gsd-pi 2.75.0 → 2.76.0-dev.b072ebb73

package/dist/resources/extensions/gsd/auto.js

@@ -45,12 +45,14 @@ import { atomicWriteSync } from "./atomic-write.js";
 import { autoCommitCurrentBranch, captureIntegrationBranch, detectWorktreeName, getCurrentBranch, getMainBranch, setActiveMilestoneId, } from "./worktree.js";
 import { GitServiceImpl } from "./git-service.js";
 import { getPriorSliceCompletionBlocker } from "./dispatch-guard.js";
-import { createAutoWorktree, enterAutoWorktree, teardownAutoWorktree, isInAutoWorktree, getAutoWorktreePath, mergeMilestoneToMain, autoWorktreeBranch, syncWorktreeStateBack, syncProjectRootToWorktree, checkResourcesStale, escapeStaleWorktree, } from "./auto-worktree.js";
+import { createAutoWorktree, enterAutoWorktree, enterBranchModeForMilestone, teardownAutoWorktree, isInAutoWorktree, getAutoWorktreePath, mergeMilestoneToMain, autoWorktreeBranch, syncWorktreeStateBack, syncProjectRootToWorktree, checkResourcesStale, escapeStaleWorktree, } from "./auto-worktree.js";
 import { pruneQueueOrder } from "./queue-order.js";
+import { startCommandPolling as _startCommandPolling, isRemoteConfigured } from "../remote-questions/manager.js";
 import { debugLog, isDebugEnabled, writeDebugSummary } from "./debug-logger.js";
 import { reconcileMergeState, } from "./auto-recovery.js";
 import { resolveDispatch, DISPATCH_RULES } from "./auto-dispatch.js";
 import { getErrorMessage } from "./error-utils.js";
+import { recoverFailedMigration } from "./migrate-external.js";
 import { initRegistry, convertDispatchRules } from "./rule-registry.js";
 import { emitJournalEvent as _emitJournalEvent } from "./journal.js";
 import { updateProgressWidget as _updateProgressWidget, updateSliceProgressCache, clearSliceProgressCache, hideFooter, } from "./auto-dashboard.js";
@@ -64,7 +66,7 @@ import { runPostUnitVerification } from "./auto-verification.js";
 import { autoCommitUnit, postUnitPreVerification, postUnitPostVerification, } from "./auto-post-unit.js";
 import { bootstrapAutoSession, openProjectDbIfPresent } from "./auto-start.js";
 import { initHealthWidget } from "./health-widget.js";
-import { autoLoop, resolveAgentEnd, resolveAgentEndCancelled, _resetPendingResolve, isSessionSwitchInFlight } from "./auto-loop.js";
+import { runLegacyAutoLoop, runUokKernelLoop, resolveAgentEnd, resolveAgentEndCancelled, _resetPendingResolve, isSessionSwitchInFlight } from "./auto-loop.js";
 import { runAutoLoopWithUok } from "./uok/kernel.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { WorktreeResolver, } from "./worktree-resolver.js";
@@ -142,6 +144,7 @@ export function startAutoDetached(ctx, pi, base, verboseMode, options) {
         debugLog("auto-start-failed", { error: message });
     });
 }
+/** Returns true if the project is configured for `isolation:worktree` mode. */
 export function shouldUseWorktreeIsolation() {
     const prefs = loadEffectiveGSDPreferences()?.preferences?.git;
     if (prefs?.isolation === "worktree")
@@ -185,6 +188,26 @@ function deregisterSigtermHandler() {
     _deregisterSigtermHandler(s.sigtermHandler);
     s.sigtermHandler = null;
 }
+/**
+ * Wrapper: start background command polling for the configured remote channel
+ * (currently Telegram only). Stores the cleanup function on the session so
+ * every exit path can stop the interval via stopCommandPolling().
+ * No-op when no remote channel is configured.
+ */
+function startAutoCommandPolling(basePath) {
+    if (!isRemoteConfigured())
+        return;
+    // Clear any existing interval before starting a new one (e.g. resume path).
+    stopAutoCommandPolling();
+    s.commandPollingCleanup = _startCommandPolling(basePath);
+}
+/** Wrapper: stop background command polling and clear the stored cleanup. */
+function stopAutoCommandPolling() {
+    if (s.commandPollingCleanup) {
+        s.commandPollingCleanup();
+        s.commandPollingCleanup = null;
+    }
+}
 export function getAutoDashboardData() {
     const ledger = getLedger();
     const totals = ledger ? getProjectTotals(ledger.units) : null;
@@ -248,6 +271,14 @@ export function getActiveRunDir() {
 export function getAutoModeStartModel() {
     return s.autoModeStartModel;
 }
+/**
+ * Update the dashboard-facing dispatched model label.
+ * Used when runtime recovery switches models mid-unit (e.g. provider fallback)
+ * so the AUTO box reflects the active model immediately.
+ */
+export function setCurrentDispatchedModelId(model) {
+    s.currentDispatchedModelId = model ? `${model.provider}/${model.id}` : null;
+}
 // Tool tracking — delegates to auto-tool-tracking.ts
 export function markToolStart(toolCallId, toolName) {
     _markToolStart(toolCallId, s.active, toolName);
@@ -392,6 +423,7 @@ function handleLostSessionLock(ctx, lockStatus) {
     s.paused = false;
     deactivateGSD();
     clearUnitTimeout();
+    stopAutoCommandPolling();
     restoreProjectRootEnv();
     restoreMilestoneLockEnv();
     deregisterSigtermHandler();
@@ -427,6 +459,7 @@ function cleanupAfterLoopExit(ctx) {
     s.active = false;
     deactivateGSD();
     clearUnitTimeout();
+    stopAutoCommandPolling();
     restoreProjectRootEnv();
     restoreMilestoneLockEnv();
     // Clear crash lock and release session lock so the next `/gsd next` does
@@ -471,6 +504,7 @@ export async function stopAuto(ctx, pi, reason) {
         // ── Step 1: Timers and locks ──
         try {
             clearUnitTimeout();
+            stopAutoCommandPolling();
             if (lockBase())
                 clearLock(lockBase());
             if (lockBase())
@@ -724,6 +758,7 @@ export async function pauseAuto(ctx, _pi, _errorContext) {
     if (!s.active)
         return;
     clearUnitTimeout();
+    stopAutoCommandPolling();
     // Flush queued follow-up messages (#3512).
     // Late async notifications (async_job_result, gsd-auto-wrapup) can trigger
     // extra LLM turns after pause. Flush them the same way run-unit.ts does.
@@ -814,6 +849,7 @@ function buildResolverDeps() {
         teardownAutoWorktree,
         createAutoWorktree,
         enterAutoWorktree,
+        enterBranchModeForMilestone,
         getAutoWorktreePath,
         autoCommitCurrentBranch,
         getCurrentBranch,
@@ -941,6 +977,11 @@ function buildLoopDeps() {
         emitJournalEvent: (entry) => _emitJournalEvent(s.basePath, entry),
     };
 }
+/**
+ * Start auto-mode. Handles both fresh-start and resume paths, sets up session
+ * state, enters the milestone worktree or branch, and dispatches the first unit.
+ * No-ops if auto-mode is already active.
+ */
 export async function startAuto(ctx, pi, base, verboseMode, options) {
     if (s.active) {
         debugLog("startAuto", { phase: "already-active", skipping: true });
@@ -956,6 +997,12 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
     }
     // Escape stale worktree cwd from a previous milestone (#608).
     base = escapeStaleWorktree(base);
+    // Heal .gsd.migrating before any branching — covers both fresh-start and
+    // resume paths (#4416). The matching call in auto-start.ts covers the
+    // bootstrap-only path; this call ensures the resume path is also protected.
+    if (recoverFailedMigration(base)) {
+        ctx.ui.notify("Recovered unfinished migration (.gsd.migrating → .gsd).", "info");
+    }
     const freshStartAssessment = interruptedAssessment
         ?? await assessInterruptedSession(base);
     if (freshStartAssessment.classification === "running") {
@@ -1112,9 +1159,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
             const level = to === "red" ? "error" : to === "yellow" ? "warning" : "info";
             ctx.ui.notify(summary, level);
         });
-        // ── Auto-worktree: re-enter worktree on resume ──
+        // ── Auto-worktree / branch-mode: re-enter on resume ──
         if (s.currentMilestoneId &&
-            shouldUseWorktreeIsolation() &&
+            getIsolationMode() !== "none" &&
             s.originalBasePath &&
             !isInAutoWorktree(s.basePath) &&
             !detectWorktreeName(s.basePath) &&
@@ -1179,12 +1226,14 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         writeLock(lockBase(), "resuming", s.currentMilestoneId ?? "unknown");
         logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "progress");
         captureProjectRootEnv(s.originalBasePath || s.basePath);
+        startAutoCommandPolling(s.basePath);
         await runAutoLoopWithUok({
             ctx,
             pi,
             s,
             deps: buildLoopDeps(),
-            runLegacyLoop: autoLoop,
+            runKernelLoop: runUokKernelLoop,
+            runLegacyLoop: runLegacyAutoLoop,
         });
         cleanupAfterLoopExit(ctx);
         return;
@@ -1208,35 +1257,18 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         logWarning("engine", `cmux sync failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
     }
     logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, requestedStepMode ? "Step-mode started." : "Auto-mode started.", "progress");
+    startAutoCommandPolling(s.basePath);
     // Dispatch the first unit
     await runAutoLoopWithUok({
         ctx,
         pi,
         s,
         deps: buildLoopDeps(),
-        runLegacyLoop: autoLoop,
+        runKernelLoop: runUokKernelLoop,
+        runLegacyLoop: runLegacyAutoLoop,
     });
     cleanupAfterLoopExit(ctx);
 }
-// ─── Agent End Handler ────────────────────────────────────────────────────────
-/**
- * Deprecated thin wrapper — kept as export for backward compatibility.
- * The actual agent_end processing now happens via resolveAgentEnd() in auto-loop.ts,
- * which is called directly from index.ts. The autoLoop() while loop handles all
- * post-unit processing (verification, hooks, dispatch) that this function used to do.
- *
- * If called by straggler code, it simply resolves the pending promise so the loop
- * can continue.
- */
-export async function handleAgentEnd(ctx, pi) {
-    if (!s.active || !s.cmdCtx) {
-        // Even when inactive, resolve any pending promise so the loop is unblocked.
-        resolveAgentEndCancelled();
-        return;
-    }
-    clearUnitTimeout();
-    resolveAgentEnd({ messages: [] });
-}
 // describeNextUnit is imported from auto-dashboard.ts and re-exported
 export { describeNextUnit } from "./auto-dashboard.js";
 /** Thin wrapper: delegates to auto-dashboard.ts, passing state accessors. */

package/dist/resources/extensions/gsd/bootstrap/agent-end-recovery.js

@@ -1,6 +1,6 @@
 import { logWarning } from "../workflow-logger.js";
 import { checkAutoStartAfterDiscuss } from "../guided-flow.js";
-import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto } from "../auto.js";
+import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
 import { isSessionSwitchInFlight, resolveAgentEnd } from "../auto-loop.js";
@@ -106,26 +106,11 @@ export async function handleAgentEnd(pi, event, ctx) {
         const explicitRetryAfterMs = ("retryAfterMs" in lastMsg && typeof lastMsg.retryAfterMs === "number") ? lastMsg.retryAfterMs : undefined;
         // ── 1. Classify using rawErrorMsg to avoid prose false-positives ────
         const cls = classifyError(rawErrorMsg, explicitRetryAfterMs);
-        // ── 1b. Defer to Core RetryHandler for transient errors ─────────────
-        // The Core RetryHandler (agent-session.ts) processes retryable errors
-        // AFTER this extension handler, in the same _processAgentEvent() call.
-        // For transient errors (overloaded, rate limit, server), the Core will
-        // retry in-context — same session, same conversation — which is strictly
-        // better than our Layer 2 pause+resume (which creates a new session).
-        //
-        // If we react here AND the Core also retries, we race: pauseAuto tears
-        // down the session while agent.continue() starts a new turn.
-        //
-        // Solution: Do nothing for transient errors. The Core RetryHandler
-        // runs next in _processAgentEvent and will either:
-        //   a) Retry successfully → new agent_end (success) → we see it next time
-        //   b) Exhaust retries → the agent stays idle, autoLoop's unit timeout
-        //      or stuck detection handles it
-        //
-        // We do NOT call resolveAgentEnd here — that would unblock autoLoop
-        // prematurely while the Core is still retrying in the same session.
-        // We do NOT call pauseAuto — that would tear down the session.
-        if (isTransient(cls)) {
+        // ── 1b. Defer to Core RetryHandler for most transient errors ────────
+        // Core retries transient failures in-session after this handler.
+        // Keep that behavior for non-rate-limit classes to avoid pause/retry races,
+        // but let rate-limit continue into model fallback logic below (#4373).
+        if (isTransient(cls) && cls.kind !== "rate-limit") {
             return;
         }
         // Cap rate-limit backoff for CLI-style providers (openai-codex, google-gemini-cli)
@@ -177,6 +162,7 @@ export async function handleAgentEnd(pi, event, ctx) {
                         if (modelToSet) {
                             const ok = await pi.setModel(modelToSet, { persist: false });
                             if (ok) {
+                                setCurrentDispatchedModelId({ provider: modelToSet.provider, id: modelToSet.id });
                                 ctx.ui.notify(`Model error${errorDetail}. Switched to fallback: ${nextModelId} and resuming.`, "warning");
                                 pi.sendMessage({ customType: "gsd-auto-timeout-recovery", content: "Continue execution.", display: false }, { triggerTurn: true });
                                 return;
@@ -193,6 +179,7 @@ export async function handleAgentEnd(pi, event, ctx) {
                     if (startModel) {
                         const ok = await pi.setModel(startModel, { persist: false });
                         if (ok) {
+                            setCurrentDispatchedModelId({ provider: startModel.provider, id: startModel.id });
                             retryState.networkRetryCount = 0;
                             retryState.currentRetryModelId = undefined;
                             ctx.ui.notify(`Model error${errorDetail}. Restored session model: ${sessionModel.provider}/${sessionModel.id} and resuming.`, "warning");

package/dist/resources/extensions/gsd/bootstrap/db-tools.js

@@ -421,10 +421,14 @@ export function registerDbTools(pi) {
                 depends: Type.Array(Type.String(), { description: "Slice dependency IDs" }),
                 demo: Type.String({ description: "Roadmap demo text / After this" }),
                 goal: Type.String({ description: "Slice goal" }),
-                successCriteria: Type.String({ description: "Slice success criteria block" }),
-                proofLevel: Type.String({ description: "Slice proof level" }),
-                integrationClosure: Type.String({ description: "Slice integration closure" }),
-                observabilityImpact: Type.String({ description: "Slice observability impact" }),
+                // ADR-011: heavy planning fields are optional for sketch slices; required for full slices.
+                successCriteria: Type.Optional(Type.String({ description: "Slice success criteria block (required for full slices; omit for sketches)" })),
+                proofLevel: Type.Optional(Type.String({ description: "Slice proof level (required for full slices; omit for sketches)" })),
+                integrationClosure: Type.Optional(Type.String({ description: "Slice integration closure (required for full slices; omit for sketches)" })),
+                observabilityImpact: Type.Optional(Type.String({ description: "Slice observability impact (required for full slices; omit for sketches)" })),
+                // ADR-011 sketch-then-refine fields.
+                isSketch: Type.Optional(Type.Boolean({ description: "ADR-011: true marks this slice as a sketch awaiting refine-slice expansion" })),
+                sketchScope: Type.Optional(Type.String({ description: "ADR-011: 2–3 sentence scope boundary, required when isSketch=true" })),
             }), { description: "Planned slices for the milestone" }),
             // ── Enrichment metadata (optional — defaults to empty) ────────────
             status: Type.Optional(Type.String({ description: "Milestone status (defaults to active)" })),
@@ -589,6 +593,20 @@ export function registerDbTools(pi) {
             keyFiles: Type.Optional(Type.Array(Type.String(), { description: "List of key files created or modified" })),
             keyDecisions: Type.Optional(Type.Array(Type.String(), { description: "List of key decisions made during this task" })),
             blockerDiscovered: Type.Optional(Type.Boolean({ description: "Whether a plan-invalidating blocker was discovered" })),
+            // ADR-011 Phase 2: mid-execution escalation — agent asks the user to resolve an ambiguity.
+            escalation: Type.Optional(Type.Object({
+                question: Type.String({ description: "The question the user needs to answer — one clear sentence." }),
+                options: Type.Array(Type.Object({
+                    id: Type.String({ description: "Short id (e.g. 'A', 'B') used by /gsd escalate resolve." }),
+                    label: Type.String({ description: "One-line label." }),
+                    tradeoffs: Type.String({ description: "1-2 sentences on the tradeoffs of this option." }),
+                }), { minItems: 2, maxItems: 4, description: "2–4 options the user can choose between." }),
+                recommendation: Type.String({ description: "Option id the executor recommends." }),
+                recommendationRationale: Type.String({ description: "Why the recommendation — 1–2 sentences." }),
+                continueWithDefault: Type.Boolean({
+                    description: "When true, loop continues (artifact logged for later review). When false, auto-mode pauses until the user resolves via /gsd escalate resolve.",
+                }),
+            }, { description: "ADR-011 Phase 2: optional escalation payload. Only honored when phases.mid_execution_escalation is true." })),
             verificationEvidence: Type.Optional(Type.Array(Type.Union([
                 Type.Object({
                     command: Type.String({ description: "Verification command that was run" }),
@@ -690,28 +708,23 @@ export function registerDbTools(pi) {
             };
         }
         try {
-            const { getSlice, updateSliceStatus } = await import("../gsd-db.js");
+            const { handleSkipSlice } = await import("../tools/skip-slice.js");
             const { invalidateStateCache } = await import("../state.js");
-            const slice = getSlice(params.milestoneId, params.sliceId);
-            if (!slice) {
-                return {
-                    content: [{ type: "text", text: `Error: Slice ${params.sliceId} not found in milestone ${params.milestoneId}` }],
-                    details: { operation: "skip_slice", error: "slice_not_found" },
-                };
-            }
-            if (slice.status === "complete" || slice.status === "done") {
-                return {
-                    content: [{ type: "text", text: `Error: Slice ${params.sliceId} is already complete — cannot skip.` }],
-                    details: { operation: "skip_slice", error: "already_complete" },
-                };
-            }
-            if (slice.status === "skipped") {
+            const result = handleSkipSlice({
+                milestoneId: params.milestoneId,
+                sliceId: params.sliceId,
+                reason: params.reason,
+            });
+            if (result.error) {
                 return {
-                    content: [{ type: "text", text: `Slice ${params.sliceId} is already skipped.` }],
-                    details: { operation: "skip_slice", sliceId: params.sliceId, milestoneId: params.milestoneId },
+                    content: [{ type: "text", text: `Error: ${result.error}` }],
+                    details: {
+                        operation: "skip_slice",
+                        error: result.error,
+                        errorCode: result.errorCode ?? "skip_failed",
+                    },
                 };
             }
-            updateSliceStatus(params.milestoneId, params.sliceId, "skipped");
             invalidateStateCache();
             // Rebuild STATE.md so it reflects the skip immediately (#3477).
             // Without this, /gsd auto reads stale STATE.md and resumes the skipped slice.
@@ -723,13 +736,20 @@ export function registerDbTools(pi) {
             catch (err) {
                 logError("tool", `skip_slice rebuildState failed: ${err.message}`, { tool: "gsd_skip_slice" });
             }
+            const suffix = result.wasAlreadySkipped
+                ? result.tasksSkipped > 0
+                    ? ` (already skipped; cascaded ${result.tasksSkipped} leftover task(s) to skipped).`
+                    : " (already skipped; no pending tasks to cascade)."
+                : ` Cascaded ${result.tasksSkipped} task(s) to skipped. Auto-mode will advance past this slice.`;
             return {
-                content: [{ type: "text", text: `Skipped slice ${params.sliceId} (${params.milestoneId}). Reason: ${params.reason ?? "User-directed skip"}. Auto-mode will advance past this slice.` }],
+                content: [{ type: "text", text: `Skipped slice ${params.sliceId} (${params.milestoneId}). Reason: ${params.reason ?? "User-directed skip"}.${suffix}` }],
                 details: {
                     operation: "skip_slice",
                     sliceId: params.sliceId,
                     milestoneId: params.milestoneId,
                     reason: params.reason,
+                    tasksSkipped: result.tasksSkipped,
+                    wasAlreadySkipped: result.wasAlreadySkipped,
                 },
             };
         }
@@ -746,12 +766,14 @@ export function registerDbTools(pi) {
         name: "gsd_skip_slice",
         label: "Skip Slice",
         description: "Mark a slice as skipped so auto-mode advances past it without executing. " +
+            "Non-closed tasks within the slice are cascaded to skipped so milestone completion is not blocked by leftover pending tasks (#4375). " +
             "The slice data is preserved for reference. The state machine treats skipped slices like completed ones for dependency satisfaction.",
         promptSnippet: "Skip a GSD slice (mark as skipped, auto-mode will advance past it)",
         promptGuidelines: [
             "Use gsd_skip_slice when a slice should be bypassed — descoped, superseded, or no longer relevant.",
             "Cannot skip a slice that is already complete.",
             "Skipped slices satisfy downstream dependencies just like completed slices.",
+            "All pending/active tasks in the slice are cascaded to skipped; completed tasks are never downgraded.",
         ],
         parameters: Type.Object({
             sliceId: Type.String({ description: "Slice ID (e.g. S02)" }),

package/dist/resources/extensions/gsd/bootstrap/memory-tools.js

@@ -0,0 +1,131 @@
+// GSD2 — Memory tool registration
+//
+// Exposes the memory-layer tools (capture_thought, memory_query, gsd_graph)
+// to the LLM over MCP. All three degrade gracefully when the GSD database
+// is unavailable.
+import { Type } from "@sinclair/typebox";
+import { ensureDbOpen } from "./dynamic-tools.js";
+import { executeGsdGraph, executeMemoryCapture, executeMemoryQuery, } from "../tools/memory-tools.js";
+export function registerMemoryTools(pi) {
+    // ─── capture_thought ────────────────────────────────────────────────────
+    pi.registerTool({
+        name: "capture_thought",
+        label: "Capture Thought",
+        description: "Record a durable piece of project knowledge (decision, convention, gotcha, pattern, " +
+            "preference, or environment detail) into the GSD memory store. Use sparingly — one memory " +
+            "per genuinely reusable insight, not per task.",
+        promptSnippet: "Capture a durable project insight into the GSD memory store (categories: architecture, convention, gotcha, pattern, preference, environment)",
+        promptGuidelines: [
+            "Use capture_thought for insights that will remain useful across future sessions.",
+            "Do NOT capture one-off bug fixes, temporary state, secrets, or task-specific details.",
+            "Keep content to 1–3 sentences.",
+            "Set confidence: 0.6 tentative, 0.8 solid, 0.95 well-confirmed (default 0.8).",
+        ],
+        parameters: Type.Object({
+            category: Type.Union([
+                Type.Literal("architecture"),
+                Type.Literal("convention"),
+                Type.Literal("gotcha"),
+                Type.Literal("preference"),
+                Type.Literal("environment"),
+                Type.Literal("pattern"),
+            ], { description: "Memory category" }),
+            content: Type.String({ description: "The memory text (1–3 sentences, no secrets)" }),
+            confidence: Type.Optional(Type.Number({ description: "0.1–0.99, default 0.8", minimum: 0.1, maximum: 0.99 })),
+            tags: Type.Optional(Type.Array(Type.String(), { description: "Free-form tags (reserved for future use)" })),
+            scope: Type.Optional(Type.String({ description: "Scope name (reserved for future use; defaults to project)" })),
+            structuredFields: Type.Optional(Type.Record(Type.String(), Type.Unknown(), {
+                description: "Optional structured payload preserved alongside content (ADR-013). Use for decisions to retain scope/decision/choice/rationale/made_by/revisable. Omit for plain captures.",
+            })),
+        }),
+        async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
+            const ok = await ensureDbOpen();
+            if (!ok) {
+                return {
+                    content: [{ type: "text", text: "Error: GSD database is not available. Cannot capture memory." }],
+                    details: { operation: "memory_capture", error: "db_unavailable" },
+                    isError: true,
+                };
+            }
+            return executeMemoryCapture(params);
+        },
+    });
+    // ─── memory_query ───────────────────────────────────────────────────────
+    pi.registerTool({
+        name: "memory_query",
+        label: "Query Memory",
+        description: "Search the GSD memory store for relevant memories. Phase 1 uses keyword matching ranked " +
+            "by confidence and reinforcement; future phases add semantic (embedding) retrieval.",
+        promptSnippet: "Search the GSD memory store by keyword; returns ranked memories with id, category, and content",
+        promptGuidelines: [
+            "Use memory_query when you need durable project context that may not be in the current prompt.",
+            "Provide a short keyword-style query — not a full question.",
+            "Use category to narrow results to gotchas, conventions, architecture notes, etc.",
+        ],
+        parameters: Type.Object({
+            query: Type.String({ description: "Keyword query (2+ char terms)" }),
+            k: Type.Optional(Type.Number({ description: "Max results (default 10, max 50)", minimum: 1, maximum: 50 })),
+            category: Type.Optional(Type.Union([
+                Type.Literal("architecture"),
+                Type.Literal("convention"),
+                Type.Literal("gotcha"),
+                Type.Literal("preference"),
+                Type.Literal("environment"),
+                Type.Literal("pattern"),
+            ], { description: "Restrict results to a single category" })),
+            scope: Type.Optional(Type.String({ description: "Only include memories with this scope (e.g. 'project', 'global')" })),
+            tag: Type.Optional(Type.String({ description: "Only include memories tagged with this value" })),
+            include_superseded: Type.Optional(Type.Boolean({ description: "Include superseded memories (default false)" })),
+            reinforce_hits: Type.Optional(Type.Boolean({ description: "Increment hit_count on returned memories (default false)" })),
+        }),
+        async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
+            const ok = await ensureDbOpen();
+            if (!ok) {
+                return {
+                    content: [{ type: "text", text: "Error: GSD database is not available. Cannot query memory." }],
+                    details: { operation: "memory_query", error: "db_unavailable" },
+                    isError: true,
+                };
+            }
+            return executeMemoryQuery(params);
+        },
+    });
+    // ─── gsd_graph ──────────────────────────────────────────────────────────
+    pi.registerTool({
+        name: "gsd_graph",
+        label: "GSD Knowledge Graph",
+        description: "Inspect the relationship graph between memories. mode=query walks supersedes edges from a " +
+            "given memoryId; mode=build is a placeholder that future phases will use to rebuild graph " +
+            "edges from milestone LEARNINGS artifacts.",
+        promptSnippet: "Query the memory relationship graph or trigger a rebuild",
+        promptGuidelines: [
+            "Use mode=query with a memoryId when you want to see how a memory relates to others.",
+            "Phase 1 only exposes supersedes edges; additional relation types arrive in later phases.",
+        ],
+        parameters: Type.Object({
+            mode: Type.Union([Type.Literal("build"), Type.Literal("query")], {
+                description: "build = recompute graph (placeholder), query = inspect edges",
+            }),
+            memoryId: Type.Optional(Type.String({ description: "Memory ID (required when mode=query)" })),
+            depth: Type.Optional(Type.Number({ description: "Hops to traverse (0–5, default 1)", minimum: 0, maximum: 5 })),
+            rel: Type.Optional(Type.Union([
+                Type.Literal("related_to"),
+                Type.Literal("depends_on"),
+                Type.Literal("contradicts"),
+                Type.Literal("elaborates"),
+                Type.Literal("supersedes"),
+            ], { description: "Only include edges with this relation type" })),
+        }),
+        async execute(_toolCallId, params, _signal, _onUpdate, _ctx) {
+            const ok = await ensureDbOpen();
+            if (!ok) {
+                return {
+                    content: [{ type: "text", text: "Error: GSD database is not available." }],
+                    details: { operation: "gsd_graph", error: "db_unavailable" },
+                    isError: true,
+                };
+            }
+            return executeGsdGraph(params);
+        },
+    });
+}

package/dist/resources/extensions/gsd/bootstrap/query-tools.js

@@ -2,6 +2,7 @@
 import { Type } from "@sinclair/typebox";
 import { ensureDbOpen } from "./dynamic-tools.js";
 import { executeMilestoneStatus } from "../tools/workflow-tool-executors.js";
+import { checkpointDatabase } from "../gsd-db.js";
 export function registerQueryTools(pi) {
     pi.registerTool({
         name: "gsd_milestone_status",
@@ -27,4 +28,32 @@ export function registerQueryTools(pi) {
             return executeMilestoneStatus(params);
         },
     });
+    pi.registerTool({
+        name: "gsd_checkpoint_db",
+        label: "Checkpoint GSD Database",
+        description: "Flush the SQLite WAL (Write-Ahead Log) into the base gsd.db file. " +
+            "Call this before `git add .gsd/gsd.db` to ensure the committed database " +
+            "contains current milestone/slice/task state rather than stale pre-session content. " +
+            "Safe to call at any time while GSD is running.",
+        promptSnippet: "Flush WAL into gsd.db so git add stages current state",
+        promptGuidelines: [
+            "Call gsd_checkpoint_db immediately before staging .gsd/gsd.db with git add.",
+            "Do not use sqlite3 or shell commands to checkpoint — they are blocked. Use this tool instead.",
+        ],
+        parameters: Type.Object({}),
+        async execute(_toolCallId, _params, _signal, _onUpdate, _ctx) {
+            const dbAvailable = await ensureDbOpen();
+            if (!dbAvailable) {
+                return {
+                    content: [{ type: "text", text: "Error: GSD database is not available. Cannot checkpoint." }],
+                    details: { operation: "checkpoint_db", error: "db_unavailable" },
+                };
+            }
+            checkpointDatabase();
+            return {
+                content: [{ type: "text", text: "WAL checkpoint complete. gsd.db is now up to date and safe to stage with git add." }],
+                details: { operation: "checkpoint_db", status: "ok" },
+            };
+        },
+    });
 }

package/dist/resources/extensions/gsd/bootstrap/register-extension.js

@@ -5,6 +5,7 @@ import { loadEcosystemExtensions } from "../ecosystem/loader.js";
 import { registerDbTools } from "./db-tools.js";
 import { registerDynamicTools } from "./dynamic-tools.js";
 import { registerJournalTools } from "./journal-tools.js";
+import { registerMemoryTools } from "./memory-tools.js";
 import { registerQueryTools } from "./query-tools.js";
 import { registerHooks } from "./register-hooks.js";
 import { registerShortcuts } from "./register-shortcuts.js";
@@ -57,6 +58,16 @@ export function registerGsdExtension(pi) {
     // so we intentionally skip it here to avoid double-registration.
     registerWorktreeCommand(pi);
     registerExitCommand(pi);
+    // Wire the Layer 2 event emitter bridge so deeply-nested GSD code can emit
+    // extension events (git lifecycle, verify, budget, milestone, unit) without
+    // threading `pi` through every call site.
+    import("../hook-emitter.js")
+        .then(({ setHookEmitter }) => setHookEmitter(pi))
+        .catch((err) => {
+        // Non-fatal — emitters simply become no-ops if this import fails, but
+        // surface the failure so silent bootstrap breakage is debuggable.
+        process.stderr.write(`[gsd] Failed to bootstrap hook-emitter bridge: ${err instanceof Error ? err.stack ?? err.message : String(err)}\n`);
+    });
     installEpipeGuard();
     // Ecosystem handlers captured by the GSDExtensionAPI wrapper for the
     // GSD-owned `before_agent_start` dispatch step (#3338).
@@ -74,6 +85,7 @@ export function registerGsdExtension(pi) {
         ["db-tools", () => registerDbTools(pi)],
         ["journal-tools", () => registerJournalTools(pi)],
         ["query-tools", () => registerQueryTools(pi)],
+        ["memory-tools", () => registerMemoryTools(pi)],
         ["shortcuts", () => registerShortcuts(pi)],
         ["hooks", () => registerHooks(pi, ecosystemHandlers)],
         ["ecosystem", () => {

package/dist/resources/extensions/gsd/bootstrap/register-hooks.js

@@ -13,6 +13,7 @@ import { loadToolApiKeys } from "../commands-config.js";
 import { loadFile, saveFile, formatContinue } from "../files.js";
 import { deriveState } from "../state.js";
 import { getAutoDashboardData, isAutoActive, isAutoPaused, markToolEnd, markToolStart, recordToolInvocationError } from "../auto.js";
+import { hideFooter } from "../auto-dashboard.js";
 import { isParallelActive, shutdownParallel } from "../parallel-orchestrator.js";
 import { checkToolCallLoop, resetToolCallLoopGuard } from "./tool-call-loop-guard.js";
 import { saveActivityLog } from "../activity-log.js";
@@ -77,6 +78,9 @@ export function registerHooks(pi, ecosystemHandlers) {
             catch { /* non-fatal */ }
         }
         loadToolApiKeys();
+        if (isAutoActive()) {
+            ctx.ui.setFooter(hideFooter);
+        }
     });
     pi.on("session_switch", async (_event, ctx) => {
         initNotificationStore(process.cwd());
@@ -96,6 +100,9 @@ export function registerHooks(pi, ecosystemHandlers) {
             prepareWorkflowMcpForProject(ctx, process.cwd());
         }
         loadToolApiKeys();
+        if (isAutoActive()) {
+            ctx.ui.setFooter(hideFooter);
+        }
     });
     pi.on("before_agent_start", async (event, ctx) => {
         // Wait for ecosystem loader to finish (no-op after first turn).
@@ -292,6 +299,7 @@ export function registerHooks(pi, ecosystemHandlers) {
     pi.on("tool_call", async (event, ctx) => {
         if (!isAutoActive())
             return;
+        markToolStart(event.toolCallId, event.toolName);
         safetyRecordToolCall(event.toolCallId, event.toolName, event.input);
         // Destructive command classification (warn only, never block)
         if (isToolCallEventType("bash", event)) {
@@ -305,6 +313,20 @@ export function registerHooks(pi, ecosystemHandlers) {
         }
     });
     pi.on("tool_result", async (event) => {
+        if (isAutoActive() && typeof event.toolCallId === "string") {
+            markToolEnd(event.toolCallId);
+        }
+        if (isAutoActive() && event.isError && event.toolName.startsWith("gsd_")) {
+            const resultPayload = ("result" in event ? event.result : undefined);
+            const errorText = typeof resultPayload === "string"
+                ? resultPayload
+                : (typeof resultPayload?.content?.[0]?.text === "string"
+                    ? resultPayload.content[0].text
+                    : (typeof event.content === "string"
+                        ? event.content
+                        : String(resultPayload ?? "")));
+            recordToolInvocationError(event.toolName, errorText);
+        }
         if (event.toolName !== "ask_user_questions")
             return;
         const milestoneId = getDiscussionMilestoneId(process.cwd());