gsd-pi 2.80.0-dev.710c06e97 → 2.80.0-dev.7582bf37a

package/src/resources/extensions/gsd/crash-recovery.ts

@@ -38,6 +38,7 @@ import { _getAdapter, isDbAvailable } from "./gsd-db.js";
 import { gsdRoot, normalizeRealPath } from "./paths.js";
 import { atomicWriteSync } from "./atomic-write.js";
 import { effectiveLockFile } from "./session-lock.js";
+import { isInFlightRuntimePhase, listUnitRuntimeRecords, type AutoUnitRuntimeRecord } from "./unit-runtime.js";
 
 export interface LockData {
   pid: number;
@@ -103,10 +104,40 @@ function getLatestDispatchForWorker(workerId: string):
   return row ?? null;
 }
 
-function workerToLockData(worker: AutoWorkerRow): LockData {
+function latestInFlightRuntimeRecord(basePath: string): AutoUnitRuntimeRecord | null {
+  const records = listUnitRuntimeRecords(basePath).filter((record) =>
+    isInFlightRuntimePhase(record.phase),
+  );
+  if (records.length === 0) return null;
+  return records.sort((a, b) => {
+    const bTime = b.updatedAt || b.startedAt || 0;
+    const aTime = a.updatedAt || a.startedAt || 0;
+    return bTime - aTime;
+  })[0] ?? null;
+}
+
+function runtimeRecordToLockData(worker: AutoWorkerRow, record: AutoUnitRuntimeRecord, sessionFile?: string): LockData {
+  const startedAt = Number.isFinite(record.startedAt)
+    ? new Date(record.startedAt).toISOString()
+    : worker.started_at;
+  return {
+    pid: worker.pid,
+    startedAt: worker.started_at,
+    unitType: record.unitType,
+    unitId: record.unitId,
+    unitStartedAt: startedAt,
+    sessionFile,
+  };
+}
+
+function workerToLockData(basePath: string, worker: AutoWorkerRow): LockData {
   const dispatch = getLatestDispatchForWorker(worker.worker_id);
   const sessionFile =
     getRuntimeKv<string>("worker", worker.worker_id, SESSION_FILE_KV_KEY) ?? undefined;
+  if (!dispatch) {
+    const runtimeRecord = latestInFlightRuntimeRecord(basePath);
+    if (runtimeRecord) return runtimeRecordToLockData(worker, runtimeRecord, sessionFile);
+  }
   return {
     pid: worker.pid,
     startedAt: worker.started_at,
@@ -204,7 +235,7 @@ export function readCrashLock(basePath: string): LockData | null {
     try {
       const projectRoot = normalizeRealPath(basePath);
       const stale = findStaleWorkerForProject(projectRoot);
-      if (stale) return workerToLockData(stale);
+      if (stale) return workerToLockData(basePath, stale);
     } catch {
       // Fall through to the legacy lock-file compatibility path.
     }
@@ -260,25 +291,48 @@ export function formatCrashInfo(lock: LockData): string {
  */
 export function emitCrashRecoveredUnitEnd(basePath: string, lock: LockData): void {
   if (!lock.unitType || !lock.unitId || lock.unitType === "starting") return;
+  emitOpenUnitEndForUnit(basePath, lock.unitType, lock.unitId, "crash-recovered");
+}
 
+export function emitOpenUnitEndForUnit(
+  basePath: string,
+  unitType: string,
+  unitId: string,
+  status: string,
+  errorContext?: { message: string; category: string; stopReason?: string; isTransient?: boolean; retryAfterMs?: number },
+): boolean {
   try {
     const all = queryJournal(basePath);
 
     const starts = all.filter(
-      (e) => e.eventType === "unit-start" && e.data?.unitId === lock.unitId,
+      (e) =>
+        e.eventType === "unit-start" &&
+        e.data?.unitType === unitType &&
+        e.data?.unitId === unitId,
     );
-    if (starts.length === 0) return;
+    if (starts.length === 0) return false;
 
-    const lastStart = starts[starts.length - 1];
+    const lastStart = [...starts].reverse().find((start) => {
+      return !all.some(
+        (e) =>
+          e.eventType === "unit-end" &&
+          e.data?.unitType === unitType &&
+          e.data?.unitId === unitId &&
+          e.causedBy?.flowId === start.flowId &&
+          e.causedBy?.seq === start.seq,
+      );
+    });
+    if (!lastStart) return false;
 
     const alreadyClosed = all.some(
       (e) =>
         e.eventType === "unit-end" &&
-        e.data?.unitId === lock.unitId &&
+        e.data?.unitType === unitType &&
+        e.data?.unitId === unitId &&
         e.causedBy?.flowId === lastStart.flowId &&
         e.causedBy?.seq === lastStart.seq,
     );
-    if (alreadyClosed) return;
+    if (alreadyClosed) return false;
 
     const maxSeq = all
       .filter((e) => e.flowId === lastStart.flowId)
@@ -290,15 +344,18 @@ export function emitCrashRecoveredUnitEnd(basePath: string, lock: LockData): voi
       seq: maxSeq + 1,
       eventType: "unit-end",
       data: {
-        unitType: lock.unitType,
-        unitId: lock.unitId,
-        status: "crash-recovered",
+        unitType,
+        unitId,
+        status,
         artifactVerified: false,
+        ...(errorContext ? { errorContext } : {}),
       },
       causedBy: { flowId: lastStart.flowId, seq: lastStart.seq },
     });
+    return true;
   } catch {
     // Never throw from crash recovery path.
+    return false;
   }
 }
 

package/src/resources/extensions/gsd/dashboard-overlay.ts

@@ -29,7 +29,7 @@ import { computeProgressScore, formatProgressLine } from "./progress-score.js";
 import { runEnvironmentChecks, type EnvironmentCheckResult } from "./doctor-environment.js";
 import { formattedShortcutPair } from "./shortcut-defs.js";
 
-function unitLabel(type: string): string {
+export function unitLabel(type: string): string {
   switch (type) {
     case "discuss-milestone":
     case "discuss-slice": return "Discuss";

package/src/resources/extensions/gsd/db/unit-dispatches.ts

@@ -98,6 +98,70 @@ function isAlreadyActiveConstraintError(err: unknown): boolean {
   return /\bUNIQUE\b|\bconstraint failed\b/i.test(msg);
 }
 
+function settleStaleActiveDispatchForUnit(input: RecordClaimInput, now: string): void {
+  const db = _getAdapter()!;
+  const active = db.prepare(
+    `SELECT id, status, worker_id, milestone_lease_token
+     FROM unit_dispatches
+     WHERE unit_id = :unit_id
+       AND status IN ('claimed','running')
+     ORDER BY id DESC
+     LIMIT 1`,
+  ).get({ ":unit_id": input.unitId }) as
+    | { id: number; status: DispatchStatus; worker_id: string; milestone_lease_token: number }
+    | undefined;
+
+  if (!active) return;
+  if (
+    active.worker_id === input.workerId &&
+    active.milestone_lease_token === input.milestoneLeaseToken
+  ) {
+    return;
+  }
+
+  const reason = "stale-dispatch-lease-takeover";
+  const result = db.prepare(
+    `UPDATE unit_dispatches
+     SET status = 'canceled',
+         ended_at = :ended_at,
+         exit_reason = :reason
+     WHERE id = :id
+       AND status IN ('claimed','running')
+       AND (worker_id != :worker_id OR milestone_lease_token != :token)`,
+  ).run({
+    ":id": active.id,
+    ":ended_at": now,
+    ":reason": reason,
+    ":worker_id": input.workerId,
+    ":token": input.milestoneLeaseToken,
+  });
+
+  const changes =
+    typeof (result as { changes?: unknown }).changes === "number"
+      ? (result as { changes: number }).changes
+      : 0;
+  if (changes < 1) return;
+
+  insertAuditEvent({
+    eventId: randomUUID(),
+    traceId: input.traceId,
+    turnId: input.turnId ?? undefined,
+    category: "orchestration",
+    type: "dispatch-stale-canceled",
+    ts: now,
+    payload: {
+      dispatchId: active.id,
+      unitId: input.unitId,
+      priorStatus: active.status,
+      priorWorkerId: active.worker_id,
+      priorMilestoneLeaseToken: active.milestone_lease_token,
+      takeoverWorkerId: input.workerId,
+      takeoverMilestoneLeaseToken: input.milestoneLeaseToken,
+      reason,
+    },
+  });
+}
+
 /**
  * Insert a new dispatch row in `claimed` state. Atomic guard against
  * double-claim (B2): the partial unique index
@@ -135,6 +199,8 @@ export function recordDispatchClaim(input: RecordClaimInput): RecordClaimResult
       };
     }
 
+    settleStaleActiveDispatchForUnit(input, now);
+
     try {
       const result = db.prepare(
         `INSERT INTO unit_dispatches (
@@ -359,6 +425,47 @@ export function markCanceled(dispatchId: number, reason: string): void {
   ).run({ ":id": dispatchId, ":ended_at": now, ":reason": reason });
 }
 
+/**
+ * Best-effort signal/crash cleanup: cancel the latest active dispatch owned by
+ * a worker when the process is exiting before the normal loop can settle it.
+ */
+export function markLatestActiveForWorkerCanceled(workerId: string, reason: string): boolean {
+  if (!isDbAvailable()) return false;
+  const now = new Date().toISOString();
+  const db = _getAdapter()!;
+  const result = transaction(() => {
+    return db.prepare(
+      `UPDATE unit_dispatches
+       SET status = 'canceled', ended_at = :ended_at, exit_reason = :reason
+       WHERE id = (
+         SELECT id FROM unit_dispatches
+         WHERE worker_id = :worker_id
+           AND status IN ('pending','claimed','running')
+         ORDER BY id DESC
+         LIMIT 1
+       )`,
+    ).run({
+      ":ended_at": now,
+      ":reason": reason,
+      ":worker_id": workerId,
+    });
+  });
+  const changes =
+    typeof (result as { changes?: unknown }).changes === "number"
+      ? (result as { changes: number }).changes
+      : 0;
+  if (changes <= 0) return false;
+  insertAuditEvent({
+    eventId: randomUUID(),
+    traceId: workerId,
+    category: "orchestration",
+    type: "dispatch-canceled",
+    ts: now,
+    payload: { workerId, reason },
+  });
+  return true;
+}
+
 /**
  * Fetch the most recent N dispatches for a unit. Used by recordDispatchClaim
  * callers to compute attempt_n and by detect-stuck.ts (B3) to consult

package/src/resources/extensions/gsd/db-base-schema.ts

@@ -57,7 +57,8 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
       slice_id TEXT DEFAULT NULL,
       task_id TEXT DEFAULT NULL,
       full_content TEXT NOT NULL DEFAULT '',
-      imported_at TEXT NOT NULL DEFAULT ''
+      imported_at TEXT NOT NULL DEFAULT '',
+      content_hash TEXT DEFAULT NULL
     )
   `);
 
@@ -76,7 +77,8 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
       hit_count INTEGER NOT NULL DEFAULT 0,
       scope TEXT NOT NULL DEFAULT 'project',
       tags TEXT NOT NULL DEFAULT '[]',
-      structured_fields TEXT DEFAULT NULL
+      structured_fields TEXT DEFAULT NULL,
+      last_hit_at TEXT DEFAULT NULL
     )
   `);
 
@@ -323,6 +325,20 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
     )
   `);
 
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS milestone_commit_attributions (
+      commit_sha TEXT NOT NULL,
+      milestone_id TEXT NOT NULL,
+      slice_id TEXT DEFAULT NULL,
+      task_id TEXT DEFAULT NULL,
+      source TEXT NOT NULL DEFAULT 'recorded',
+      confidence REAL NOT NULL DEFAULT 1.0,
+      files_json TEXT NOT NULL DEFAULT '[]',
+      created_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (commit_sha, milestone_id)
+    )
+  `);
+
   db.exec(`
     CREATE TABLE IF NOT EXISTS audit_events (
       event_id TEXT PRIMARY KEY,
@@ -359,6 +375,7 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
   db.exec("CREATE INDEX IF NOT EXISTS idx_gate_runs_turn ON gate_runs(trace_id, turn_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_gate_runs_lookup ON gate_runs(milestone_id, slice_id, task_id, gate_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_turn_git_tx_turn ON turn_git_transactions(trace_id, turn_id)");
+  db.exec("CREATE INDEX IF NOT EXISTS idx_milestone_commit_attr_milestone ON milestone_commit_attributions(milestone_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_trace ON audit_events(trace_id, ts)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_turn ON audit_events(trace_id, turn_id, ts)");
 

package/src/resources/extensions/gsd/db-migration-steps.ts

@@ -399,6 +399,31 @@ export function applyMigrationV23MilestoneQueue(db: DbAdapter): void {
   ensureColumn(db, "milestones", "sequence", "ALTER TABLE milestones ADD COLUMN sequence INTEGER DEFAULT 0");
 }
 
+export function applyMigrationV26MilestoneCommitAttributions(db: DbAdapter): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS milestone_commit_attributions (
+      commit_sha TEXT NOT NULL,
+      milestone_id TEXT NOT NULL,
+      slice_id TEXT DEFAULT NULL,
+      task_id TEXT DEFAULT NULL,
+      source TEXT NOT NULL DEFAULT 'recorded',
+      confidence REAL NOT NULL DEFAULT 1.0,
+      files_json TEXT NOT NULL DEFAULT '[]',
+      created_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (commit_sha, milestone_id)
+    )
+  `);
+  db.exec("CREATE INDEX IF NOT EXISTS idx_milestone_commit_attr_milestone ON milestone_commit_attributions(milestone_id)");
+}
+
+export function applyMigrationV27ArtifactHash(db: DbAdapter): void {
+  ensureColumn(db, "artifacts", "content_hash", "ALTER TABLE artifacts ADD COLUMN content_hash TEXT DEFAULT NULL");
+}
+
+export function applyMigrationV28MemoryLastHitAt(db: DbAdapter): void {
+  ensureColumn(db, "memories", "last_hit_at", "ALTER TABLE memories ADD COLUMN last_hit_at TEXT DEFAULT NULL");
+}
+
 export interface MigrationV22Hooks {
   copyQualityGateRowsToRepairedTable(db: DbAdapter): void;
 }

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

@@ -6,6 +6,7 @@
  * flow to show when entering a project directory.
  */
 
+import { execFileSync } from "node:child_process";
 import { existsSync, openSync, readSync, closeSync, readdirSync, readFileSync, statSync } from "node:fs";
 import { dirname, join, parse as parsePath } from "node:path";
 import { homedir } from "node:os";
@@ -72,6 +73,22 @@ export interface ProjectSignals {
   verificationCommands: string[];
 }
 
+export type ProjectClassificationKind =
+  | "invalid-repo"
+  | "greenfield"
+  | "untyped-existing"
+  | "typed-existing";
+
+export interface ProjectClassification {
+  kind: ProjectClassificationKind;
+  signals: ProjectSignals;
+  trackedFiles: string[];
+  untrackedFiles: string[];
+  contentFiles: string[];
+  markers: string[];
+  reason: string;
+}
+
 // ─── Project File Markers ───────────────────────────────────────────────────────
 
 export const PROJECT_FILES = [
@@ -243,6 +260,7 @@ const TEST_MARKERS = [
 const RECURSIVE_SCAN_IGNORED_DIRS = new Set([
   ".git",
   ".gsd",
+  ".bg-shell",
   ".planning",
   ".plans",
   ".claude",
@@ -267,6 +285,8 @@ const RECURSIVE_SCAN_IGNORED_DIRS = new Set([
   "out",
 ]) as ReadonlySet<string>;
 
+const PROJECT_CONTENT_EXCLUDE_DIRS = RECURSIVE_SCAN_IGNORED_DIRS;
+
 /** Project file markers safe to detect recursively via suffix matching. */
 const ROOT_ONLY_PROJECT_FILES = new Set<string>([
   ".github/workflows",
@@ -536,6 +556,114 @@ export function detectProjectSignals(basePath: string): ProjectSignals {
   };
 }
 
+function normalizeGitPath(file: string): string {
+  return file.replaceAll("\\", "/").replace(/^\.\//, "");
+}
+
+function isProjectContentFile(file: string): boolean {
+  const normalized = normalizeGitPath(file);
+  if (!normalized || normalized.endsWith("/")) return false;
+  if (normalized === ".gitignore" || normalized === ".gitattributes") return false;
+  const parts = normalized.split("/");
+  if (parts.some((part) => PROJECT_CONTENT_EXCLUDE_DIRS.has(part))) return false;
+  if (normalized.endsWith(".DS_Store")) return false;
+  return true;
+}
+
+function runGitLines(basePath: string, args: string[]): string[] {
+  try {
+    const output = execFileSync("git", args, {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "ignore"],
+      encoding: "utf-8",
+    }).trim();
+    return output ? output.split("\n").map((line) => line.trim()).filter(Boolean) : [];
+  } catch {
+    return [];
+  }
+}
+
+function listTrackedProjectFiles(basePath: string): string[] {
+  return runGitLines(basePath, ["ls-files"])
+    .map(normalizeGitPath)
+    .filter(isProjectContentFile);
+}
+
+function listUntrackedProjectFiles(basePath: string): string[] {
+  return runGitLines(basePath, ["ls-files", "--others", "--exclude-standard"])
+    .map(normalizeGitPath)
+    .filter(isProjectContentFile);
+}
+
+function hasKnownProjectMarkers(basePath: string, signals: ProjectSignals): boolean {
+  if (signals.detectedFiles.length > 0) return true;
+  if (signals.xcodePlatforms.length > 0) return true;
+  return false;
+}
+
+/**
+ * Classify repo presence separately from ecosystem/tooling markers.
+ *
+ * Known project files identify tooling. Git-tracked/non-ignored content
+ * identifies whether this is an existing project at all. This keeps small
+ * static or documentation repos from being mislabeled as greenfield.
+ */
+export function classifyProject(basePath: string): ProjectClassification {
+  const signals = detectProjectSignals(basePath);
+  const markers = [...signals.detectedFiles];
+
+  if (!signals.isGitRepo) {
+    return {
+      kind: "invalid-repo",
+      signals,
+      trackedFiles: [],
+      untrackedFiles: [],
+      contentFiles: [],
+      markers,
+      reason: "missing .git",
+    };
+  }
+
+  const trackedFiles = listTrackedProjectFiles(basePath);
+  const untrackedFiles = listUntrackedProjectFiles(basePath);
+  const contentFiles = [...new Set([...trackedFiles, ...untrackedFiles])];
+  const hasMarkers = hasKnownProjectMarkers(basePath, signals);
+
+  if (hasMarkers) {
+    return {
+      kind: "typed-existing",
+      signals,
+      trackedFiles,
+      untrackedFiles,
+      contentFiles,
+      markers,
+      reason: markers.length > 0 ? `detected markers: ${markers.join(", ")}` : "detected project structure",
+    };
+  }
+
+  if (contentFiles.length > 0) {
+    return {
+      kind: "untyped-existing",
+      signals,
+      trackedFiles,
+      untrackedFiles,
+      contentFiles,
+      markers,
+      reason: "project content exists but no recognized tooling markers were found",
+    };
+  }
+
+  return {
+    kind: "greenfield",
+    signals,
+    trackedFiles,
+    untrackedFiles,
+    contentFiles,
+    markers,
+    reason: "no tracked or non-ignored project content",
+  };
+}
+
 // ─── Xcode Platform Detection ───────────────────────────────────────────────────
 
 /** Known SDKROOT values → canonical platform names. */

package/src/resources/extensions/gsd/ecosystem/gsd-extension-api.ts

@@ -204,6 +204,9 @@ export function createGSDExtensionAPI(
     getAllTools: () => pi.getAllTools(),
     setActiveTools: (...args: Parameters<ExtensionAPI["setActiveTools"]>) =>
       pi.setActiveTools(...args),
+    getVisibleSkills: () => pi.getVisibleSkills(),
+    setVisibleSkills: (...args: Parameters<ExtensionAPI["setVisibleSkills"]>) =>
+      pi.setVisibleSkills(...args),
     getCommands: () => pi.getCommands(),
 
     // ── Model & thinking ───────────────────────────────────────────────

package/src/resources/extensions/gsd/git-service.ts

@@ -1,3 +1,5 @@
+// Project/App: GSD-2
+// File Purpose: Git operations, commit-message formatting, and turn git actions.
 /**
  * GSD Git Service
  *
@@ -14,6 +16,7 @@ import { isAbsolute, join, normalize, relative, resolve, sep } from "node:path";
 import { gsdRoot } from "./paths.js";
 import { GIT_NO_PROMPT_ENV } from "./git-constants.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
+import { logWarning } from "./workflow-logger.js";
 
 
 import {
@@ -128,6 +131,11 @@ export interface TurnGitActionResult {
 export interface TaskCommitContext {
   taskId: string;
   taskTitle: string;
+  milestoneId?: string;
+  milestoneTitle?: string;
+  sliceId?: string;
+  sliceTitle?: string;
+  taskDisplayId?: string;
   /** The one-liner from the task summary (e.g. "Added retry-aware worker status logging") */
   oneLiner?: string;
   /** Files modified by this task (from task summary frontmatter) */
@@ -169,6 +177,11 @@ export function buildTaskCommitMessage(ctx: TaskCommitContext): string {
     bodyParts.push(fileLines);
   }
 
+  const contextLines = buildTaskCommitContextLines(ctx);
+  if (contextLines.length > 0) {
+    bodyParts.push(`GSD context:\n${contextLines.join("\n")}`);
+  }
+
   // Trailers: GSD-Task first, then Resolves
   bodyParts.push(`GSD-Task: ${ctx.taskId}`);
 
@@ -179,6 +192,28 @@ export function buildTaskCommitMessage(ctx: TaskCommitContext): string {
   return `${subject}\n\n${bodyParts.join("\n\n")}`;
 }
 
+function buildTaskCommitContextLines(ctx: TaskCommitContext): string[] {
+  const lines: string[] = [];
+  const milestone = formatNamedContext(ctx.milestoneId, ctx.milestoneTitle);
+  const slice = formatNamedContext(ctx.sliceId, ctx.sliceTitle);
+  const taskId = ctx.taskDisplayId ?? ctx.taskId.split("/").pop();
+  const task = formatNamedContext(taskId, ctx.taskTitle);
+
+  if (milestone) lines.push(`- Milestone: ${milestone}`);
+  if (slice) lines.push(`- Slice: ${slice}`);
+  if (task) lines.push(`- Task: ${task}`);
+  return lines;
+}
+
+function formatNamedContext(id: string | undefined, title: string | undefined): string | null {
+  const cleanId = id?.trim();
+  const cleanTitle = title?.trim();
+  if (!cleanId && !cleanTitle) return null;
+  if (!cleanId) return cleanTitle ?? null;
+  if (!cleanTitle || cleanTitle === cleanId) return cleanId;
+  return `${cleanId} - ${cleanTitle}`;
+}
+
 function sanitizeCommitSubjectDescription(value: string): string {
   const cleaned = value
     .replace(/[\x00-\x1F\x7F]+/g, " ")
@@ -722,16 +757,53 @@ export class GitServiceImpl {
     if (keyFiles.length === 0) return false;
 
     const allExclusions = [...RUNTIME_EXCLUSION_PATHS, ...extraExclusions];
-    const paths = Array.from(new Set(
-      keyFiles
-        .map(file => normalizeRepoRelativePath(this.basePath, file))
-        .filter((file): file is string => file !== null)
-        .filter(file => !isExcludedScopedPath(file, allExclusions)),
-    ));
+    const normalized = keyFiles
+      .map(file => normalizeRepoRelativePath(this.basePath, file))
+      .filter((file): file is string => file !== null)
+      .filter(file => !isExcludedScopedPath(file, allExclusions));
+
+    // Drop entries that don't exist on disk. The LLM occasionally lists files
+    // it intended to write but didn't (or names them with wrong casing/path).
+    // Pre-`b304f738b` `git add -A` swallowed these silently; the scoped
+    // pathspec form passes each path explicitly, so a single bad entry made
+    // the whole commit fail (see #5500). Filter so valid paths still commit.
+    const missing: string[] = [];
+    const existing: string[] = [];
+    for (const path of normalized) {
+      if (existsSync(join(this.basePath, path))) {
+        existing.push(path);
+      } else {
+        missing.push(path);
+      }
+    }
+    if (missing.length > 0) {
+      logWarning(
+        "engine",
+        `scoped stage: dropping ${missing.length} non-existent keyFile(s) from task commit: ${missing.join(", ")}`,
+        { file: "git-service.ts" },
+      );
+    }
+
+    const paths = Array.from(new Set(existing));
     if (paths.length === 0) return false;
 
-    nativeAddPaths(this.basePath, paths);
-    return true;
+    try {
+      nativeAddPaths(this.basePath, paths);
+      return true;
+    } catch (err) {
+      // Defense-in-depth: even after existence filtering, libgit2/git can
+      // still reject paths (gitignore matches, case-only differences on
+      // case-insensitive FS, submodule boundaries). Returning false lets
+      // autoCommit fall through to smartStage so the commit still goes out
+      // — restoring the resilience the unscoped path used to provide.
+      const msg = err instanceof Error ? err.message : String(err);
+      logWarning(
+        "engine",
+        `scoped stage failed (${msg}); falling back to smartStage`,
+        { file: "git-service.ts" },
+      );
+      return false;
+    }
   }
 
   /** Tracks whether runtime file cleanup has run this session. */
@@ -1035,7 +1107,7 @@ export function createDraftPR(
   milestoneId: string,
   title: string,
   body: string,
-  opts?: { head?: string; base?: string },
+  opts?: { head?: string; base?: string; env?: NodeJS.ProcessEnv },
 ): string | null {
   try {
     const args = [
@@ -1045,7 +1117,12 @@ export function createDraftPR(
     ];
     if (opts?.head) args.push("--head", opts.head);
     if (opts?.base) args.push("--base", opts.base);
-    const result = execFileSync("gh", args, { cwd: basePath, encoding: "utf8", timeout: 30000, env: GIT_NO_PROMPT_ENV });
+    const result = execFileSync("gh", args, {
+      cwd: basePath,
+      encoding: "utf8",
+      timeout: 30000,
+      env: opts?.env ?? GIT_NO_PROMPT_ENV,
+    });
     return result.trim();
   } catch {
     return null;