const engineeringView = shared.db.messages.listAgentMessages(shared.companyId, { agentId: engineeringLeadId });
     expect(engineeringView.some((message) => message.id === deptMessageId)).toBe(true);
     expect(engineeringView.some((message) => message.id === projectMessageId)).toBe(true);
 
-    const productView = shared.db.listAgentMessages(shared.companyId, { agentId: productLeadId });
+    const productView = shared.db.messages.listAgentMessages(shared.companyId, { agentId: productLeadId });
     expect(productView.some((message) => message.id === deptMessageId)).toBe(false);
     expect(productView.some((message) => message.id === projectMessageId)).toBe(false);
   });
 
   it("filters messages by channel", () => {
-    shared.db.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, subject: "Dept update", body: "All good", channel: "department", channelTargetId: "engineering" });
-    shared.db.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, toAgentId: agentBId, subject: "DM", body: "Hey", channel: "direct" });
+    shared.db.messages.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, subject: "Dept update", body: "All good", channel: "department", channelTargetId: "engineering" });
+    shared.db.messages.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, toAgentId: agentBId, subject: "DM", body: "Hey", channel: "direct" });
 
-    const deptMsgs = shared.db.listAgentMessages(shared.companyId, { channel: "department" });
+    const deptMsgs = shared.db.messages.listAgentMessages(shared.companyId, { channel: "department" });
     expect(deptMsgs).toHaveLength(1);
     expect(deptMsgs[0].subject).toBe("Dept update");
 
-    const directMsgs = shared.db.listAgentMessages(shared.companyId, { channel: "direct" });
+    const directMsgs = shared.db.messages.listAgentMessages(shared.companyId, { channel: "direct" });
     expect(directMsgs).toHaveLength(1);
     expect(directMsgs[0].subject).toBe("DM");
   });
 
   it("appears in snapshot", () => {
-    shared.db.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, channel: "company", subject: "Snapshot test", body: "Hi" });
+    shared.db.messages.sendAgentMessage({ companyId: shared.companyId, fromAgentId: agentAId, channel: "company", subject: "Snapshot test", body: "Hi" });
     const snapshot = shared.db.listSnapshot();
     expect(snapshot.agentMessages.length).toBeGreaterThanOrEqual(1);
     expect(snapshot.agentMessages[0].subject).toBe("Snapshot test");

tests/integration/autonomous-chain/crash-recovery.spec.ts

@@ -23,7 +23,7 @@ describe("Step 7: Worker crash recovery (database layer)", () => {
       status: "in_progress",
     });
 
-    const run = shared.db.createRun({
+    const run = shared.db.runs.createRun({
       companyId: shared.companyId,
       taskId,
       agentId,
@@ -31,7 +31,7 @@ describe("Step 7: Worker crash recovery (database layer)", () => {
       connectorId: "openai-codex",
     });
 
-    shared.db.markRunStatus(run.id, "running", "Started");
+    shared.db.runs.markRunStatus(run.id, "running", "Started");
 
     // Verify it's running
     let snapshot = shared.db.listSnapshot();
@@ -61,7 +61,7 @@ describe("Step 7: Worker crash recovery (database layer)", () => {
       status: "in_progress",
     });
 
-    const run = shared.db.createRun({
+    const run = shared.db.runs.createRun({
       companyId: shared.companyId,
       taskId,
       agentId,
@@ -69,10 +69,10 @@ describe("Step 7: Worker crash recovery (database layer)", () => {
       connectorId: "openai-codex",
     });
 
-    shared.db.markRunStatus(run.id, "running", "Started");
+    shared.db.runs.markRunStatus(run.id, "running", "Started");
 
     // Simulate crash recovery - mark as interrupted
-    shared.db.finishRun({
+    shared.db.runs.finishRun({
       runId: run.id,
       status: "interrupted",
       summary: "Worker process crashed.",

tests/integration/autonomous-chain/e2e-flows.spec.ts

@@ -31,7 +31,7 @@ describe("E2E: Full autonomous CEO cold start flow", () => {
     const cmoId = createAgent({ name: "Aria", role: "CMO", reportsTo: ceoId, status: "pending_approval" as "idle" });
 
     // 3. CEO submits org strategy approval
-    const orgApprovalId = shared.db.requestApproval({
+    const orgApprovalId = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "approve_ceo_strategy",
@@ -64,7 +64,7 @@ describe("E2E: Full autonomous CEO cold start flow", () => {
     expect(phase1Prompt).toContain("Awaiting Org Strategy Approval");
 
     // 4. Board approves hires
-    const hireApprovalCTO = shared.db.requestApproval({
+    const hireApprovalCTO = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "hire_agent",
@@ -72,9 +72,9 @@ describe("E2E: Full autonomous CEO cold start flow", () => {
       impactSummary: "Test",
       payloadJson: JSON.stringify({ agentId: ctoId }),
     });
-    shared.db.decideApproval({ approvalId: hireApprovalCTO, state: "approved", decisionNote: "Approved" });
+    shared.db.approvalsMod.decideApproval({ approvalId: hireApprovalCTO, state: "approved", decisionNote: "Approved" });
 
-    const hireApprovalCMO = shared.db.requestApproval({
+    const hireApprovalCMO = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "hire_agent",
@@ -82,14 +82,14 @@ describe("E2E: Full autonomous CEO cold start flow", () => {
       impactSummary: "Test",
       payloadJson: JSON.stringify({ agentId: cmoId }),
     });
-    shared.db.decideApproval({ approvalId: hireApprovalCMO, state: "approved", decisionNote: "Approved" });
+    shared.db.approvalsMod.decideApproval({ approvalId: hireApprovalCMO, state: "approved", decisionNote: "Approved" });
 
     // Agents now idle
     expect(shared.db.entityCrud.getAgent(ctoId).status).toBe("idle");
     expect(shared.db.entityCrud.getAgent(cmoId).status).toBe("idle");
 
     // 5. Board approves org strategy
-    shared.db.decideApproval({ approvalId: orgApprovalId, state: "approved", decisionNote: "Go ahead" });
+    shared.db.approvalsMod.decideApproval({ approvalId: orgApprovalId, state: "approved", decisionNote: "Go ahead" });
 
     // 6. CEO now in Phase 2
     const updatedCto = shared.db.entityCrud.getAgent(ctoId);
@@ -287,7 +287,7 @@ describe("Review Fix: Rejected approval wakes agent", () => {
   it("decideApproval with rejected state still triggers wake (tested via DB)", () => {
     const ceoId = createAgent({ name: "CEO", role: "CEO" });
 
-    const approvalId = shared.db.requestApproval({
+    const approvalId = shared.db.approvalsMod.requestApproval({
       companyId: shared.companyId,
       requestedByAgentId: ceoId,
       type: "approve_ceo_strategy",
@@ -295,14 +295,14 @@ describe("Review Fix: Rejected approval wakes agent", () => {
       impactSummary: "test",
     });
 
-    shared.db.decideApproval({
+    shared.db.approvalsMod.decideApproval({
       approvalId,
       state: "rejected",
       decisionNote: "Not ready",
     });
 
     // Verify approval state
-    const approval = shared.db.getApprovalRecord(approvalId);
+    const approval = shared.db.approvalsMod.getApprovalRecord(approvalId);
     expect(approval.state).toBe("rejected");
     // The IPC handler in index.ts now wakes on rejected too —
     // we verify the DB layer works; the wakeAgentIfPossible call is in index.ts

tests/integration/autonomous-chain/run-failure.spec.ts

@@ -22,7 +22,7 @@ describe("Step 6: Run failure escalation (database layer)", () => {
       status: "in_progress",
     });
 
-    const run = shared.db.createRun({
+    const run = shared.db.runs.createRun({
       companyId: shared.companyId,
       taskId,
       agentId,
@@ -30,9 +30,9 @@ describe("Step 6: Run failure escalation (database layer)", () => {
       connectorId: "openai-codex",
     });
 
-    shared.db.markRunStatus(run.id, "running", "Started");
+    shared.db.runs.markRunStatus(run.id, "running", "Started");
 
-    const outcome = shared.db.finishRun({
+    const outcome = shared.db.runs.finishRun({
       runId: run.id,
       status: "failed",
       summary: null,

tests/integration/autonomous-chain/shared-setup.ts

@@ -54,7 +54,7 @@ export function installSharedSetup(): SharedHandle {
     state.db = new AppDatabase(profileDir);
     state.db.init();
 
-    state.companyId = state.db.saveCompany({
+    state.companyId = state.db.company.saveCompany({
       name: "Autonomous Test Corp",
       description: "Test company for autonomous chain",
       status: "active",

tests/integration/connector-model-enforcement.spec.ts

@@ -57,7 +57,7 @@ function createOrchestrationHarness(db: AppDatabase) {
     runDispatch.resolveWorkspace,
     runDispatch.getRunEligibilityFailure,
     runDispatch.dispatchRunToWorker,
-    (filter) => db.hasActiveRun(filter),
+    (filter) => db.runs.hasActiveRun(filter),
   );
 
   return { deps, taskRunner };
@@ -77,7 +77,7 @@ describe("connector model enforcement", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Runtime Enforcement Co",
       description: "Blocks runs when agent models are disabled",
       status: "active",
@@ -141,7 +141,7 @@ describe("connector model enforcement", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Recovered Run Co",
       description: "Rejects invalid queued runs during recovery",
       status: "active",
@@ -177,7 +177,7 @@ describe("connector model enforcement", () => {
       status: "todo",
     });
 
-    const run = db.createRun({
+    const run = db.runs.createRun({
       companyId,
       taskId,
       agentId,

tests/integration/cross-subsystem.spec.ts

@@ -64,7 +64,7 @@ function scaffold(db: AppDatabase, budgetAmountCents = 500): ScaffoldResult {
     notes: "Non-exempt connector for session rotation tests",
   });
 
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Pipeline Test Corp",
     description: "Cross-subsystem pipeline integration tests",
     status: "active",
@@ -187,7 +187,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     });
 
     // 2. CAS checkout: create run and checkout task
-    const { id: runId } = db.createRun({
+    const { id: runId } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: s.agentId,
@@ -207,9 +207,9 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     expect(budgetResult.blockedBy).toHaveLength(0);
 
     // 4. Execute run
-    db.markRunStatus(runId, "running", "Starting");
-    db.recordCostEntry({ runId, companyId: s.companyId, agentId: s.agentId, taskId, connectorId: "gemini-cli", amountUsd: 0.05, unattributed: false });
-    db.finishRun({
+    db.runs.markRunStatus(runId, "running", "Starting");
+    db.runs.recordCostEntry({ runId, companyId: s.companyId, agentId: s.agentId, taskId, connectorId: "gemini-cli", amountUsd: 0.05, unattributed: false });
+    db.runs.finishRun({
       runId,
       status: "succeeded",
       summary: "Login page built with form validation",
@@ -229,7 +229,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     sessionService.accumulateTokenUsage(sessionId, 5000, 2000, runId);
 
     // 6. Verify final state
-    const run = db.getRun(runId);
+    const run = db.runs.getRun(runId);
     expect(run.status).toBe("succeeded");
 
     const task = db.entityCrud.getTask(taskId);
@@ -266,7 +266,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     });
 
     // First agent checks out
-    const { id: runId1 } = db.createRun({
+    const { id: runId1 } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: s.agentId,
@@ -289,7 +289,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       capabilities: "Backend development",
       budgetMonthlyUsd: 100,
     });
-    const { id: runId2 } = db.createRun({
+    const { id: runId2 } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: agent2Id,
@@ -322,7 +322,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       status: "todo",
     });
 
-    const { id: runId } = db.createRun({
+    const { id: runId } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: s.agentId,
@@ -331,9 +331,9 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     });
 
     db.tasks.checkoutTask(taskId, runId);
-    db.markRunStatus(runId, "running", "Starting");
-    db.recordCostEntry({ runId, companyId: s.companyId, agentId: s.agentId, taskId, connectorId: s.connectorId, amountUsd: 1.5, unattributed: false });
-    db.finishRun({
+    db.runs.markRunStatus(runId, "running", "Starting");
+    db.runs.recordCostEntry({ runId, companyId: s.companyId, agentId: s.agentId, taskId, connectorId: s.connectorId, amountUsd: 1.5, unattributed: false });
+    db.runs.finishRun({
       runId,
       status: "succeeded",
       summary: "Done",
@@ -382,7 +382,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     });
 
     // Run 1: create run and accumulate tokens
-    const { id: runId1 } = db.createRun({
+    const { id: runId1 } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: s.agentId,
@@ -392,7 +392,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
     sessionService.accumulateTokenUsage(sessionId, 5000, 2000, runId1);
 
     // Run 2: create another run and accumulate more tokens
-    const { id: runId2 } = db.createRun({
+    const { id: runId2 } = db.runs.createRun({
       companyId: s.companyId,
       taskId,
       agentId: s.agentId,
@@ -432,7 +432,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       status: "todo",
     });
 
-    const { id: runId1 } = db.createRun({
+    const { id: runId1 } = db.runs.createRun({
       companyId: s.companyId,
       taskId: taskId1,
       agentId: s.agentId,
@@ -440,9 +440,9 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       connectorId: s.connectorId,
     });
     db.tasks.checkoutTask(taskId1, runId1);
-    db.markRunStatus(runId1, "running", "Starting");
-    db.recordCostEntry({ runId: runId1, companyId: s.companyId, agentId: s.agentId, taskId: taskId1, connectorId: s.connectorId, amountUsd: 3.0, unattributed: false });
-    db.finishRun({
+    db.runs.markRunStatus(runId1, "running", "Starting");
+    db.runs.recordCostEntry({ runId: runId1, companyId: s.companyId, agentId: s.agentId, taskId: taskId1, connectorId: s.connectorId, amountUsd: 3.0, unattributed: false });
+    db.runs.finishRun({
       runId: runId1,
       status: "succeeded",
       summary: "First task done",
@@ -473,7 +473,7 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       status: "todo",
     });
 
-    const { id: runId2 } = db.createRun({
+    const { id: runId2 } = db.runs.createRun({
       companyId: s.companyId,
       taskId: taskId2,
       agentId: s.agentId,
@@ -481,9 +481,9 @@ describe("Cross-Subsystem Pipeline (D-04)", () => {
       connectorId: s.connectorId,
     });
     db.tasks.checkoutTask(taskId2, runId2);
-    db.markRunStatus(runId2, "running", "Starting");
-    db.recordCostEntry({ runId: runId2, companyId: s.companyId, agentId: s.agentId, taskId: taskId2, connectorId: s.connectorId, amountUsd: 3.0, unattributed: false });
-    db.finishRun({
+    db.runs.markRunStatus(runId2, "running", "Starting");
+    db.runs.recordCostEntry({ runId: runId2, companyId: s.companyId, agentId: s.agentId, taskId: taskId2, connectorId: s.connectorId, amountUsd: 3.0, unattributed: false });
+    db.runs.finishRun({
       runId: runId2,
       status: "succeeded",
       summary: "Second task done",

tests/integration/database.spec.ts

@@ -37,7 +37,7 @@ describe("AppDatabase", () => {
     const db = new AppDatabase(profileDir);
     db.init();
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Orbit Foundry",
       description: "Test company",
       status: "active",
@@ -113,7 +113,7 @@ describe("AppDatabase", () => {
       OPENAI_API_KEY: "sk-test-123",
     });
 
-    const run = db.createRun({
+    const run = db.runs.createRun({
       companyId,
       taskId,
       agentId,
@@ -121,11 +121,11 @@ describe("AppDatabase", () => {
       connectorId: "openai-codex",
     });
 
-    await db.appendRunLog(run.id, "stdout", "hello from run\n");
-    expect(db.readRunLog(run.id)).toContain("hello from run");
+    await db.runs.appendRunLog(run.id, "stdout", "hello from run\n");
+    expect(db.runs.readRunLog(run.id)).toContain("hello from run");
 
-    db.markRunStatus(run.id, "running", "Connector launched");
-    db.finishRun({
+    db.runs.markRunStatus(run.id, "running", "Connector launched");
+    db.runs.finishRun({
       runId: run.id,
       status: "succeeded",
       summary: "Completed successfully",
@@ -143,7 +143,7 @@ describe("AppDatabase", () => {
 
     await db.exportBackup(backupDir);
 
-    db.saveCompany({
+    db.company.saveCompany({
       name: "Temporary company",
       description: "Should disappear after restore",
       status: "active",
@@ -164,13 +164,13 @@ describe("AppDatabase", () => {
     const db = new AppDatabase(profileDir);
     db.init();
 
-    const alphaCompanyId = db.saveCompany({
+    const alphaCompanyId = db.company.saveCompany({
       name: "Alpha",
       description: "Alpha company",
       status: "active",
     });
 
-    const betaCompanyId = db.saveCompany({
+    const betaCompanyId = db.company.saveCompany({
       name: "Beta",
       description: "Beta company",
       status: "active",

tests/integration/document-run-provenance.spec.ts

@@ -34,7 +34,7 @@ async function createHarness() {
     lastError: null,
   });
 
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Document Provenance Co",
     description: "Tests document revision provenance through run completion",
     status: "active",
@@ -82,7 +82,7 @@ async function createHarness() {
     status: "draft",
   });
 
-  const run = db.createRun({
+  const run = db.runs.createRun({
     companyId,
     taskId,
     agentId,
@@ -284,7 +284,7 @@ describe("document run provenance", () => {
   it("creates deliverable review approvals that stay linked to the originating task", async () => {
     const harness = await createHarness();
     try {
-      harness.db.saveCompany({
+      harness.db.company.saveCompany({
         id: harness.companyId,
         name: "Document Provenance Co",
         description: "Tests document review task linkage",

tests/integration/process-recovery.spec.ts

@@ -62,7 +62,7 @@ function scaffold(db: AppDatabase): ScaffoldResult {
   });
 
   // Company
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Recovery Test Corp",
     description: "Process recovery integration tests",
     status: "active",
@@ -157,7 +157,7 @@ function createAndStartRun(
       status: "todo",
     });
 
-  const { id: runId } = db.createRun({
+  const { id: runId } = db.runs.createRun({
     companyId: opts.companyId,
     taskId,
     agentId: opts.agentId,
@@ -166,7 +166,7 @@ function createAndStartRun(
   });
 
   db.tasks.checkoutTask(taskId, runId);
-  db.markRunStatus(runId, "running", "Starting execution");
+  db.runs.markRunStatus(runId, "running", "Starting execution");
 
   if (opts.claimWorkspace !== false) {
     db.claimWorkspaceLock(opts.workspaceId, runId);
@@ -278,8 +278,8 @@ describe("Process Recovery -- Worker Crash Detection", () => {
     const interruptedCount = simulateWorkerCrash(db);
 
     expect(interruptedCount).toBe(2);
-    expect(db.getRun(run1.runId).status).toBe("interrupted");
-    expect(db.getRun(run2.runId).status).toBe("interrupted");
+    expect(db.runs.getRun(run1.runId).status).toBe("interrupted");
+    expect(db.runs.getRun(run2.runId).status).toBe("interrupted");
   });
 
   it("releases task locks after crash", () => {
@@ -378,7 +378,7 @@ describe("Process Recovery -- Worker Crash Detection", () => {
       priority: "medium",
       status: "todo",
     });
-    const { id: newRunId } = db.createRun({
+    const { id: newRunId } = db.runs.createRun({
       companyId: s.companyId,
       taskId: taskId2,
       agentId: agent2Id,
@@ -530,7 +530,7 @@ describe("Process Recovery -- Multiple Concurrent Runs", () => {
 
     expect(interruptedCount).toBe(3);
     for (const run of runs) {
-      expect(db.getRun(run.runId).status).toBe("interrupted");
+      expect(db.runs.getRun(run.runId).status).toBe("interrupted");
     }
   });
 

tests/integration/skill-aware-assignment.spec.ts

@@ -32,7 +32,7 @@ describe("skill-aware capability registry", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Skill Match Co",
       description: "Tests skill-aware assignment",
       status: "active",
@@ -122,7 +122,7 @@ describe("skill-aware capability registry", () => {
       lastError: null,
     });
 
-    const companyId = db.saveCompany({
+    const companyId = db.company.saveCompany({
       name: "Registry Co",
       description: "Tests capability registry prompt injection",
       status: "active",

tests/integration/thread-wait-heartbeat.spec.ts

@@ -36,7 +36,7 @@ function createScaffold(db: AppDatabase) {
     lastError: null,
   });
 
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Thread Wait Co",
     description: "Tests cofounder wait states and replies",
     status: "active",
@@ -204,7 +204,7 @@ describe("thread wait + heartbeat integration", () => {
       throw new Error("Expected a task thread to exist for approval resolution testing.");
     }
 
-    const approvalId = db.requestApproval({
+    const approvalId = db.approvalsMod.requestApproval({
       companyId,
       relatedTaskId: taskId,
       requestedByAgentId: engineerId,
@@ -238,7 +238,7 @@ describe("thread wait + heartbeat integration", () => {
     expect(waitStates).toHaveLength(1);
     expect(checkpointEngine.shouldPauseHeartbeat(companyId, engineerId)).toBe(true);
 
-    db.decideApproval({
+    db.approvalsMod.decideApproval({
       approvalId,
       state: "approved",
       decisionNote: "Approved by board",

tests/integration/work-products-lifecycle.spec.ts

@@ -53,7 +53,7 @@ async function createHarness(): Promise<Harness> {
     lastError: null,
   });
 
-  const companyId = db.saveCompany({
+  const companyId = db.company.saveCompany({
     name: "Work Products Co",
     description: "Tests archived visibility, bulk retirement, deliverable signal",
     status: "active",
@@ -88,7 +88,7 @@ async function createHarness(): Promise<Harness> {
     priority: "medium",
     status: "in_progress",
   });
-  const run = db.createRun({
+  const run = db.runs.createRun({
     companyId,
     taskId,
     agentId,