gsd-pi 2.81.0 → 2.82.0-dev.20138ae42

package/src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts

@@ -12,7 +12,14 @@ import {
   resetEmptyTurnCounter,
 } from "../guided-flow.js";
 import { clearPathCache } from "../paths.js";
-import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
+import {
+  getAutoDashboardData,
+  getAutoModeStartModel,
+  isAutoActive,
+  isAutoCompletionStopInProgress,
+  pauseAuto,
+  setCurrentDispatchedModelId,
+} from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
 import {
@@ -25,6 +32,7 @@ import { shouldIgnoreAgentEndForActiveUnit } from "../auto/unit-runner-events.js
 import { resolveModelId } from "../auto-model-selection.js";
 import { resolveProjectRoot } from "../worktree.js";
 import { clearDiscussionFlowState } from "./write-gate.js";
+import { clearGuidedUnitContext } from "../guided-unit-context.js";
 import { resumeAutoAfterProviderDelay } from "./provider-error-resume.js";
 import {
   classifyError,
@@ -41,6 +49,11 @@ const MAX_NETWORK_RETRIES = 2;
 function isObjectRecord(value: unknown): value is Record<string, unknown> {
   return !!value && typeof value === "object";
 }
+
+export function _hasEmptyAgentEndContent(content: unknown): boolean {
+  return content == null || (Array.isArray(content) && content.length === 0);
+}
+
 /**
  * Cap on auto-resume attempts for sustained transient-provider errors.
  *
@@ -146,8 +159,7 @@ export function isBareClaudeCodeStreamAbortPlaceholder(lastMsg: unknown): boolea
  * Claude Code abort markers are intentionally ignored when the abort fires
  * while the session-switch is in flight: the abort is the expected side-effect
  * of the transition, not a user signal. Other branches (genuine `stopReason
- * === "aborted"` with diagnostic content/errorMessage) preserve the prior
- * behavior.
+ * === "aborted"` with explicit errorMessage) preserve the prior behavior.
  */
 export function _handleSessionSwitchAgentEnd(
   lastMsg: unknown,
@@ -171,10 +183,8 @@ export function _handleSessionSwitchAgentEnd(
   }
 
   if (m.stopReason === "aborted") {
-    const content = m.content;
-    const hasEmptyContent = Array.isArray(content) && content.length === 0;
     const hasErrorMessage = !!m.errorMessage;
-    if (!hasEmptyContent || hasErrorMessage) {
+    if (hasErrorMessage) {
       resolveCancelled(_buildAbortedPauseContext(m as { errorMessage?: unknown }));
     }
   }
@@ -192,6 +202,14 @@ export function resolveAgentEndErrorDisplay(
   return rawErrorMsg;
 }
 
+export function isTerminalDeletedWorktreeProviderError(
+  message: string | undefined | null,
+): boolean {
+  if (!message) return false;
+  if (!/\bdoes not exist\b/i.test(message)) return false;
+  return /[/\\]\.gsd[/\\](?:projects[/\\][^/\\]+[/\\])?worktrees[/\\][^/\\\s"']+/i.test(message);
+}
+
 async function pauseTransientWithBackoff(
   cls: ErrorClass,
   pi: ExtensionAPI,
@@ -240,9 +258,11 @@ export async function handleAgentEnd(
   // falsely report files as missing — producing a spurious "ready signal
   // rejected" loop even though the files are on disk.
   clearPathCache();
+  const basePath = resolveAgentEndBasePath();
+  clearGuidedUnitContext(basePath);
 
   try {
-    if (await checkDeepProjectSetupAfterTurn(event, ctx, resolveAgentEndBasePath())) {
+    if (await checkDeepProjectSetupAfterTurn(event, ctx, basePath)) {
       return;
     }
   } catch (err) {
@@ -250,8 +270,8 @@ export async function handleAgentEnd(
     logWarning("bootstrap", `checkDeepProjectSetupAfterTurn failed: ${message}`);
   }
 
-  if (checkAutoStartAfterDiscuss()) {
-    clearDiscussionFlowState(resolveAgentEndBasePath() ?? process.cwd());
+  if (checkAutoStartAfterDiscuss(basePath)) {
+    clearDiscussionFlowState(basePath ?? process.cwd());
     return;
   }
 
@@ -259,14 +279,14 @@ export async function handleAgentEnd(
   // are missing, `checkAutoStartAfterDiscuss` returns false silently. Surface
   // that and nudge the LLM to complete the writes before the user hits the
   // downstream "All milestones complete" warning loop.
-  if (maybeHandleReadyPhraseWithoutFiles(event)) return;
+  if (maybeHandleReadyPhraseWithoutFiles(event, basePath)) return;
 
   // #4573 — Empty-turn recovery: if the LLM announced intent in prose but
   // emitted no tool calls, nudge it to execute. Fires only when auto-mode is
   // active or a discussion autostart is pending (non-auto interactive discuss
   // is user-driven). Runs before `isAutoActive` early return so pending
   // discussions (where isAutoActive may be false) still get recovered.
-  if (maybeHandleEmptyIntentTurn(event, isAutoActive())) return;
+  if (maybeHandleEmptyIntentTurn(event, isAutoActive(), basePath)) return;
 
   if (!isAutoActive()) return;
 
@@ -295,12 +315,18 @@ export async function handleAgentEnd(
   }
 
   if (isObjectRecord(lastMsg) && "stopReason" in lastMsg && lastMsg.stopReason === "aborted") {
+    if (isAutoCompletionStopInProgress()) {
+      resetRetryState(retryState);
+      resolveAgentEnd(event);
+      return;
+    }
+
     // Empty content with aborted stopReason is a non-fatal agent stop (the LLM
     // chose to end without producing output). Only pause on genuine fatal aborts
     // that carry error context — e.g. errorMessage field or non-empty content
     // indicating a mid-stream failure. (#2695)
     const content = "content" in lastMsg ? lastMsg.content : undefined;
-    const hasEmptyContent = Array.isArray(content) && content.length === 0;
+    const hasEmptyContent = _hasEmptyAgentEndContent(content);
     const hasErrorMessage = "errorMessage" in lastMsg && !!lastMsg.errorMessage;
 
     if (hasEmptyContent && !hasErrorMessage) {
@@ -326,6 +352,11 @@ export async function handleAgentEnd(
     // errorMessage looks uninformative.
     const rawErrorMsg = ("errorMessage" in lastMsg && lastMsg.errorMessage) ? String(lastMsg.errorMessage) : "";
     if (isUserInitiatedAbortMessage(rawErrorMsg)) {
+      if (isAutoCompletionStopInProgress()) {
+        resetRetryState(retryState);
+        resolveAgentEnd(event);
+        return;
+      }
       resolveAgentEndCancelled({
         message: rawErrorMsg,
         category: "aborted",
@@ -340,6 +371,17 @@ export async function handleAgentEnd(
       rawErrorMsg,
       "content" in lastMsg ? lastMsg.content : undefined,
     );
+    if (
+      isAutoCompletionStopInProgress() &&
+      isTerminalDeletedWorktreeProviderError(`${rawErrorMsg}\n${displayMsg}`)
+    ) {
+      resetRetryState(retryState);
+      logWarning(
+        "bootstrap",
+        `Ignoring stale deleted-worktree provider error during terminal completion reroot: ${displayMsg || rawErrorMsg}`,
+      );
+      return;
+    }
     const errorDetail = displayMsg ? `: ${displayMsg}` : "";
     const explicitRetryAfterMs = ("retryAfterMs" in lastMsg && typeof lastMsg.retryAfterMs === "number") ? lastMsg.retryAfterMs : undefined;
 

package/src/resources/extensions/gsd/bootstrap/db-tools.ts

@@ -487,17 +487,18 @@ export function registerDbTools(pi: ExtensionAPI): void {
     promptGuidelines: [
       "Use gsd_plan_milestone for milestone planning instead of writing ROADMAP.md directly.",
       "Keep parameters flat and provide the full milestone planning payload, including slices.",
+      "Milestone and slice titles must not contain forward slash (/), en dash, or em dash characters.",
       "The tool validates input, writes milestone and slice planning data transactionally, renders ROADMAP.md from DB, and clears both state and parse caches after success.",
       "Use the canonical name gsd_plan_milestone; gsd_milestone_plan is only an alias.",
     ],
     parameters: Type.Object({
       // ── Core identification + content (required) ──────────────────────
       milestoneId: Type.String({ description: "Milestone ID (e.g. M001)" }),
-      title: Type.String({ description: "Milestone title" }),
+      title: Type.String({ description: "Milestone title; must not contain forward slash (/), en dash, or em dash characters" }),
       vision: Type.String({ description: "Milestone vision" }),
       slices: Type.Array(Type.Object({
         sliceId: Type.String({ description: "Slice ID (e.g. S01)" }),
-        title: Type.String({ description: "Slice title" }),
+        title: Type.String({ description: "Slice title; must not contain forward slash (/), en dash, or em dash characters" }),
         risk: Type.String({ description: "Slice risk" }),
         depends: Type.Array(Type.String(), { description: "Slice dependency IDs" }),
         demo: Type.String({ description: "Roadmap demo text / After this" }),
@@ -570,10 +571,10 @@ export function registerDbTools(pi: ExtensionAPI): void {
         title: Type.String({ description: "Task title" }),
         description: Type.String({ description: "Task description / steps block" }),
         estimate: Type.String({ description: "Task estimate string" }),
-        files: Type.Array(Type.String(), { description: "Files likely touched" }),
+        files: Type.Array(Type.String(), { description: "Array<string> of files likely touched; pass [\"path\"] or [], never a single string" }),
         verify: Type.String({ description: "Verification command or block" }),
-        inputs: Type.Array(Type.String(), { description: "Input files or references" }),
-        expectedOutput: Type.Array(Type.String(), { description: "Expected output files or artifacts" }),
+        inputs: Type.Array(Type.String(), { description: "Array<string> of input files or references; pass [\"path\"] or [], never a single string" }),
+        expectedOutput: Type.Array(Type.String(), { description: "Array<string> of expected output files or artifacts; pass [\"path\"] or [], never a single string" }),
         observabilityImpact: Type.Optional(Type.String({ description: "Task observability impact" })),
       }), { description: "Planned tasks for the slice" }),
       // ── Enrichment metadata (optional — defaults to empty) ────────────
@@ -650,10 +651,10 @@ export function registerDbTools(pi: ExtensionAPI): void {
       title: Type.String({ description: "Task title" }),
       description: Type.String({ description: "Task description / steps block" }),
       estimate: Type.String({ description: "Task estimate string" }),
-      files: Type.Array(Type.String(), { description: "Files likely touched" }),
+      files: Type.Array(Type.String(), { description: "Array<string> of files likely touched; pass [\"path\"] or [], never a single string" }),
       verify: Type.String({ description: "Verification command or block" }),
-      inputs: Type.Array(Type.String(), { description: "Input files or references" }),
-      expectedOutput: Type.Array(Type.String(), { description: "Expected output files or artifacts" }),
+      inputs: Type.Array(Type.String(), { description: "Array<string> of input files or references; pass [\"path\"] or [], never a single string" }),
+      expectedOutput: Type.Array(Type.String(), { description: "Array<string> of expected output files or artifacts; pass [\"path\"] or [], never a single string" }),
       observabilityImpact: Type.Optional(Type.String({ description: "Task observability impact" })),
       // Single-writer v3 audit trail (Stream 2): caller-provided actor identity + causation.
       actorName: Type.Optional(Type.String({ description: "Caller-provided actor identity for the audit trail (e.g. 'executor-01', 'gsd-orchestrator')" })),

package/src/resources/extensions/gsd/bootstrap/register-hooks.ts

@@ -16,7 +16,7 @@ import { canonicalToolName, clearDiscussionFlowState, isDepthConfirmationAnswer,
 import { resolveManifest } from "../unit-context-manifest.js";
 import { isBlockedStateFile, isBashWriteToStateFile, BLOCKED_WRITE_ERROR } from "../write-intercept.js";
 import { loadFile, saveFile, formatContinue } from "../files.js";
-import { getAutoRuntimeSnapshot, isAutoActive, isAutoPaused, markToolEnd, markToolStart, recordToolInvocationError } from "../auto-runtime-state.js";
+import { clearToolInvocationError, getAutoRuntimeSnapshot, isAutoActive, isAutoPaused, markToolEnd, markToolStart, recordToolInvocationError } from "../auto-runtime-state.js";
 
 import { checkToolCallLoop, resetToolCallLoopGuard } from "./tool-call-loop-guard.js";
 import { saveActivityLog } from "../activity-log.js";
@@ -31,6 +31,7 @@ import { resolveWorktreeProjectRoot } from "../worktree-root.js";
 import { extractSubagentAgentClasses } from "./subagent-input.js";
 import { approvalGateIdForUnit, isExplicitApprovalResponse, shouldPauseForUserApprovalQuestion } from "../user-input-boundary.js";
 import { resolveSkillManifest } from "../skill-manifest.js";
+import { getGuidedUnitContext } from "../guided-unit-context.js";
 
 let approvalQuestionAbortInFlight = false;
 
@@ -143,7 +144,7 @@ const AUTO_UNIT_SCOPED_TOOLS: Record<string, readonly string[]> = {
   "plan-slice": ["gsd_plan_slice", "gsd_plan_task", "gsd_decision_save"],
   "refine-slice": ["gsd_plan_slice", "gsd_plan_task", "gsd_decision_save"],
   "replan-slice": ["gsd_replan_slice", "gsd_plan_task", "gsd_decision_save"],
-  "complete-slice": ["gsd_slice_complete", "gsd_decision_save", "gsd_requirement_update", "subagent"],
+  "complete-slice": ["gsd_slice_complete", "gsd_task_reopen", "gsd_replan_slice", "gsd_decision_save", "gsd_requirement_update", "subagent"],
   "reassess-roadmap": ["gsd_reassess_roadmap"],
   "execute-task": ["gsd_task_complete", "gsd_decision_save"],
   "execute-task-simple": ["gsd_task_complete", "gsd_decision_save"],
@@ -423,6 +424,10 @@ export function registerHooks(
   pi: ExtensionAPI,
   ecosystemHandlers: GSDEcosystemBeforeAgentStartHandler[],
 ): void {
+  // ADR-005 Phase 3b: surface pi-ai ProviderSwitchReport via audit, notification, and counter.
+  // Idempotent — only the first registerHooks call installs.
+  void import("../provider-switch-observer.js").then((m) => m.installProviderSwitchObserver());
+
   pi.on("session_start", async (_event, ctx) => {
     const basePath = contextBasePath(ctx);
     initSessionNotifications(ctx);
@@ -480,6 +485,8 @@ export function registerHooks(
     }
     await loadToolApiKeysForSession();
     if (!isAutoActive()) {
+      ctx.ui.setWidget("gsd-progress", undefined);
+      ctx.ui.setWidget("gsd-outcome", undefined);
       const { initHealthWidget } = await import("../health-widget.js");
       initHealthWidget(ctx);
     } else {
@@ -766,7 +773,8 @@ export function registerHooks(
     // subagent dispatch. Closes the b23 bug class where a discuss-milestone
     // turn used the host Edit tool to modify user source files.
     const dash = getAutoRuntimeSnapshot();
-    const activeUnitType = dash.currentUnit?.type;
+    const guidedUnit = getGuidedUnitContext(discussionBasePath);
+    const activeUnitType = dash.currentUnit?.type ?? guidedUnit?.unitType;
     if (activeUnitType) {
       const manifest = resolveManifest(activeUnitType);
       if (manifest) {
@@ -785,7 +793,7 @@ export function registerHooks(
         const planningGuard = shouldBlockPlanningUnit(
           event.toolName,
           planningInput,
-          dash.basePath || discussionBasePath,
+          dash.basePath || guidedUnit?.basePath || discussionBasePath,
           activeUnitType,
           manifest.tools,
           agentClasses,
@@ -892,6 +900,8 @@ export function registerHooks(
       // Let recordToolInvocationError classify the failure so non-gsd_ harness
       // errors and deterministic policy rejections are handled consistently.
       recordToolInvocationError(event.toolName, errorText);
+    } else if (isAutoActive()) {
+      clearToolInvocationError();
     }
     const toolName = canonicalToolName(event.toolName);
     if (toolName !== "ask_user_questions") return;
@@ -1009,6 +1019,8 @@ export function registerHooks(
       // Let recordToolInvocationError classify the failure so non-gsd_ harness
       // errors and deterministic policy rejections are handled consistently.
       recordToolInvocationError(event.toolName, errorText);
+    } else if (isAutoActive()) {
+      clearToolInvocationError();
     }
     // Safety harness: record tool execution results for evidence cross-referencing
     if (isAutoActive()) {

package/src/resources/extensions/gsd/bootstrap/register-shortcuts.ts

@@ -1,3 +1,6 @@
+// Project/App: GSD-2
+// File Purpose: Registers GSD keyboard shortcuts for dashboard, notifications, and parallel overlays.
+
 import { existsSync } from "node:fs";
 import { join } from "node:path";
 
@@ -39,18 +42,12 @@ export function registerShortcuts(pi: ExtensionAPI): void {
   };
 
   const openNotificationsOverlay = async (ctx: ExtensionContext) => {
-    const { GSDNotificationOverlay } = await import("../notification-overlay.js");
+    const { GSDNotificationOverlay, notificationOverlayOptions } = await import("../notification-overlay.js");
     await ctx.ui.custom<boolean>(
       (tui, theme, _kb, done) => new GSDNotificationOverlay(tui, theme, () => done(true)),
       {
         overlay: true,
-        overlayOptions: {
-          width: "80%",
-          minWidth: 60,
-          maxHeight: "88%",
-          anchor: "center",
-          backdrop: true,
-        },
+        overlayOptions: notificationOverlayOptions(),
       },
     );
   };

package/src/resources/extensions/gsd/bootstrap/subagent-input.ts

@@ -1,20 +1,32 @@
 export function extractSubagentAgentClasses(input: unknown): string[] {
   if (!input || typeof input !== "object") return [];
 
-  const record = input as Record<string, unknown>;
   const agentClasses: string[] = [];
+  const visited = new WeakSet<object>();
   const addAgentClass = (value: unknown): void => {
-    if (typeof value === "string" && value.trim().length > 0) agentClasses.push(value.trim());
+    if (typeof value !== "string") return;
+    const normalized = value.trim().replace(/\.md$/i, "");
+    if (normalized.length > 0) agentClasses.push(normalized);
   };
-  const addFromItems = (value: unknown): void => {
+
+  const visitItems = (value: unknown): void => {
     if (!Array.isArray(value)) return;
     for (const item of value) {
-      if (item && typeof item === "object") addAgentClass((item as Record<string, unknown>).agent);
+      visit(item);
     }
   };
 
-  addAgentClass(record.agent);
-  addFromItems(record.tasks);
-  addFromItems(record.chain);
+  const visit = (value: unknown): void => {
+    if (!value || typeof value !== "object") return;
+    if (visited.has(value)) return;
+    visited.add(value);
+    const record = value as Record<string, unknown>;
+    addAgentClass(record.agent);
+    visitItems(record.tasks);
+    visitItems(record.chain);
+    visitItems(record.parallel);
+  };
+
+  visit(input);
   return agentClasses;
 }

package/src/resources/extensions/gsd/bootstrap/system-context.ts

@@ -13,6 +13,7 @@ import { resolveAllSkillReferences, renderPreferencesForSystemPrompt, loadEffect
 import { resolveModelWithFallbacksForUnit } from "../preferences-models.js";
 import { resolveSkillReference } from "../preferences-skills.js";
 import { resolveGsdRootFile, resolveSliceFile, resolveSlicePath, resolveTaskFile, resolveTaskFiles, resolveTasksDir, relSliceFile, relSlicePath, relTaskFile } from "../paths.js";
+import { extractIntroAndRules } from "../knowledge-parser.js";
 import { ensureCodebaseMapFresh, readCodebaseMap } from "../codebase-generator.js";
 import { hasSkillSnapshot, detectNewSkills, formatSkillsXml } from "../skill-discovery.js";
 import { getActiveAutoWorktreeContext } from "../auto-worktree.js";
@@ -131,9 +132,14 @@ export async function buildBeforeAgentStartResult(
     logWarning("bootstrap", `cmux prompt setup skipped: ${(e as Error).message}`);
   }
 
+  const ctxProjectRoot = (ctx as { projectRoot?: unknown }).projectRoot;
+  const basePath = typeof ctxProjectRoot === "string" && ctxProjectRoot.length > 0
+    ? ctxProjectRoot
+    : process.cwd();
+
   let preferenceBlock = "";
   if (loadedPreferences) {
-    const cwd = process.cwd();
+    const cwd = basePath;
     const report = resolveAllSkillReferences(loadedPreferences.preferences, cwd);
     preferenceBlock = `\n\n${renderPreferencesForSystemPrompt(loadedPreferences.preferences, report.resolutions)}`;
     if (report.warnings.length > 0) {
@@ -144,14 +150,6 @@ export async function buildBeforeAgentStartResult(
     }
   }
 
-  const { block: knowledgeBlock, globalSizeKb } = loadKnowledgeBlock(gsdHome(), process.cwd());
-  if (globalSizeKb > 4) {
-    ctx.ui.notify(
-      `GSD: ~/.gsd/agent/KNOWLEDGE.md is ${globalSizeKb.toFixed(1)}KB — consider trimming to keep system prompt lean.`,
-      "warning",
-    );
-  }
-
   // ADR-013 step 5: opportunistic decisions->memories backfill. Idempotent
   // and best-effort — first run absorbs the existing decisions table into
   // the memory store; subsequent runs are a single sentinel SELECT.
@@ -159,12 +157,50 @@ export async function buildBeforeAgentStartResult(
     const { backfillDecisionsToMemories } = await import("../memory-backfill.js");
     const written = backfillDecisionsToMemories();
     if (written > 0) {
-      ctx.ui.notify(`GSD: backfilled ${written} decision${written === 1 ? "" : "s"} into the memory store (ADR-013).`, "info");
+      ctx.ui.notify(`GSD: backfilled ${written} decision${written === 1 ? "" : "s"} into the memory store.`, "info");
     }
   } catch (e) {
     logWarning("bootstrap", `decisions backfill failed: ${(e as Error).message}`);
   }
 
+  // ADR-013 Stage 2b: KNOWLEDGE.md Patterns + Lessons backfill, then
+  // re-render the hybrid projection (manual Rules + projected Patterns +
+  // projected Lessons). Both are idempotent and best-effort — failures here
+  // can't block agent startup.
+  try {
+    const { backfillKnowledgeToMemories } = await import("../knowledge-backfill.js");
+    const writtenK = backfillKnowledgeToMemories(basePath);
+    if (writtenK > 0) {
+      ctx.ui.notify(`GSD: backfilled ${writtenK} KNOWLEDGE.md row${writtenK === 1 ? "" : "s"} into the memory store.`, "info");
+    }
+  } catch (e) {
+    logWarning("bootstrap", `KNOWLEDGE.md backfill failed: ${(e as Error).message}`);
+  }
+  try {
+    const { renderKnowledgeProjection } = await import("../knowledge-projection.js");
+    renderKnowledgeProjection(basePath);
+  } catch (e) {
+    logWarning("bootstrap", `KNOWLEDGE.md projection render failed: ${(e as Error).message}`);
+  }
+
+  // ADR-013 step 6 preflight: warn when decisions / KNOWLEDGE.md rows are not
+  // yet in the memories table. Read-only; never throws. Runs after the two
+  // backfills above so the gap report reflects post-backfill state.
+  try {
+    const { reportConsolidationGaps } = await import("../memory-consolidation-scanner.js");
+    reportConsolidationGaps(basePath);
+  } catch (e) {
+    logWarning("bootstrap", `memory consolidation scan failed: ${(e as Error).message}`);
+  }
+
+  const { block: knowledgeBlock, globalSizeKb } = loadKnowledgeBlock(gsdHome(), basePath);
+  if (globalSizeKb > 4) {
+    ctx.ui.notify(
+      `GSD: ~/.gsd/agent/KNOWLEDGE.md is ${globalSizeKb.toFixed(1)}KB — consider trimming to keep system prompt lean.`,
+      "warning",
+    );
+  }
+
   let newSkillsBlock = "";
   if (hasSkillSnapshot()) {
     const newSkills = detectNewSkills();
@@ -370,7 +406,9 @@ export async function loadMemoryBlock(
 }
 
 export function loadKnowledgeBlock(gsdHomeDir: string, cwd: string): { block: string; globalSizeKb: number } {
-  // 1. Global knowledge (~/.gsd/agent/KNOWLEDGE.md) — cross-project, user-maintained
+  // 1. Global knowledge (~/.gsd/agent/KNOWLEDGE.md) — cross-project,
+  //    user-maintained. NOT migrated to memories (which are project-scoped),
+  //    so the full file is injected unchanged.
   let globalKnowledge = "";
   let globalSizeKb = 0;
   const globalKnowledgePath = join(gsdHomeDir, "agent", "KNOWLEDGE.md");
@@ -386,13 +424,18 @@ export function loadKnowledgeBlock(gsdHomeDir: string, cwd: string): { block: st
     }
   }
 
-  // 2. Project knowledge (.gsd/KNOWLEDGE.md) — project-specific
+  // 2. Project knowledge (.gsd/KNOWLEDGE.md) — project-specific.
+  //    ADR-013 Stage 2b: Patterns and Lessons are projected from the
+  //    memories table and already reach the LLM via loadMemoryBlock. Inject
+  //    only the intro prose + `## Rules` section here to avoid duplicating
+  //    Patterns/Lessons content in the prompt. Rules stay manual per
+  //    ADR-013 line 39 and have no memory equivalent.
   let projectKnowledge = "";
   const knowledgePath = resolveGsdRootFile(cwd, "KNOWLEDGE");
   if (existsSync(knowledgePath)) {
     try {
-      const content = readFileSync(knowledgePath, "utf-8").trim();
-      if (content) projectKnowledge = content;
+      const raw = readFileSync(knowledgePath, "utf-8").trim();
+      if (raw) projectKnowledge = extractIntroAndRules(raw).trim();
     } catch (e) {
       logWarning("bootstrap", `project knowledge file read failed: ${(e as Error).message}`);
     }
@@ -411,7 +454,7 @@ export function loadKnowledgeBlock(gsdHomeDir: string, cwd: string): { block: st
   }
   const body = limitKnowledgeBlock(parts.join("\n\n"), getKnowledgeCharLimit());
   return {
-    block: `\n\n[KNOWLEDGE — Rules, patterns, and lessons learned]\n\n${body}`,
+    block: `\n\n[KNOWLEDGE — Rules from KNOWLEDGE.md (Patterns and Lessons reach the LLM via the memory block)]\n\n${body}`,
     globalSizeKb,
   };
 }

package/src/resources/extensions/gsd/bootstrap/write-gate.ts

@@ -5,7 +5,7 @@ import { isAbsolute, join, relative, resolve, sep } from "node:path";
 import { minimatch } from "minimatch";
 
 import { getIsolationMode } from "../preferences.js";
-import type { ToolsPolicy } from "../unit-context-manifest.js";
+import { compileSubagentPermissionContract, type ToolsPolicy } from "../unit-context-manifest.js";
 import { logWarning } from "../workflow-logger.js";
 import { isGsdWorktreePath, resolveWorktreeProjectRoot } from "../worktree-root.js";
 
@@ -65,6 +65,7 @@ const QUEUE_SAFE_TOOLS = new Set([
  *   true / false        — shell no-ops / test exit codes
  */
 const BASH_READ_ONLY_RE = /^\s*(cat|head|tail|less|more|wc|file|stat|du|df|which|type|echo|printf|ls|find|grep|rg|awk|sed\b(?!.*-i)|sort|uniq|diff|comm|tr|cut|tee\s+-a\s+\/dev\/null|git\s+(log|show|diff|status|branch|tag|remote|rev-parse|ls-files|blame|shortlog|describe|stash\s+list|config\s+--get|cat-file)|gh\s+(issue|pr|api|repo|release)\s+(view|list|diff|status|checks)|mkdir\s+-p\s+\.gsd|rtk\s|npm\s+run\s+(test|test:\w+|lint|lint:\w+|typecheck|type-check|type-check:\w+|check|verify|audit|outdated|format:check|ci|validate)\b|npm\s+(ls|list|info|view|show|outdated|audit|explain|doctor|ping|--version|-v)\b|npx\s|tsx\s|node\s+(--print|--version|-v\b)|python[23]?\s+(-c\s+'[^']*'|--version|-V\b|-m\s+(pip\s+show|pip\s+list|site))|pip[23]?\s+(show|list|freeze|check|index\s+versions)\b|jq\s|yq\s|curl\s+(-s\b|--silent\b)(?!\s+[^|>]*\s-[oO]\b)(?!\s+[^|>]*\s--output\b)[^|>]*$|openssl\s+(version|x509|s_client)|env\b|printenv\b|true\b|false\b)/;
+const BASH_VERIFICATION_RE = /^\s*(npm\s+(run\s+(build|test|test:\w+|lint|lint:\w+|typecheck|type-check|verify|ci|validate)\b|test\b)|pnpm\s+(build|test|lint|typecheck|verify)\b|yarn\s+(build|test|lint|typecheck|verify)\b|vitest\b|jest\b|go\s+test\b)/;
 
 interface InMemoryWriteGateState {
   verifiedDepthMilestones: Set<string>;
@@ -767,6 +768,9 @@ function blockReason(unitType: string, mode: string, what: string): string {
  *                    and listed in the policy's allowedSubagents.
  *   - "docs"       → like "planning" but also allows writes to paths
  *                    matching `allowedPathGlobs` relative to basePath.
+ *   - "verification"
+ *                  → allows Bash for project verification commands, but keeps
+ *                    writes restricted to .gsd/ and blocks subagent dispatch.
  *
  * `pathOrCommand` is the file path for write/edit-shaped tools and the
  * shell command for bash. Other tools ignore this argument.
@@ -804,14 +808,15 @@ export function shouldBlockPlanningUnit(
     return { block: true, reason: blockReason(unitType, policy.mode, `tool "${tool}" is not on the read-only allowlist`) };
   }
 
-  // planning / planning-dispatch / docs modes share the same surface for safe tools, bash, and subagent.
+  // planning / planning-dispatch / docs / verification modes share the same surface for safe tools, bash, and subagent.
   if (PLANNING_SAFE_TOOLS.has(tool)) return { block: false };
   if (tool.startsWith("gsd_")) return { block: false };
 
   if (PLANNING_SUBAGENT_TOOLS.has(tool)) {
     if (policy.mode === "planning-dispatch") {
       const requested = (agentClasses ?? []).map(a => a.trim()).filter(Boolean);
-      const allowedSubagents = Array.isArray(policy.allowedSubagents) ? policy.allowedSubagents : [];
+      const dispatchContract = compileSubagentPermissionContract(policy);
+      const allowedSubagents = dispatchContract.allowedSubagents;
       const allowed = new Set(allowedSubagents);
       // When agentClasses is undefined, the caller has not been updated to extract
       // agent identities yet. Block and warn so stale callers surface in telemetry
@@ -861,6 +866,17 @@ export function shouldBlockPlanningUnit(
   }
 
   if (tool === "bash") {
+    if (policy.mode === "verification") {
+      if (BASH_VERIFICATION_RE.test(pathOrCommand) || BASH_READ_ONLY_RE.test(pathOrCommand)) return { block: false };
+      return {
+        block: true,
+        reason: blockReason(
+          unitType,
+          policy.mode,
+          `bash is restricted to build/test verification commands (npm run build, npm test, etc.); cannot run "${pathOrCommand.slice(0, 80)}${pathOrCommand.length > 80 ? "…" : ""}"`,
+        ),
+      };
+    }
     if (BASH_READ_ONLY_RE.test(pathOrCommand)) return { block: false };
     return {
       block: true,