@stigmer/runner 3.0.9-dev.20260615153829 → 3.1.0

package/dist/activities/execute-deep-agent/hitl.js

@@ -31,9 +31,13 @@ const ACTION_MAP = new Map([
  * Returns a `Command(resume=...)` if there are pending interrupts with
  * matching approval decisions, or a fresh user message input if this is
  * not a resume scenario.
+ *
+ * The graph checkpoint snapshot is read once by the caller and passed in: the
+ * same snapshot also decides whether status must be seeded from the persisted
+ * transcript (see `index.ts`), and on the durable (http) saver an extra
+ * `getState` is a network round-trip best avoided.
  */
-export async function resolveResumeInput(execution, agentGraph, langgraphConfig, userMessage) {
-    const graphState = await agentGraph.getState(langgraphConfig);
+export function resolveResumeInput(execution, graphState, userMessage) {
     const pendingInterrupts = extractPendingInterrupts(graphState);
     if (pendingInterrupts.length === 0) {
         return {
@@ -101,7 +105,11 @@ function extractPendingInterrupts(state) {
             if (typeof value === "object" && value !== null) {
                 const toolCallId = value.tool_call_id;
                 if (typeof toolCallId === "string" && toolCallId) {
-                    result.push({ interruptId: task.id, toolCallId });
+                    // Key on the interrupt's own id (falling back to task.id for the
+                    // parent-level case where they coincide). This is what makes a
+                    // sub-agent approval resume into the nested interrupt rather than
+                    // being dropped — see InterruptValue.id.
+                    result.push({ interruptId: intr.id ?? task.id, toolCallId });
                 }
             }
         }

package/dist/activities/execute-deep-agent/hitl.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hitl.js","sourceRoot":"","sources":["../../../src/activities/execute-deep-agent/hitl.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AAE/C,OAAO,EACL,cAAc,EACd,cAAc,GACf,MAAM,8DAA8D,CAAC;AAGtE,qEAAqE;AACrE,yEAAyE;AACzE,yEAAyE;AACzE,oEAAoE;AACpE,0BAA0B;AAC1B,MAAM,UAAU,GAAwC,IAAI,GAAG,CAAC;IAC9D,CAAC,cAAc,CAAC,OAAO,EAAE,SAAS,CAAC;IACnC,CAAC,cAAc,CAAC,WAAW,EAAE,SAAS,CAAC;IACvC,CAAC,cAAc,CAAC,IAAI,EAAE,MAAM,CAAC;IAC7B,CAAC,cAAc,CAAC,MAAM,EAAE,QAAQ,CAAC;CAClC,CAAC,CAAC;AAkCH;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,kBAAkB,CAChC,SAAyB,EACzB,UAA8B,EAC9B,WAAmB;IAEnB,MAAM,iBAAiB,GAAG,wBAAwB,CAAC,UAAU,CAAC,CAAC;IAC/D,IAAI,iBAAiB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACnC,OAAO;YACL,UAAU,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,CAAC,EAAE;YAClE,oBAAoB,EAAE,KAAK;YAC3B,YAAY,EAAE,KAAK;YACnB,eAAe,EAAE,EAAE;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,SAAS,GAAG,wBAAwB,CAAC,SAAS,CAAC,CAAC;IACtD,IAAI,SAAS,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO;YACL,UAAU,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,CAAC,EAAE;YAClE,oBAAoB,EAAE,KAAK;YAC3B,YAAY,EAAE,KAAK;YACnB,eAAe,EAAE,EAAE;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,UAAU,GAAyD,EAAE,CAAC;IAC5E,IAAI,YAAY,GAAG,KAAK,CAAC;IACzB,IAAI,eAAe,GAAG,EAAE,CAAC;IAEzB,KAAK,MAAM,IAAI,IAAI,iBAAiB,EAAE,CAAC;QACrC,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,CAAC;QACnC,MAAM,QAAQ,GAAG,SAAS,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QAC3C,IAAI,CAAC,QAAQ;YAAE,SAAS;QAExB,MAAM,SAAS,GAAG,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;QAClD,IAAI,CAAC,SAAS;YAAE,SAAS;QAEzB,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,GAAG;YAC7B,MAAM,EAAE,SAAS;YACjB,GAAG,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,QAAQ,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SAC3D,CAAC;QAEF,IAAI,QAAQ,CAAC,MAAM,KAAK,cAAc,CAAC,MAAM,EAAE,CAAC;YAC9C,YAAY,GAAG,IAAI,CAAC;YACpB,eAAe,GAAG,QAAQ,CAAC,OAAO,IAAI,kBAAkB,CAAC;QAC3D,CAAC;IACH,CAAC;IAED,IAAI,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzC,OAAO;YACL,UAAU,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,CAAC,EAAE;YAClE,oBAAoB,EAAE,KAAK;YAC3B,YAAY,EAAE,KAAK;YACnB,eAAe,EAAE,EAAE;SACpB,CAAC;IACJ,CAAC;IAED,OAAO,CAAC,GAAG,CACT,8BAA8B,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,MAAM,iBAAiB;QAC7E,aAAa,YAAY,EAAE,CAC5B,CAAC;IAEF,OAAO;QACL,UAAU,EAAE,IAAI,OAAO,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;QAC/C,oBAAoB,EAAE,IAAI;QAC1B,YAAY;QACZ,eAAe;KAChB,CAAC;AACJ,CAAC;AAOD,SAAS,wBAAwB,CAAC,KAAyB;IACzD,MAAM,MAAM,GAAuB,EAAE,CAAC;IAEtC,KAAK,MAAM,IAAI,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;QAC/B,IAAI,CAAC,IAAI,CAAC,UAAU;YAAE,SAAS;QAC/B,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;YACnC,IAAI,IAAI,CAAC,WAAW,KAAK,SAAS;gBAAE,SAAS;YAE7C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;YACzB,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;gBAChD,MAAM,UAAU,GAAI,KAAiC,CAAC,YAAY,CAAC;gBACnE,IAAI,OAAO,UAAU,KAAK,QAAQ,IAAI,UAAU,EAAE,CAAC;oBACjD,iEAAiE;oBACjE,+DAA+D;oBAC/D,kEAAkE;oBAClE,yCAAyC;oBACzC,MAAM,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,EAAE,EAAE,UAAU,EAAE,CAAC,CAAC;gBAC/D,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAOD,SAAS,wBAAwB,CAC/B,SAAyB;IAEzB,MAAM,SAAS,GAAG,IAAI,GAAG,EAAiC,CAAC;IAC3D,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC;IAChC,IAAI,CAAC,MAAM;QAAE,OAAO,SAAS,CAAC;IAE9B,KAAK,MAAM,OAAO,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;QACtC,KAAK,MAAM,EAAE,IAAI,OAAO,CAAC,SAAS,EAAE,CAAC;YACnC,IACE,EAAE,CAAC,cAAc,KAAK,cAAc,CAAC,WAAW;gBAChD,EAAE,CAAC,MAAM,KAAK,cAAc,CAAC,0BAA0B,EACvD,CAAC;gBACD,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;oBACnB,MAAM,EAAE,EAAE,CAAC,cAAc;oBACzB,OAAO,EAAE,EAAE;iBACZ,CAAC,CAAC;YACL,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,yBAAyB,CACvC,SAAwC,EACxC,SAAqD;IAErD,KAAK,MAAM,CAAC,UAAU,EAAE,QAAQ,CAAC,IAAI,SAAS,EAAE,CAAC;QAC/C,MAAM,EAAE,GAAG,SAAS,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QACrC,IAAI,CAAC,EAAE;YAAE,SAAS;QAElB,QAAQ,QAAQ,CAAC,MAAM,EAAE,CAAC;YACxB,KAAK,cAAc,CAAC,OAAO,CAAC;YAC5B,KAAK,cAAc,CAAC,WAAW;gBAC7B,EAAE,CAAC,MAAM,GAAG,cAAc,CAAC,iBAAiB,CAAC;gBAC7C,MAAM;YACR,KAAK,cAAc,CAAC,IAAI;gBACtB,EAAE,CAAC,MAAM,GAAG,cAAc,CAAC,iBAAiB,CAAC;gBAC7C,MAAM;YACR,KAAK,cAAc,CAAC,MAAM;gBACxB,EAAE,CAAC,MAAM,GAAG,cAAc,CAAC,gBAAgB,CAAC;gBAC5C,EAAE,CAAC,KAAK,GAAG,qBAAqB,QAAQ,CAAC,OAAO,IAAI,iBAAiB,EAAE,CAAC;gBACxE,MAAM;QACV,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/activities/execute-deep-agent/index.d.ts

@@ -8,7 +8,8 @@
  * Phase 3b-iii: full middleware stack + artifact storage, inline publishing,
  * incremental git writeback, and post-stream safety net.
  */
+import { type ExecuteActivityInput } from "../../shared/activity-input.js";
 import type { Config } from "../../config.js";
 export declare function createDeepAgentActivities(config: Config): {
-    ExecuteDeepAgent: (executionId: string, threadId: string) => Promise<unknown>;
+    ExecuteDeepAgent: (arg0: ExecuteActivityInput | string, arg1?: string) => Promise<unknown>;
 };

package/dist/activities/execute-deep-agent/index.js

@@ -8,15 +8,19 @@
  * Phase 3b-iii: full middleware stack + artifact storage, inline publishing,
  * incremental git writeback, and post-stream safety net.
  */
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
 import { Context, CancelledFailure } from "@temporalio/activity";
-import { create } from "@bufbuild/protobuf";
+import { create, clone } from "@bufbuild/protobuf";
 import { AgentExecutionStatusSchema } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/api_pb";
 import { AgentMessageSchema, ToolCallSchema } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/message_pb";
-import { ExecutionPhase, InteractionMode, MessageType, ToolCallStatus } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/enum_pb";
+import { ExecutionPhase, FileCaptureClass, FileChangeSetStatus, InteractionMode, MessageType, ToolCallStatus } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/enum_pb";
 import { activityStarted, activityFinished } from "../../idle-watchdog.js";
+import { normalizeActivityInput } from "../../shared/activity-input.js";
 import { persistStatus, slimStatus, utcTimestamp } from "../../shared/status.js";
 import { publishPlanArtifact } from "../../shared/plan-artifact.js";
 import { classifyTool } from "../../shared/tool-kind.js";
+import { POLICY_ENGINE_VERSION, toProtoPolicySource, } from "../../shared/approval-policy.js";
 import { StigmerClient } from "../../client/stigmer-client.js";
 import { performSetup } from "./setup.js";
 import { streamExecution } from "./streaming.js";
@@ -26,6 +30,15 @@ import { InlinePublisher } from "./inline-publisher.js";
 import { WriteBackCoordinator } from "./writeback-coordinator.js";
 import { processPostStream } from "./post-stream.js";
 import { resolveResumeInput } from "./hitl.js";
+import { captureApprovalArtifacts } from "./approval-file-change.js";
+import { applyCaptureDecisions, captureBaselineToLedger, captureCandidateToLedger, } from "../../shared/filereview/capture.js";
+import { hasCandidateCaptured } from "../../shared/filereview/events.js";
+import { casBlobReader } from "../../shared/filereview/cas-substrate.js";
+import { partitionIgnoredPathsBySecret } from "../../shared/filereview/secret-paths.js";
+import { collectSubAgentToolCallIds } from "../../shared/tool-row.js";
+import { stampFlowedFileEditRows, stampFlowedSubAgentFileEditRows } from "./stamp-flowed-rows.js";
+/** The harness id stamped on the deep-agent's file-review ledger events. */
+const DEEP_AGENT_HARNESS_ID = "deep-agent";
 export function createDeepAgentActivities(config) {
     const client = new StigmerClient({
         endpoint: config.stigmerBackendEndpoint,
@@ -34,7 +47,12 @@ export function createDeepAgentActivities(config) {
     });
     const streamingConfig = loadStreamingConfig();
     return {
-        ExecuteDeepAgent: async (executionId, threadId) => {
+        // Accepts the new typed object OR the legacy positional args (transitional
+        // dual-shape so the runner can deploy before the control planes — see
+        // shared/activity-input.ts). Drop the positional arm once both control
+        // planes send the object.
+        ExecuteDeepAgent: async (arg0, arg1) => {
+            const { executionId, threadId, turnSeq } = normalizeActivityInput(arg0, arg1);
             activityStarted();
             let setup = null;
             try {
@@ -44,19 +62,32 @@ export function createDeepAgentActivities(config) {
                 // oversized tool outputs (e.g. computer-use screenshots) to artifact
                 // storage so the UI can render them, and keep the status under the
                 // gRPC cap. Threaded into the streaming loop and reused for the
-                // terminal persists below so the guard is never skipped.
-                const statusOffload = {
-                    artifactStorage: setup.artifactStorage,
-                    executionId,
-                };
-                const initialStatus = create(AgentExecutionStatusSchema, {});
+                // terminal persists below so the guard is never skipped. Undefined when
+                // there is no artifact store (proxy misconfig): offload is then disabled,
+                // but persistStatus still enforces the aggregate size cap, so persistence
+                // can never silently blow past the gRPC limit.
+                const statusOffload = setup.artifactStorage
+                    ? { artifactStorage: setup.artifactStorage, executionId }
+                    : undefined;
+                // Read the graph checkpoint once, to resolve how a pending approval
+                // interrupt continues (Command(resume) vs a fresh replay). Reading once
+                // avoids a redundant round-trip on the durable (http) saver.
+                const graphState = await setup.agentGraph.getState(setup.langgraphConfig);
+                // Seed from the persisted transcript whenever the execution already has
+                // committed history, so streamed deltas append onto it instead of
+                // replacing it. This holds for every re-invocation — durable resume and
+                // memory-checkpointer replay alike — and is a no-op on a first run.
+                const initialStatus = shouldSeedFromPersistedTranscript(setup.execution)
+                    ? seedStatusFromExecution(setup.execution)
+                    : create(AgentExecutionStatusSchema, {});
                 const statusBuilder = new StatusBuilder(executionId, initialStatus);
                 statusBuilder.setApprovalProvider({
                     policies: setup.approvalPolicies,
                     toolServerMap: setup.toolServerMap,
-                    autoApproveAll: setup.autoApproveAll,
+                    leasedCategories: setup.leasedCategories,
+                    globalBypass: setup.globalBypass,
                 });
-                const resume = await resolveResumeInput(setup.execution, setup.agentGraph, setup.langgraphConfig, setup.execution.spec.message);
+                const resume = resolveResumeInput(setup.execution, graphState, setup.execution.spec.message);
                 if (resume.hasRejection) {
                     const failedStatus = create(AgentExecutionStatusSchema, {
                         phase: ExecutionPhase.EXECUTION_FAILED,
@@ -92,6 +123,112 @@ export function createDeepAgentActivities(config) {
                         workspaceBackend: setup.workspaceBackend,
                     })
                     : null;
+                // Apply-then-review capture identity + substrate root for this turn.
+                const gitRoot = setup.workspaceBackend.rootDir;
+                const changeSetId = `${executionId}:${turnSeq}`;
+                // (1) Capture-mode resume — reconcile any DECIDED change set FIRST (this
+                // drops the per-execution refs), before the next baseline re-pins them
+                // (refs are executionId-keyed). Then (2) short-circuit a pure file-review
+                // resume — the agent already finished in a prior segment, so finalize with
+                // NO model re-invocation. A mixed turn (a tool gate is also pending) falls
+                // through to resume the graph for the gated tool.
+                if (setup.captureMode) {
+                    const decidedSets = (setup.execution.status?.fileChangeSets ?? []).filter((cs) => cs.status === FileChangeSetStatus.DECIDED);
+                    let reconciledAny = false;
+                    let reconcileFailed = false;
+                    let reconcileFailureDetail = "";
+                    // The CAS blob reader reconciles ignored-file decisions from the durable
+                    // manifest (git-only turns have no manifest, so the CAS branch no-ops).
+                    // Undefined with no store: this block still runs for a git workspace
+                    // whose captureMode is true without storage, but such a turn captures no
+                    // CAS files (captureIgnored is off), so its change set carries no CAS ref
+                    // and applyCaptureDecisions never needs the reader.
+                    const casReadBlob = setup.artifactStorage
+                        ? casBlobReader(setup.artifactStorage)
+                        : undefined;
+                    for (const changeSet of decidedSets) {
+                        const capResult = await applyCaptureDecisions({
+                            status: initialStatus,
+                            gitRoot,
+                            executionId,
+                            changeSet,
+                            harnessId: DEEP_AGENT_HARNESS_ID,
+                            storage: setup.artifactStorage,
+                            readBlob: casReadBlob,
+                            gitWorkspace: setup.gitWorkspace,
+                        });
+                        if (!capResult.isCaptureTurn)
+                            continue;
+                        reconciledAny = true;
+                        if (capResult.failed) {
+                            reconcileFailed = true;
+                            reconcileFailureDetail =
+                                capResult.failureDetail ?? "file review reconcile failed";
+                        }
+                    }
+                    if (reconciledAny) {
+                        if (reconcileFailed) {
+                            // What-you-approve-is-what-applies failed: nothing was applied.
+                            initialStatus.phase = ExecutionPhase.EXECUTION_FAILED;
+                            initialStatus.error = `File review reconcile failed: ${reconcileFailureDetail}`;
+                            initialStatus.completedAt = utcTimestamp();
+                            await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
+                            return slimStatus(initialStatus);
+                        }
+                        if (!hasPendingToolApprovals(setup.execution)) {
+                            // Pure file review: the agent's final answer + outputs already rode
+                            // the prior segment's persisted status (seeded into initialStatus).
+                            // Complete now and push only the approved tree — NO model re-run.
+                            //
+                            // The discriminator is the PERSISTED transcript, not the live graph
+                            // checkpoint: the memory checkpointer (OSS local / desktop) recreates
+                            // the checkpoint empty each invocation, so a graphState-based check
+                            // would wrongly fire for a mixed turn. A mixed turn leaves
+                            // WAITING_APPROVAL tool rows in the transcript; a pure file-review
+                            // turn leaves none.
+                            initialStatus.phase = ExecutionPhase.EXECUTION_COMPLETED;
+                            initialStatus.completedAt = utcTimestamp();
+                            if (writebackCoordinator) {
+                                await processCaptureWriteback(writebackCoordinator, executionId);
+                            }
+                            await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
+                            // Surface the agent's final outputs (computed in the prior segment,
+                            // carried on the seeded status) the same way a normal completion does.
+                            const slim = slimStatus(initialStatus);
+                            const lastAi = [...initialStatus.messages]
+                                .reverse()
+                                .find((m) => m.type === MessageType.MESSAGE_AI);
+                            if (lastAi?.content)
+                                slim.final_text = lastAi.content;
+                            if (initialStatus.structuredOutput !== undefined) {
+                                slim.structured = initialStatus.structuredOutput;
+                            }
+                            return slim;
+                        }
+                        // else: mixed turn — fall through; the graph resumes for the gated
+                        // tool and a new baseline is taken below for the continuation segment.
+                    }
+                }
+                // Turn start (capture mode): pin the pre-turn tree + author BASELINE. Taken
+                // AFTER any reconcile above and AFTER performSetup's workspace writes, so
+                // the baseline absorbs the reconciled state and the runner-owned files.
+                let captureBaselineTree = "";
+                // Snapshot the sub-agent tool-call ids that exist BEFORE this turn's
+                // stream, so the turn-boundary stamp scopes itself to sub-agent rows
+                // created this turn (empty here by construction — this harness never
+                // seeds prior sub-agents — but computed, not assumed, so it stays correct
+                // if that ever changes; see collectSubAgentToolCallIds).
+                const priorSubAgentToolCallIds = collectSubAgentToolCallIds(initialStatus.subAgentExecutions);
+                if (setup.captureMode) {
+                    captureBaselineTree = await captureBaselineToLedger({
+                        status: initialStatus,
+                        gitRoot,
+                        executionId,
+                        changeSetId,
+                        harnessId: DEEP_AGENT_HARNESS_ID,
+                        gitWorkspace: setup.gitWorkspace,
+                    });
+                }
                 const cancellationSignal = Context.current().cancellationSignal;
                 const result = await streamExecution({
                     agentGraph: setup.agentGraph,
@@ -104,45 +241,98 @@ export function createDeepAgentActivities(config) {
                     offload: statusOffload,
                     gracefulStop: setup.gracefulStop,
                     inlinePublisher,
-                    writebackCoordinator: writebackCoordinator ?? undefined,
+                    // Capture mode: never push speculative edits during the turn. Writeback
+                    // is deferred until the approved tree is reconciled (post-decision).
+                    writebackCoordinator: setup.captureMode ? undefined : (writebackCoordinator ?? undefined),
                     heartbeatFn: (details) => Context.current().heartbeat(details),
                     isCancelledFn: () => cancellationSignal.aborted,
                     approvalProvider: {
                         policies: setup.approvalPolicies,
                         toolServerMap: setup.toolServerMap,
-                        autoApproveAll: setup.autoApproveAll,
+                        leasedCategories: setup.leasedCategories,
+                        globalBypass: setup.globalBypass,
                     },
                     streamVersion: setup.streamVersion,
                 });
                 await processPostStream({
                     status: initialStatus,
                     inlinePublisher,
-                    writebackCoordinator,
+                    // Capture mode: suppress the post-stream writeback finalize — the edits
+                    // on disk are still speculative until reviewed. Writeback runs only on
+                    // the approved tree (processCaptureWriteback, after reconcile).
+                    writebackCoordinator: setup.captureMode ? null : writebackCoordinator,
                     pendingPublishPromises: result.pendingPublishPromises,
                     pendingWritebackPromises: result.pendingWritebackPromises,
                     executionId,
                 });
+                // Turn boundary (capture mode): capture the candidate change set from the
+                // git diff and author CANDIDATE_CAPTURED, then stamp the flowed file-edit
+                // rows with the change set id — they stay visible in place as
+                // observational records while file_change_sets remains the single
+                // decision surface. Skipped on an abnormal terminal (pause / stop /
+                // recursion limit) — there is no review to open. `fileReviewPending`
+                // then composes with any tool gate below.
+                let fileReviewPending = false;
+                const abnormalTerminal = !!result.terminalStatus &&
+                    initialStatus.phase !== ExecutionPhase.EXECUTION_WAITING_FOR_APPROVAL;
+                if (setup.captureMode && !abnormalTerminal) {
+                    // Compose the CAS-captured paths (before-bytes from the observer,
+                    // after-bytes re-read from disk) and the secret-blocked paths into the
+                    // change set. The substrate class labels their provenance:
+                    // GIT_IGNORED_CAPTURED for a git tree's ignored paths, NON_GIT_CAS for a
+                    // non-git workspace (where these ARE the whole change set). In a git turn
+                    // they compose with the git-tracked diff into one hybrid set; in a non-git
+                    // turn they are the entire (CAS-only) set.
+                    const casCaptureClass = setup.gitWorkspace
+                        ? FileCaptureClass.GIT_IGNORED_CAPTURED
+                        : FileCaptureClass.NON_GIT_CAS;
+                    const { casCaptures, unreviewablePaths } = await buildCasTurnCaptures(setup.casObserver, gitRoot, casCaptureClass);
+                    await captureCandidateToLedger({
+                        status: initialStatus,
+                        gitRoot,
+                        executionId,
+                        changeSetId,
+                        baselineTree: captureBaselineTree,
+                        harnessId: DEEP_AGENT_HARNESS_ID,
+                        casCaptures,
+                        storage: setup.artifactStorage,
+                        unreviewablePaths,
+                        unreviewableCaptureClass: casCaptureClass,
+                        gitWorkspace: setup.gitWorkspace,
+                    });
+                    // Review is pending iff a CANDIDATE was actually authored (the seam
+                    // drops no-op captures), so a turn that only touched-then-unchanged an
+                    // ignored file does not open an empty review. Stamping is gated on the
+                    // same signal: a row must never reference a change set that does not
+                    // exist.
+                    fileReviewPending = hasCandidateCaptured(initialStatus, changeSetId);
+                    if (fileReviewPending) {
+                        stampFlowedFileEditRows(initialStatus.messages, changeSetId);
+                        stampFlowedSubAgentFileEditRows(initialStatus.subAgentExecutions, changeSetId, priorSubAgentToolCallIds);
+                    }
+                }
                 if (result.terminalStatus) {
                     if (initialStatus.phase === ExecutionPhase.EXECUTION_PAUSED) {
                         await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
                         console.log(`[ExecuteDeepAgent] Paused for execution ${executionId}: events=${result.eventsProcessed}`);
                         throw new CancelledFailure("Activity paused by orchestrator");
                     }
+                    // Capture mode: a tool gate set WAITING during the stream while file
+                    // edits also flowed this turn. The CANDIDATE event + stamped file-edit
+                    // rows post-date the stream's slim, so persist + return the current
+                    // status (both review surfaces — the file change set and the tool gate —
+                    // are now pending). `!abnormalTerminal` means the capture block ran.
+                    if (setup.captureMode && !abnormalTerminal) {
+                        await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
+                        return slimStatus(initialStatus);
+                    }
                     return result.terminalStatus;
                 }
-                if (!setup.autoApproveAll) {
-                    const graphState = await setup.agentGraph.getState(setup.langgraphConfig);
-                    const pendingInterrupts = graphState.tasks?.flatMap((task) => (task.interrupts ?? [])
-                        .filter((intr) => intr.resumeValue === undefined)
-                        .map((intr) => {
-                        const val = intr.value;
-                        return {
-                            toolCallId: val?.tool_call_id ?? "",
-                            toolName: val?.tool_name ?? "",
-                            mcpServerSlug: val?.mcp_server_slug ?? "",
-                            message: val?.message ?? "",
-                        };
-                    })) ?? [];
+                if (!setup.globalBypass) {
+                    const postStreamGraphState = await setup.agentGraph.getState(setup.langgraphConfig);
+                    const graphMessages = postStreamGraphState.values.messages;
+                    const aiMessages = Array.isArray(graphMessages) ? graphMessages : [];
+                    const pendingInterrupts = detectPendingInterrupts(postStreamGraphState);
                     if (pendingInterrupts.length > 0) {
                         console.log(`[ExecuteDeepAgent] Detected ${pendingInterrupts.length} pending interrupt(s) ` +
                             `for execution ${executionId} — setting WAITING_FOR_APPROVAL`);
@@ -154,7 +344,7 @@ export function createDeepAgentActivities(config) {
                             isStreaming: false,
                         });
                         for (const intr of pendingInterrupts) {
-                            aiMsg.toolCalls.push(create(ToolCallSchema, {
+                            const toolCall = create(ToolCallSchema, {
                                 id: intr.toolCallId,
                                 name: intr.toolName,
                                 status: ToolCallStatus.TOOL_CALL_WAITING_APPROVAL,
@@ -164,15 +354,37 @@ export function createDeepAgentActivities(config) {
                                 mcpServerSlug: intr.mcpServerSlug,
                                 startedAt: utcTimestamp(),
                                 toolKind: classifyTool(intr.toolName, intr.mcpServerSlug),
-                            }));
+                                approvalPolicySource: toProtoPolicySource(intr.policySource),
+                                policyEngineVersion: intr.policySource ? POLICY_ENGINE_VERSION : "",
+                            });
+                            // Capture a sanitized args preview while the graph is paused, so the
+                            // approval UI renders the proposed change before the tool runs. Args
+                            // are correlated from the AI-message tool call in graph state (the
+                            // single source of truth).
+                            const { argsPreview } = captureApprovalArtifacts({
+                                toolCallId: intr.toolCallId,
+                                messages: aiMessages,
+                            });
+                            if (argsPreview)
+                                toolCall.argsPreview = argsPreview;
+                            aiMsg.toolCalls.push(toolCall);
                         }
                         initialStatus.messages.push(aiMsg);
                         await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
                         return slimStatus(initialStatus);
                     }
                 }
-                initialStatus.phase = ExecutionPhase.EXECUTION_COMPLETED;
-                initialStatus.completedAt = utcTimestamp();
+                // Capture mode: file edits flowed but no tool gate fired — open file
+                // review instead of completing. The agent's final answer + outputs are
+                // still computed and persisted below, so the pure-file-review resume can
+                // complete from the seeded status with no model re-invocation.
+                const completeNow = !fileReviewPending;
+                initialStatus.phase = completeNow
+                    ? ExecutionPhase.EXECUTION_COMPLETED
+                    : ExecutionPhase.EXECUTION_WAITING_FOR_APPROVAL;
+                if (completeNow) {
+                    initialStatus.completedAt = utcTimestamp();
+                }
                 let structuredOutput;
                 let finalText;
                 const lastAiMsg = [...initialStatus.messages]
@@ -213,8 +425,12 @@ export function createDeepAgentActivities(config) {
                 // first-class plan.md artifact so the UI can render a reviewable Plan
                 // card and a follow-up Implement run can reference it. Read-only mode
                 // produces no file to auto-publish, so this is the only artifact path.
+                // Requires artifact storage; with none (proxy misconfig) the plan text
+                // still lives in the final message — only the reviewable artifact is
+                // skipped (mirrors Cursor's storage-guarded plan publish).
                 if (setup.execution.spec?.executionConfig?.interactionMode === InteractionMode.PLAN &&
-                    finalText) {
+                    finalText &&
+                    setup.artifactStorage) {
                     await publishPlanArtifact({
                         status: initialStatus,
                         executionId,
@@ -222,13 +438,25 @@ export function createDeepAgentActivities(config) {
                         artifactStorage: setup.artifactStorage,
                     });
                 }
+                // Capture mode: push the approved tree exactly once, on terminal
+                // completion — never the speculative mid-turn edits.
+                if (setup.captureMode && completeNow && writebackCoordinator) {
+                    await processCaptureWriteback(writebackCoordinator, executionId);
+                }
                 await persistStatus(client, executionId, initialStatus, { offload: statusOffload });
-                console.log(`[ExecuteDeepAgent] Completed for execution ${executionId}: ` +
+                console.log(`[ExecuteDeepAgent] ${completeNow ? "Completed" : "Awaiting file review for"} ` +
+                    `execution ${executionId}: ` +
                     `events=${result.eventsProcessed}, ` +
                     `messages=${initialStatus.messages.length}, ` +
                     `artifacts=${initialStatus.artifacts.length}, ` +
                     `writebacks=${initialStatus.workspaceWriteBacks.length}, ` +
                     `hasStructuredOutput=${structuredOutput !== undefined}`);
+                // A WAITING (file-review) return carries no final outputs yet — those are
+                // surfaced when the pure-file-review resume completes from this persisted
+                // status. The COMPLETED return enriches the slim with final text/outputs.
+                if (!completeNow) {
+                    return slimStatus(initialStatus);
+                }
                 const slim = slimStatus(initialStatus);
                 if (finalText !== undefined) {
                     slim.final_text = finalText;
@@ -281,6 +509,138 @@ export function createDeepAgentActivities(config) {
         },
     };
 }
+/**
+ * Normalize the graph checkpoint's un-resumed interrupts into pending approvals.
+ * Used both before streaming (to detect whether a resume is a pure file review)
+ * and after (to seed the WAITING_FOR_APPROVAL tool rows).
+ */
+function detectPendingInterrupts(graphState) {
+    const tasks = graphState.tasks;
+    return (tasks?.flatMap((task) => (task.interrupts ?? [])
+        .filter((intr) => intr.resumeValue === undefined)
+        .map((intr) => {
+        const val = intr.value;
+        return {
+            toolCallId: val?.tool_call_id ?? "",
+            toolName: val?.tool_name ?? "",
+            mcpServerSlug: val?.mcp_server_slug ?? "",
+            message: val?.message ?? "",
+            policySource: val?.policy_source || undefined,
+        };
+    })) ?? []);
+}
+/**
+ * Whether the persisted transcript holds any tool call awaiting approval — the
+ * checkpointer-independent signal that a resume must drive a tool gate (resume
+ * the graph), not just a file review. Scans root + sub-agent messages. A tool
+ * keeps `WAITING_APPROVAL` after the user decides (the decision rides
+ * `approval_action`) until the runner reconciles it, so this is true for a mixed
+ * turn's resume and false for a pure file-review turn.
+ */
+function hasPendingToolApprovals(execution) {
+    const status = execution.status;
+    if (!status)
+        return false;
+    const anyWaiting = (msgs) => msgs.some((m) => m.toolCalls.some((tc) => tc.status === ToolCallStatus.TOOL_CALL_WAITING_APPROVAL));
+    if (anyWaiting(status.messages))
+        return true;
+    return status.subAgentExecutions.some((sa) => anyWaiting(sa.messages));
+}
+/**
+ * Assemble the turn's CAS captures and secret-blocked paths from the shared
+ * observer (the pre-turn bytes recorded by the parent AND every sub-agent CAS
+ * backend, plus the gate's secret-blocked set).
+ *
+ * For each observed CAS-owned path the after-bytes are re-read from disk (the
+ * authoritative net result of the turn; `null` when the file is gone). A path
+ * that is secret-like is diverted to `unreviewablePaths` and its before-bytes are
+ * dropped — the fail-closed backstop that holds even under the global bypass,
+ * where the gate did not run to block it up front. The result composes into the
+ * change set in {@link captureCandidateToLedger}.
+ *
+ * `captureClass` is the turn's CAS substrate class — GIT_IGNORED_CAPTURED for a
+ * git work tree's ignored paths, NON_GIT_CAS for a non-git workspace (where these
+ * ARE the whole change set) — so each captured path carries its true provenance.
+ */
+async function buildCasTurnCaptures(observer, workspaceRoot, captureClass) {
+    // The secret partition (pure, corpus-lockable) decides what may be captured;
+    // this shell only performs the IO for the capturable set. The backstop that
+    // withholds a secret observed under the global bypass lives in the partition.
+    const { capturablePaths, unreviewablePaths } = partitionIgnoredPathsBySecret(observer.before.keys(), observer.blockedSecretPaths);
+    const casCaptures = [];
+    for (const relPath of capturablePaths) {
+        const after = await readFileOrNull(join(workspaceRoot, relPath));
+        casCaptures.push({
+            path: relPath,
+            before: observer.before.get(relPath) ?? null,
+            after,
+            captureClass,
+        });
+    }
+    return { casCaptures, unreviewablePaths: [...unreviewablePaths] };
+}
+/** Raw bytes of a file, or `null` when it does not exist (a DELETE). */
+async function readFileOrNull(absolutePath) {
+    try {
+        return await readFile(absolutePath);
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Push the reconciled (approved) tree exactly once, on terminal completion in
+ * capture mode. The coordinator's {@link WriteBackCoordinator.finalize} commits +
+ * pushes whatever uncommitted changes remain — which, post-reconcile, is exactly
+ * the approved content (rejected files were already snapped back to baseline).
+ * Speculative mid-turn edits never reach here (writeback is suppressed during the
+ * turn). Fire-and-forget by the coordinator's own contract (errors logged).
+ */
+async function processCaptureWriteback(writebackCoordinator, executionId) {
+    await writebackCoordinator.finalize();
+    console.log(`[ExecuteDeepAgent] capture writeback finalized for execution ${executionId}`);
+}
+/**
+ * Whether to seed the initial status from the persisted execution transcript.
+ *
+ * The Temporal workflow re-invokes ExecuteDeepAgent with the same thread_id on
+ * every continuation — HITL approval, pause/resume, and transient recovery. The
+ * runner owns the transcript and the server enforces it as append-only at
+ * identity, so any continuation must build ON the committed history rather than
+ * rebuilding from an empty proto and replacing it.
+ *
+ * The decision is therefore driven solely by whether the server already holds
+ * committed history for this execution — NOT by the live graph checkpoint, which
+ * the two checkpointers leave in different states for the same continuation:
+ *   - durable (http): the checkpoint survives, the graph resumes via
+ *     Command(resume), and streamEvents re-emits only post-checkpoint events;
+ *   - memory (the OSS local / desktop default): the checkpoint is recreated
+ *     empty every invocation, so the graph REPLAYS from scratch and the blind
+ *     FIFO turns advance one gate at a time.
+ * Keying on the live checkpoint skipped seeding on that memory-replay path, so a
+ * second sequential gate emitted a transcript holding only the new gate, dropped
+ * the first gate's committed tool-call id, and tripped the server's append-only
+ * guard — the silent sequential-gate skip. Seeding whenever persisted history
+ * exists covers both paths; a re-emitted prior turn reconciles in place by
+ * tool-call id (StatusBuilder.rebuildToolCallIndex), so seeding never
+ * duplicates. False on a first run (no persisted messages), preserving the
+ * original start-from-empty behavior.
+ */
+function shouldSeedFromPersistedTranscript(execution) {
+    return (execution.status?.messages.length ?? 0) > 0;
+}
+/**
+ * Seed a fresh status from the persisted execution transcript so streamed
+ * deltas append onto existing history rather than replacing it. The clone keeps
+ * the persisted proto immutable. Terminal fields are cleared because the resumed
+ * run is in progress again; the StatusBuilder constructor re-sets the phase.
+ */
+function seedStatusFromExecution(execution) {
+    const seeded = clone(AgentExecutionStatusSchema, execution.status);
+    seeded.completedAt = "";
+    seeded.error = "";
+    return seeded;
+}
 async function cleanup(setup) {
     if (!setup)
         return;