gsd-pi 2.73.1 → 2.74.0-dev.b741afb

package/src/resources/extensions/gsd/auto-post-unit.ts

@@ -104,6 +104,7 @@ import {
   updateSliceProgressCache,
   unitVerb,
   hideFooter,
+  describeNextUnit,
 } from "./auto-dashboard.js";
 import { existsSync, unlinkSync } from "node:fs";
 import { join } from "node:path";
@@ -233,6 +234,18 @@ export function detectRogueFileWrites(
   return rogues;
 }
 
+export const STEP_COMPLETE_FALLBACK_MESSAGE =
+  "Step complete. Run /clear, then /gsd to continue (or /gsd auto to run continuously).";
+
+export function buildStepCompleteMessage(nextState: import("./types.js").GSDState): string {
+  if (nextState.phase === "complete") {
+    return "Step complete — milestone finished. Run /gsd status to review, or start the next milestone.";
+  }
+  const next = describeNextUnit(nextState);
+  return `Step complete. Next: ${next.label}\n`
+    + `Run /clear, then /gsd to continue (or /gsd auto to run continuously).`;
+}
+
 export interface PreVerificationOpts {
   skipSettleDelay?: boolean;
   skipWorktreeSync?: boolean;
@@ -249,6 +262,65 @@ export interface PostUnitContext {
   updateProgressWidget: (ctx: ExtensionContext, unitType: string, unitId: string, state: import("./types.js").GSDState) => void;
 }
 
+export async function autoCommitUnit(
+  basePath: string,
+  unitType: string,
+  unitId: string,
+  ctx?: ExtensionContext,
+): Promise<string | null> {
+  try {
+    let taskContext: TaskCommitContext | undefined;
+
+    if (unitType === "execute-task") {
+      const { milestone: mid, slice: sid, task: tid } = parseUnitId(unitId);
+      if (mid && sid && tid) {
+        const summaryPath = resolveTaskFile(basePath, mid, sid, tid, "SUMMARY");
+        if (summaryPath) {
+          try {
+            const summaryContent = await loadFile(summaryPath);
+            if (summaryContent) {
+              const summary = parseSummary(summaryContent);
+              let ghIssueNumber: number | undefined;
+              try {
+                const { getTaskIssueNumberForCommit } = await import("../github-sync/sync.js");
+                ghIssueNumber = getTaskIssueNumberForCommit(basePath, mid, sid, tid) ?? undefined;
+              } catch (err) {
+                logWarning("engine", `GitHub issue lookup failed: ${err instanceof Error ? err.message : String(err)}`);
+              }
+
+              taskContext = {
+                taskId: `${sid}/${tid}`,
+                taskTitle: summary.title?.replace(/^T\d+:\s*/, "") || tid,
+                oneLiner: summary.oneLiner || undefined,
+                keyFiles: summary.frontmatter.key_files?.filter(f => !f.includes("{{")) || undefined,
+                issueNumber: ghIssueNumber,
+              };
+            }
+          } catch (e) {
+            debugLog("postUnit", { phase: "task-summary-parse", error: String(e) });
+          }
+        }
+      }
+    }
+
+    _resetHasChangesCache();
+
+    if (LIFECYCLE_ONLY_UNITS.has(unitType)) {
+      return null;
+    }
+
+    const commitMsg = autoCommitCurrentBranch(basePath, unitType, unitId, taskContext);
+    if (commitMsg) {
+      ctx?.ui.notify(`Committed: ${commitMsg.split("\n")[0]}`, "info");
+    }
+    return commitMsg;
+  } catch (e) {
+    debugLog("postUnit", { phase: "auto-commit", error: String(e) });
+    ctx?.ui.notify(`Auto-commit failed: ${String(e).split("\n")[0]}`, "warning");
+    return null;
+  }
+}
+
 /**
  * Pre-verification processing: parallel worker signal check, cache invalidation,
  * auto-commit, doctor run, state rebuild, worktree sync, artifact verification.
@@ -288,63 +360,7 @@ export async function postUnitPreVerification(pctx: PostUnitContext, opts?: PreV
   // Auto-commit
   if (s.currentUnit) {
     const unit = s.currentUnit;
-    try {
-      let taskContext: TaskCommitContext | undefined;
-
-      if (s.currentUnit.type === "execute-task") {
-        const { milestone: mid, slice: sid, task: tid } = parseUnitId(s.currentUnit.id);
-        if (mid && sid && tid) {
-          const summaryPath = resolveTaskFile(s.basePath, mid, sid, tid, "SUMMARY");
-          if (summaryPath) {
-            try {
-              const summaryContent = await loadFile(summaryPath);
-              if (summaryContent) {
-                const summary = parseSummary(summaryContent);
-                // Look up GitHub issue number for commit linking
-                let ghIssueNumber: number | undefined;
-                try {
-                  const { getTaskIssueNumberForCommit } = await import("../github-sync/sync.js");
-                  ghIssueNumber = getTaskIssueNumberForCommit(s.basePath, mid, sid, tid) ?? undefined;
-                } catch (err) {
-                  // GitHub sync not available — skip
-                  logWarning("engine", `GitHub issue lookup failed: ${err instanceof Error ? err.message : String(err)}`);
-                }
-
-                taskContext = {
-                  taskId: `${sid}/${tid}`,
-                  taskTitle: summary.title?.replace(/^T\d+:\s*/, "") || tid,
-                  oneLiner: summary.oneLiner || undefined,
-                  keyFiles: summary.frontmatter.key_files?.filter(f => !f.includes("{{")) || undefined,
-                  issueNumber: ghIssueNumber,
-                };
-              }
-            } catch (e) {
-              debugLog("postUnit", { phase: "task-summary-parse", error: String(e) });
-            }
-          }
-        }
-      }
-
-      // Invalidate the nativeHasChanges cache before auto-commit (#1853).
-      // The cache has a 10-second TTL and is keyed by basePath.  A stale
-      // `false` result causes autoCommit to skip staging entirely, leaving
-      // code files only in the working tree where they are destroyed by
-      // `git worktree remove --force` during teardown.
-      _resetHasChangesCache();
-
-      // Skip auto-commit for lifecycle-only units (#2553) — they only touch
-      // `.gsd/` internal state files. Those files are picked up by the next
-      // actual task commit via smartStage().
-      if (!LIFECYCLE_ONLY_UNITS.has(s.currentUnit.type)) {
-        const commitMsg = autoCommitCurrentBranch(s.basePath, s.currentUnit.type, s.currentUnit.id, taskContext);
-        if (commitMsg) {
-          ctx.ui.notify(`Committed: ${commitMsg.split("\n")[0]}`, "info");
-        }
-      }
-    } catch (e) {
-      debugLog("postUnit", { phase: "auto-commit", error: String(e) });
-      ctx.ui.notify(`Auto-commit failed: ${String(e).split("\n")[0]}`, "warning");
-    }
+    await autoCommitUnit(s.basePath, unit.type, unit.id, ctx);
 
     // GitHub sync (non-blocking, opt-in)
     await runSafely("postUnit", "github-sync", async () => {
@@ -619,6 +635,30 @@ export async function postUnitPreVerification(pctx: PostUnitContext, opts?: PreV
           s.verificationRetryCount.set(retryKey, attempt);
 
           if (attempt > MAX_VERIFICATION_RETRIES) {
+            // #4175: For complete-milestone, a blocker placeholder is harmful —
+            // the stub SUMMARY has no recovery value (milestone is terminal),
+            // it does not update DB status (so deriveState never advances),
+            // and it fools stopAuto's presence check into merging a milestone
+            // that was never legitimately completed. Pause auto-mode with a
+            // clear single failure signal and preserve the worktree branch.
+            if (s.currentUnit.type === "complete-milestone") {
+              debugLog("postUnit", {
+                phase: "artifact-verify-pause-complete-milestone",
+                unitType: s.currentUnit.type,
+                unitId: s.currentUnit.id,
+                attempt,
+                maxRetries: MAX_VERIFICATION_RETRIES,
+              });
+              s.verificationRetryCount.delete(retryKey);
+              s.pendingVerificationRetry = null;
+              ctx.ui.notify(
+                `Milestone ${s.currentUnit.id} verification failed after ${MAX_VERIFICATION_RETRIES} retries — worktree branch preserved. Re-run /gsd auto once blockers are resolved.`,
+                "error",
+              );
+              await pauseAuto(ctx, pi);
+              return "dispatched";
+            }
+
             // Retries exhausted — write a blocker placeholder so the pipeline
             // can advance past this stuck unit (#2653).
             debugLog("postUnit", {
@@ -1025,8 +1065,17 @@ export async function postUnitPostVerification(pctx: PostUnitContext): Promise<"
     }
   }
 
-  // Step mode → show wizard instead of dispatch
+  // Step mode → show wizard instead of dispatch.
+  // Without this notify(), /gsd in step mode finishes a unit and silently
+  // exits the loop, leaving the user with no hint to /clear and /gsd again.
   if (s.stepMode) {
+    try {
+      const nextState = await deriveState(s.basePath);
+      ctx.ui.notify(buildStepCompleteMessage(nextState), "info");
+    } catch (e) {
+      debugLog("postUnit", { phase: "step-wizard-notify", error: String(e) });
+      ctx.ui.notify(STEP_COMPLETE_FALLBACK_MESSAGE, "info");
+    }
     return "step-wizard";
   }
 

package/src/resources/extensions/gsd/auto-prompts.ts

@@ -34,6 +34,7 @@ import {
 import { formatDecisionsCompact, formatRequirementsCompact } from "./structured-data-formatter.js";
 import { readPhaseAnchor, formatAnchorForPrompt } from "./phase-anchor.js";
 import { logWarning } from "./workflow-logger.js";
+import { inlineGraphSubgraph } from "./graph-context.js";
 
 // ─── Preamble Cap ─────────────────────────────────────────────────────────────
 
@@ -1175,6 +1176,10 @@ export async function buildResearchSlicePrompt(
   const knowledgeInlineRS = await inlineKnowledgeScoped(base, keywords);
   if (knowledgeInlineRS) inlined.push(knowledgeInlineRS);
 
+  // Knowledge graph: subgraph for this slice (graceful — skipped if no graph.json)
+  const graphBlockRS = await inlineGraphSubgraph(base, `${sid} ${sTitle}`, { budget: 3000 });
+  if (graphBlockRS) inlined.push(graphBlockRS);
+
   inlined.push(inlineTemplate("research", "Research"));
 
   const depContent = await inlineDependencySummaries(mid, sid, base);
@@ -1250,6 +1255,10 @@ export async function buildPlanSlicePrompt(
   const knowledgeInlinePS = await inlineKnowledgeScoped(base, keywordsPS);
   if (knowledgeInlinePS) inlined.push(knowledgeInlinePS);
 
+  // Knowledge graph: subgraph for this slice (graceful — skipped if no graph.json)
+  const graphBlockPS = await inlineGraphSubgraph(base, `${sid} ${sTitle}`, { budget: 3000 });
+  if (graphBlockPS) inlined.push(graphBlockPS);
+
   inlined.push(inlineTemplate("plan", "Slice Plan"));
   if (inlineLevel === "full") {
     inlined.push(inlineTemplate("task-plan", "Task Plan"));
@@ -1366,12 +1375,16 @@ export async function buildExecuteTaskPrompt(
   // Only include if it has content (not a "not found" result)
   const knowledgeContent = knowledgeInlineET && !knowledgeInlineET.includes("not found") ? knowledgeInlineET : null;
 
+  // Knowledge graph: tight subgraph for this task (graceful — skipped if no graph.json)
+  const graphBlockET = await inlineGraphSubgraph(base, `${tid} ${tTitle}`, { budget: 2000 });
+
   const inlinedTemplates = inlineLevel === "minimal"
     ? inlineTemplate("task-summary", "Task Summary")
     : [
         inlineTemplate("task-summary", "Task Summary"),
         inlineTemplate("decisions", "Decisions"),
         ...(knowledgeContent ? [knowledgeContent] : []),
+        ...(graphBlockET ? [graphBlockET] : []),
       ].join("\n\n---\n\n");
 
   const taskSummaryPath = join(base, `${relSlicePath(base, mid, sid)}/tasks/${tid}-SUMMARY.md`);

package/src/resources/extensions/gsd/auto-start.ts

@@ -83,7 +83,11 @@ import { join } from "node:path";
 import { sep as pathSep } from "node:path";
 
 import { resolveProjectRootDbPath } from "./bootstrap/dynamic-tools.js";
-import { resolveDefaultSessionModel, resolveDynamicRoutingConfig } from "./preferences-models.js";
+import {
+  isCustomProvider,
+  resolveDefaultSessionModel,
+  resolveDynamicRoutingConfig,
+} from "./preferences-models.js";
 import type { WorktreeResolver } from "./worktree-resolver.js";
 import { getSessionModelOverride } from "./session-model-override.js";
 
@@ -274,8 +278,18 @@ export async function bootstrapAutoSession(
   //
   // This preserves #3517 defaults while honoring explicit runtime model
   // selection for subsequent /gsd runs in the same session.
+  //
+  // Exception (#4122): when the session provider is a custom provider declared
+  // in ~/.gsd/agent/models.json (Ollama, vLLM, OpenAI-compatible proxy, etc.),
+  // PREFERENCES.md is skipped entirely. PREFERENCES.md cannot reference custom
+  // providers, so honoring it would silently reroute auto-mode to a built-in
+  // provider the user is not logged into and surface as "Not logged in · Please
+  // run /login" before pausing and resetting to claude-code/claude-sonnet-4-6.
   const manualSessionOverride = getSessionModelOverride(ctx.sessionManager.getSessionId());
-  const preferredModel = resolveDefaultSessionModel(ctx.model?.provider);
+  const sessionProviderIsCustom = isCustomProvider(ctx.model?.provider);
+  const preferredModel = sessionProviderIsCustom
+    ? null
+    : resolveDefaultSessionModel(ctx.model?.provider);
   // Validate the preferred model against the live registry + provider auth so
   // an unconfigured PREFERENCES.md entry (no API key / OAuth) can't become the
   // start-model snapshot. Without this, every subsequent unit would try to
@@ -792,6 +806,9 @@ export async function bootstrapAutoSession(
 
     ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
     ctx.ui.setFooter(hideFooter);
+    // Hide gsd-health during AUTO — gsd-progress is the single source of truth
+    // for last-commit / cost / health signal while auto is running.
+    ctx.ui.setWidget("gsd-health", undefined);
     const modeLabel = s.stepMode ? "Step-mode" : "Auto-mode";
     const pendingCount = (state.registry ?? []).filter(
       (m) => m.status !== "complete" && m.status !== "parked",
@@ -811,12 +828,19 @@ export async function bootstrapAutoSession(
       ? `${s.autoModeStartModel.provider}/${s.autoModeStartModel.id}`
       : ctx.model ? `${ctx.model.provider}/${ctx.model.id}` : "default";
 
-    // Flat-rate providers (e.g. GitHub Copilot, claude-code) suppress routing
-    // at dispatch time (#3453) — reflect that in the banner.
-    const { isFlatRateProvider } = await import("./auto-model-selection.js");
+    // Flat-rate providers (e.g. GitHub Copilot, claude-code, user-declared
+    // subscription proxies, externalCli CLIs) suppress routing at dispatch
+    // time (#3453) — reflect that in the banner.  Thread the same
+    // FlatRateContext used by selectAndApplyModel so user-declared
+    // flat-rate providers and externalCli auto-detection are respected.
+    const { isFlatRateProvider, buildFlatRateContext } = await import("./auto-model-selection.js");
+    const bannerPrefs = loadEffectiveGSDPreferences()?.preferences;
     const effectiveProvider = s.autoModeStartModel?.provider ?? ctx.model?.provider;
     const effectivelyEnabled = routingConfig.enabled
-      && !(effectiveProvider && isFlatRateProvider(effectiveProvider));
+      && !(effectiveProvider && isFlatRateProvider(
+        effectiveProvider,
+        buildFlatRateContext(effectiveProvider, ctx, bannerPrefs),
+      ));
 
     // The actual ceiling may come from tier_models.heavy, not the start model.
     const effectiveCeiling = (routingConfig.enabled && routingConfig.tier_models?.heavy)

package/src/resources/extensions/gsd/auto-timeout-recovery.ts

@@ -230,6 +230,23 @@ export async function recoverTimedOutUnit(
     return "recovered";
   }
 
+  // #4175: For complete-milestone, never write a blocker placeholder — a stub
+  // SUMMARY has no recovery value (milestone is terminal), it does not update
+  // DB status, and downstream merge paths can treat the stub as a legitimate
+  // completion signal. Pause instead so the worktree branch is preserved.
+  if (unitType === "complete-milestone") {
+    writeUnitRuntimeRecord(basePath, unitType, unitId, currentUnitStartedAt, {
+      phase: "paused",
+      recoveryAttempts: recoveryAttempts + 1,
+      lastRecoveryReason: reason,
+    });
+    ctx.ui.notify(
+      `Milestone ${unitId} ${reason}-recovery exhausted ${maxRecoveryAttempts} attempt(s) — worktree branch preserved. Re-run /gsd auto once blockers are resolved.`,
+      "error",
+    );
+    return "paused";
+  }
+
   // Retries exhausted — write a blocker placeholder and advance the pipeline
   // instead of silently stalling.
   const placeholder = writeBlockerPlaceholder(

package/src/resources/extensions/gsd/auto-verification.ts

@@ -12,10 +12,15 @@
 
 import type { ExtensionContext, ExtensionAPI } from "@gsd/pi-coding-agent";
 import { mkdirSync, writeFileSync } from "node:fs";
-import { resolveSliceFile, resolveSlicePath } from "./paths.js";
+import { resolveSliceFile, resolveSlicePath, resolveMilestoneFile } from "./paths.js";
 import { parseUnitId } from "./unit-id.js";
-import { isDbAvailable, getTask, getSliceTasks, type TaskRow } from "./gsd-db.js";
+import { isDbAvailable, getTask, getSliceTasks, getMilestoneSlices, type TaskRow } from "./gsd-db.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
+import { extractVerdict } from "./verdict-parser.js";
+import { isClosedStatus } from "./status-guards.js";
+import { loadFile } from "./files.js";
+import { parseRoadmap } from "./parsers-legacy.js";
+import { isMilestoneComplete } from "./state.js";
 import {
   runVerificationGate,
   formatFailureContext,
@@ -43,6 +48,88 @@ function isInfraVerificationFailure(stderr: string): boolean {
   );
 }
 
+/**
+ * Post-unit guard for `validate-milestone` units (#4094).
+ *
+ * When validate-milestone writes verdict=needs-remediation, the agent is
+ * expected to also call gsd_reassess_roadmap in the same turn to add
+ * remediation slices. If they don't, the state machine re-derives
+ * `phase: validating-milestone` indefinitely (all slices still complete +
+ * verdict still needs-remediation), wasting ~3 dispatches before the stuck
+ * detector fires.
+ *
+ * This guard fires immediately on the first occurrence: if VALIDATION.md
+ * verdict is needs-remediation and no incomplete slices exist for the
+ * milestone, pause the auto-loop with a clear blocker.
+ */
+async function runValidateMilestonePostCheck(
+  vctx: VerificationContext,
+  pauseAuto: (ctx?: ExtensionContext, pi?: ExtensionAPI) => Promise<void>,
+): Promise<VerificationResult> {
+  const { s, ctx, pi } = vctx;
+  if (!s.currentUnit) return "continue";
+
+  const { milestone: mid } = parseUnitId(s.currentUnit.id);
+  if (!mid) return "continue";
+
+  const validationFile = resolveMilestoneFile(s.basePath, mid, "VALIDATION");
+  if (!validationFile) return "continue";
+
+  const validationContent = await loadFile(validationFile);
+  if (!validationContent) return "continue";
+
+  const verdict = extractVerdict(validationContent);
+  if (verdict !== "needs-remediation") return "continue";
+
+  const incompleteSliceCount = await countIncompleteSlices(s.basePath, mid);
+
+  // If any non-closed slices exist, the agent successfully queued remediation
+  // work — proceed normally. The state machine will execute those slices and
+  // re-validate per the #3596/#3670 fix.
+  if (incompleteSliceCount > 0) return "continue";
+
+  ctx.ui.notify(
+    `Milestone ${mid} validation returned verdict=needs-remediation but no remediation slices were added. Pausing for human review.`,
+    "error",
+  );
+  process.stderr.write(
+    `validate-milestone: pausing — verdict=needs-remediation with no incomplete slices for ${mid}. ` +
+      `The agent must call gsd_reassess_roadmap to add remediation slices before re-validation.\n`,
+  );
+  await pauseAuto(ctx, pi);
+  return "pause";
+}
+
+/**
+ * Count slices for a milestone that are not in a closed status.
+ * DB-backed projects are authoritative (#4094 peer review); falls back to
+ * roadmap parsing only when the DB is unavailable.
+ */
+async function countIncompleteSlices(basePath: string, milestoneId: string): Promise<number> {
+  if (isDbAvailable()) {
+    const slices = getMilestoneSlices(milestoneId);
+    if (slices.length === 0) {
+      // No DB rows — treat as "unknown", do not pause.
+      return 1;
+    }
+    return slices.filter((slice) => !isClosedStatus(slice.status)).length;
+  }
+
+  // Filesystem fallback: parse the roadmap markdown.
+  try {
+    const roadmapFile = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
+    if (!roadmapFile) return 1;
+    const roadmapContent = await loadFile(roadmapFile);
+    if (!roadmapContent) return 1;
+    const roadmap = parseRoadmap(roadmapContent);
+    if (roadmap.slices.length === 0) return 1;
+    return isMilestoneComplete(roadmap) ? 0 : 1;
+  } catch {
+    // Parsing failures should not cause false-positive pauses.
+    return 1;
+  }
+}
+
 /**
  * Run the verification gate for the current execute-task unit.
  * Returns:
@@ -56,7 +143,15 @@ export async function runPostUnitVerification(
 ): Promise<VerificationResult> {
   const { s, ctx, pi } = vctx;
 
-  if (!s.currentUnit || s.currentUnit.type !== "execute-task") {
+  if (!s.currentUnit) {
+    return "continue";
+  }
+
+  if (s.currentUnit.type === "validate-milestone") {
+    return await runValidateMilestonePostCheck(vctx, pauseAuto);
+  }
+
+  if (s.currentUnit.type !== "execute-task") {
     return "continue";
   }
 

package/src/resources/extensions/gsd/auto.ts

@@ -187,7 +187,7 @@ import {
   deregisterSigtermHandler as _deregisterSigtermHandler,
   detectWorkingTreeActivity,
 } from "./auto-supervisor.js";
-import { isDbAvailable } from "./gsd-db.js";
+import { isDbAvailable, getMilestone } from "./gsd-db.js";
 import { countPendingCaptures } from "./captures.js";
 import { clearCmuxSidebar, logCmuxEvent, syncCmuxSidebar } from "../cmux/index.js";
 
@@ -195,10 +195,12 @@ import { clearCmuxSidebar, logCmuxEvent, syncCmuxSidebar } from "../cmux/index.j
 import { startUnitSupervision } from "./auto-timers.js";
 import { runPostUnitVerification } from "./auto-verification.js";
 import {
+  autoCommitUnit,
   postUnitPreVerification,
   postUnitPostVerification,
 } from "./auto-post-unit.js";
 import { bootstrapAutoSession, openProjectDbIfPresent, type BootstrapDeps } from "./auto-start.js";
+import { initHealthWidget } from "./health-widget.js";
 import { autoLoop, resolveAgentEnd, resolveAgentEndCancelled, _resetPendingResolve, isSessionSwitchInFlight, type LoopDeps, type ErrorContext } from "./auto-loop.js";
 // Slice-level parallelism (#2340)
 import { getEligibleSlices } from "./slice-parallel-eligibility.js";
@@ -650,6 +652,7 @@ function handleLostSessionLock(
   ctx?.ui.setStatus("gsd-auto", undefined);
   ctx?.ui.setWidget("gsd-progress", undefined);
   ctx?.ui.setFooter(undefined);
+  if (ctx) initHealthWidget(ctx);
 }
 
 /**
@@ -684,6 +687,7 @@ function cleanupAfterLoopExit(ctx: ExtensionContext): void {
     ctx.ui.setStatus("gsd-auto", undefined);
     ctx.ui.setWidget("gsd-progress", undefined);
     ctx.ui.setFooter(undefined);
+    initHealthWidget(ctx);
   }
 
   // Restore CWD out of worktree back to original project root
@@ -758,24 +762,36 @@ export async function stopAuto(
           : { notify: () => {} };
         const resolver = buildResolver();
 
-        // Check if the milestone is complete — SUMMARY file is the authoritative signal.
+        // Check if the milestone is complete. DB status is the authoritative
+        // signal — only a successful gsd_complete_milestone call flips it to
+        // "complete" (tools/complete-milestone.ts). SUMMARY file presence is
+        // NOT sufficient: a blocker placeholder stub or a partial write can
+        // leave a file behind without the milestone actually being done,
+        // which previously caused stopAuto to merge a failed milestone and
+        // emit a misleading metadata-only merge warning (#4175).
+        // DB-unavailable projects fall back to SUMMARY-file presence.
         let milestoneComplete = false;
         try {
-          const summaryPath = resolveMilestoneFile(
-            s.originalBasePath || s.basePath,
-            s.currentMilestoneId,
-            "SUMMARY",
-          );
-          if (!summaryPath) {
-            // Also check in the worktree path (SUMMARY may not be synced yet)
-            const wtSummaryPath = resolveMilestoneFile(
-              s.basePath,
+          if (isDbAvailable()) {
+            const dbRow = getMilestone(s.currentMilestoneId);
+            milestoneComplete = dbRow?.status === "complete";
+          } else {
+            const summaryPath = resolveMilestoneFile(
+              s.originalBasePath || s.basePath,
               s.currentMilestoneId,
               "SUMMARY",
             );
-            milestoneComplete = wtSummaryPath !== null;
-          } else {
-            milestoneComplete = true;
+            if (!summaryPath) {
+              // Also check in the worktree path (SUMMARY may not be synced yet)
+              const wtSummaryPath = resolveMilestoneFile(
+                s.basePath,
+                s.currentMilestoneId,
+                "SUMMARY",
+              );
+              milestoneComplete = wtSummaryPath !== null;
+            } else {
+              milestoneComplete = true;
+            }
           }
         } catch (err) {
           // Non-fatal — fall through to preserveBranch path
@@ -943,6 +959,7 @@ export async function stopAuto(
     ctx?.ui.setStatus("gsd-auto", undefined);
     ctx?.ui.setWidget("gsd-progress", undefined);
     ctx?.ui.setFooter(undefined);
+    if (ctx) initHealthWidget(ctx);
     restoreProjectRootEnv();
     restoreMilestoneLockEnv();
 
@@ -1044,6 +1061,7 @@ export async function pauseAuto(
   ctx?.ui.setStatus("gsd-auto", "paused");
   ctx?.ui.setWidget("gsd-progress", undefined);
   ctx?.ui.setFooter(undefined);
+  if (ctx) initHealthWidget(ctx);
   const resumeCmd = s.stepMode ? "/gsd next" : "/gsd auto";
   ctx?.ui.notify(
     `${s.stepMode ? "Step" : "Auto"}-mode paused (Escape). Type to interact, or ${resumeCmd} to resume.`,
@@ -1163,6 +1181,7 @@ function buildLoopDeps(): LoopDeps {
     getMainBranch,
     // Unit closeout + runtime records
     closeoutUnit,
+    autoCommitUnit,
     recordOutcome,
     writeLock,
     captureAvailableSkills,
@@ -1383,6 +1402,11 @@ export async function startAuto(
     s.stepMode = requestedStepMode;
     s.cmdCtx = ctx;
     s.basePath = base;
+    // Ensure the workflow-logger audit log is pinned to the project root
+    // even when auto-mode is entered via a path that bypasses the
+    // bootstrap/dynamic-tools ensureDbOpen() → setLogBasePath() chain
+    // (e.g. /clear resume, hot-reload).
+    setLogBasePath(base);
     s.unitDispatchCount.clear();
     s.unitLifetimeDispatches.clear();
     if (!getLedger()) initMetrics(base);

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

@@ -2,7 +2,6 @@
 
 import type { ExtensionAPI, ExtensionCommandContext } from "@gsd/pi-coding-agent";
 
-import { registerGSDCommand } from "../commands.js";
 import { registerExitCommand } from "../exit-command.js";
 import { registerWorktreeCommand } from "../worktree-command.js";
 import { registerDbTools } from "./db-tools.js";
@@ -12,6 +11,7 @@ import { registerQueryTools } from "./query-tools.js";
 import { registerHooks } from "./register-hooks.js";
 import { registerShortcuts } from "./register-shortcuts.js";
 import { writeCrashLog } from "./crash-log.js";
+import { logWarning } from "../workflow-logger.js";
 
 export { writeCrashLog } from "./crash-log.js";
 
@@ -58,7 +58,8 @@ function installEpipeGuard(): void {
 }
 
 export function registerGsdExtension(pi: ExtensionAPI): void {
-  registerGSDCommand(pi);
+  // Note: registerGSDCommand is called by index.ts before this function,
+  // so we intentionally skip it here to avoid double-registration.
   registerWorktreeCommand(pi);
   registerExitCommand(pi);
 
@@ -71,10 +72,25 @@ export function registerGsdExtension(pi: ExtensionAPI): void {
     },
   });
 
-  registerDynamicTools(pi);
-  registerDbTools(pi);
-  registerJournalTools(pi);
-  registerQueryTools(pi);
-  registerShortcuts(pi);
-  registerHooks(pi);
+  // Wrap non-critical registrations individually so one failure
+  // doesn't prevent the others from loading.
+  const nonCriticalRegistrations: Array<[string, () => void]> = [
+    ["dynamic-tools", () => registerDynamicTools(pi)],
+    ["db-tools", () => registerDbTools(pi)],
+    ["journal-tools", () => registerJournalTools(pi)],
+    ["query-tools", () => registerQueryTools(pi)],
+    ["shortcuts", () => registerShortcuts(pi)],
+    ["hooks", () => registerHooks(pi)],
+  ];
+
+  for (const [name, register] of nonCriticalRegistrations) {
+    try {
+      register();
+    } catch (err) {
+      logWarning(
+        "bootstrap",
+        `Failed to register ${name}: ${err instanceof Error ? err.message : String(err)}`,
+      );
+    }
+  }
 }