gsd-pi 2.80.0-dev.c5f2443b3 → 2.80.0-dev.f55d16d13

package/src/resources/extensions/gsd/clean-root-preflight.ts

@@ -21,10 +21,34 @@ import { nativeHasChanges } from "./native-git-bridge.js";
 export interface PreflightResult {
   /** true when a stash was pushed and postflightPopStash should be called */
   stashPushed: boolean;
+  /** Unique marker embedded in the stash message for targeted restoration */
+  stashMarker?: string;
   /** human-readable summary of what happened (empty string for clean trees) */
   summary: string;
 }
 
+function findPreflightStashRef(basePath: string, milestoneId: string, stashMarker?: string): string | null {
+  const markerPrefix = `gsd-preflight-stash:${milestoneId}:`;
+  let fallbackRef: string | null = null;
+  try {
+    const list = execFileSync("git", ["stash", "list", "--format=%gd%x00%s"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+      env: GIT_NO_PROMPT_ENV,
+    });
+    for (const line of list.split("\n")) {
+      const [ref, subject] = line.split("\x00");
+      if (!ref || !subject) continue;
+      if (stashMarker && subject.includes(stashMarker)) return ref;
+      if (!fallbackRef && subject.includes(markerPrefix)) fallbackRef = ref;
+    }
+  } catch (err) {
+    logWarning("preflight", `stash list failed before restore: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  return fallbackRef;
+}
+
 /**
  * Check the working tree for dirty files before a milestone merge.
  *
@@ -62,7 +86,8 @@ export function preflightCleanRoot(
 
   // Push the stash
   try {
-    execFileSync("git", ["stash", "push", "--include-untracked", "-m", "gsd-preflight-stash"], {
+    const stashMarker = `gsd-preflight-stash:${milestoneId}:${process.pid}:${Date.now()}:${process.hrtime.bigint().toString(36)}`;
+    execFileSync("git", ["stash", "push", "--include-untracked", "-m", `gsd-preflight-stash [${stashMarker}]`], {
       cwd: basePath,
       stdio: ["ignore", "pipe", "pipe"],
       encoding: "utf-8",
@@ -70,6 +95,7 @@ export function preflightCleanRoot(
     });
     return {
       stashPushed: true,
+      stashMarker,
       summary: `Stashed uncommitted changes before merge (milestone ${milestoneId}).`,
     };
   } catch (err) {
@@ -91,10 +117,19 @@ export function preflightCleanRoot(
 export function postflightPopStash(
   basePath: string,
   milestoneId: string,
+  stashMarker: string | undefined,
   notify: (message: string, level: "info" | "warning" | "error") => void,
 ): void {
+  let stashRef: string | null = null;
   try {
-    execFileSync("git", ["stash", "pop"], {
+    stashRef = findPreflightStashRef(basePath, milestoneId, stashMarker);
+    if (!stashRef) {
+      const msg = `No matching GSD preflight stash found for milestone ${milestoneId}; leaving stash list untouched.`;
+      logWarning("preflight", msg);
+      notify(msg, "warning");
+      return;
+    }
+    execFileSync("git", ["stash", "pop", stashRef], {
       cwd: basePath,
       stdio: ["ignore", "pipe", "pipe"],
       encoding: "utf-8",
@@ -104,7 +139,10 @@ export function postflightPopStash(
   } catch (err) {
     // Pop conflicts mean the merged code collides with the stashed changes.
     // Log a warning — the user needs to resolve manually, but the merge succeeded.
-    const msg = `git stash pop failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. Run "git stash pop" manually to restore your changes.`;
+    const restoreHint = stashRef
+      ? `Run "git stash pop ${stashRef}" or "git stash apply ${stashRef}" manually to restore the correct stash.`
+      : `Run "git stash list" to find the matching GSD preflight stash before restoring manually.`;
+    const msg = `git stash pop ${stashRef ?? ""}`.trim() + ` failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. ${restoreHint}`;
     logWarning("preflight", msg);
     notify(msg, "warning");
   }

package/src/resources/extensions/gsd/commands-extract-learnings.ts

@@ -222,14 +222,19 @@ Using the \`write\` tool, persist the full structured report to
 LEARNINGS.md is the full, cited audit trail. Write it first — subsequent steps
 feed from its content.
 
-### Step 3 — Optionally pre-query the memory store for semantic duplicates
+### Step 3 — Run one bounded duplicate check
 
-Before persisting any extracted item in Steps 4–6, you may call
-\`memory_query\` with 2–3 keywords from the item to check whether the
-memory store already holds a semantically equivalent entry at high
-confidence. Skip those items in their respective steps. The memory store
-is the single source of truth for cross-session durable knowledge — no
-other persistence call is part of this flow.
+Before persisting extracted items in Steps 4–6, do at most one duplicate-check
+pass for the durable Decisions, Lessons, and Patterns from this milestone. Use
+the already-written LEARNINGS.md content and call \`memory_query\` once with a
+compact keyword summary for the whole batch. If that result clearly shows a
+semantically equivalent high-confidence memory for an item, mark only that item
+as already captured and skip it in its respective persistence step.
+
+Do not re-read milestone artefacts or repeat memory queries category-by-category
+after this point. The memory store is the single source of truth for
+cross-session durable knowledge — no other persistence call is part of this
+flow.
 
 ### Step 4 — Persist Patterns via \`capture_thought\`
 
@@ -268,11 +273,11 @@ later projection back to a human-visible decisions register stays lossless
 
 ### Step 7 — Deduplication rule (applies to Steps 4, 5, 6)
 
-Before each \`capture_thought\` call, optionally call \`memory_query\` with 2–3
-keywords from the entry. If a semantically equivalent memory is returned at
-high confidence, skip the capture entirely. Prefer skipping a near-duplicate
-over creating a second slightly-different row — redundancy degrades the
-signal.
+Use only the duplicate-check result from Step 3. If that bounded check returned
+a semantically equivalent memory at high confidence for an extracted item, skip
+the capture entirely. Otherwise, persist the item once via \`capture_thought\`.
+Prefer skipping a near-duplicate over creating a second slightly-different row
+— redundancy degrades the signal.
 
 ### Step 8 — Surprises stay only in LEARNINGS.md
 

package/src/resources/extensions/gsd/custom-workflow-engine.ts

@@ -29,6 +29,7 @@ import {
   markStepActive,
   markStepComplete,
   expandIteration,
+  isTerminalStepStatus,
   type WorkflowGraph,
 } from "./graph.js";
 import { injectContext } from "./context-injector.js";
@@ -40,6 +41,24 @@ import { withFileLock } from "./file-lock.js";
 // Re-export for downstream consumers
 export { readFrozenDefinition } from "./definition-io.js";
 
+function formatBlockedWorkflowReason(graph: WorkflowGraph): string {
+  const statusById = new Map(graph.steps.map((step) => [step.id, step.status]));
+  const blockedSteps = graph.steps
+    .filter((step) => step.status === "pending")
+    .map((step) => {
+      const blockers = step.dependsOn
+        .filter((depId) => !isTerminalStepStatus(statusById.get(depId)))
+        .map((depId) => `${depId} (${statusById.get(depId) ?? "missing"})`);
+      return blockers.length > 0
+        ? `${step.id} waiting on ${blockers.join(", ")}`
+        : `${step.id} has no runnable dependency path`;
+    });
+
+  return blockedSteps.length > 0
+    ? `Workflow blocked: no pending steps are ready. Blocked steps: ${blockedSteps.join("; ")}`
+    : "Workflow blocked: no pending steps are ready.";
+}
+
 export class CustomWorkflowEngine implements WorkflowEngine {
   readonly engineId = "custom";
   private readonly runDir: string;
@@ -114,7 +133,11 @@ export class CustomWorkflowEngine implements WorkflowEngine {
           (step) => step.status === "complete" || step.status === "expanded",
         );
         if (!allDone) {
-          return { action: "skip" };
+          return {
+            action: "stop",
+            reason: formatBlockedWorkflowReason(graph),
+            level: "error",
+          };
         }
         return {
           action: "stop",

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

@@ -323,6 +323,20 @@ 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 +373,7 @@ 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 +399,23 @@ 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 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/graph.ts

@@ -31,7 +31,7 @@ export interface GraphStep {
   status: "pending" | "active" | "complete" | "expanded";
   /** The prompt to dispatch for this step. */
   prompt: string;
-  /** IDs of steps that must be "complete" before this step can run. */
+  /** IDs of steps that must be terminal before this step can run. */
   dependsOn: string[];
   /** For iteration instances: ID of the parent step that was expanded. */
   parentStepId?: string;
@@ -152,10 +152,17 @@ export function writeGraph(runDir: string, graph: WorkflowGraph): void {
 }
 
 /**
- * Get the next pending step whose dependencies are all complete.
+ * Return whether a graph step status satisfies dependency edges.
+ */
+export function isTerminalStepStatus(status: GraphStep["status"] | undefined): boolean {
+  return status === "complete" || status === "expanded";
+}
+
+/**
+ * Get the next pending step whose dependencies are all terminal.
  *
  * Returns the first step (in array order) with status "pending" where
- * every step in its `dependsOn` list has status "complete".
+ * every step in its `dependsOn` list has status "complete" or "expanded".
  *
  * @param graph — the workflow graph to query
  * @returns The next dispatchable step, or null if none available
@@ -165,8 +172,8 @@ export function getNextPendingStep(graph: WorkflowGraph): GraphStep | null {
 
   for (const step of graph.steps) {
     if (step.status !== "pending") continue;
-    const depsComplete = step.dependsOn.every(
-      (depId) => statusMap.get(depId) === "complete",
+    const depsComplete = step.dependsOn.every((depId) =>
+      isTerminalStepStatus(statusMap.get(depId)),
     );
     if (depsComplete) return step;
   }

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

@@ -77,6 +77,7 @@ import {
   applyMigrationV21StructuredMemories,
   applyMigrationV22QualityGateRepair,
   applyMigrationV23MilestoneQueue,
+  applyMigrationV26MilestoneCommitAttributions,
 } from "./db-migration-steps.js";
 import { isMemoriesFtsAvailableSchema, tryCreateMemoriesFtsSchema } from "./db-memory-fts-schema.js";
 import { createDbOpenState, type DbOpenPhase } from "./db-open-state.js";
@@ -105,7 +106,7 @@ const providerLoader = createSqliteProviderLoader({
   writeStderr: (message: string) => process.stderr.write(message),
 });
 
-export const SCHEMA_VERSION = 25;
+export const SCHEMA_VERSION = 26;
 
 function initSchema(db: DbAdapter, fileBacked: boolean): void {
   if (fileBacked) db.exec("PRAGMA journal_mode=WAL");
@@ -329,6 +330,11 @@ function migrateSchema(db: DbAdapter): void {
       recordSchemaVersion(db, 25);
     }
 
+    if (currentVersion < 26) {
+      applyMigrationV26MilestoneCommitAttributions(db);
+      recordSchemaVersion(db, 26);
+    }
+
     db.exec("COMMIT");
   } catch (err) {
     db.exec("ROLLBACK");
@@ -1349,6 +1355,45 @@ export function getSliceTasks(milestoneId: string, sliceId: string): TaskRow[] {
   return rows.map(rowToTask);
 }
 
+export function getCompletedMilestoneTaskFileHints(milestoneId: string): string[] {
+  if (!currentDb) return [];
+  const rows = currentDb.prepare(
+    `SELECT files, key_files
+     FROM tasks
+     WHERE milestone_id = :mid AND status IN ('complete', 'done')`,
+  ).all({ ":mid": milestoneId }) as Array<Record<string, unknown>>;
+
+  const hints = new Set<string>();
+  for (const row of rows) {
+    for (const raw of [row["files"], row["key_files"]]) {
+      for (const file of parseStringArrayColumn(raw)) {
+        const normalized = normalizeRepoPath(file);
+        if (normalized) hints.add(normalized);
+      }
+    }
+  }
+  return [...hints];
+}
+
+function parseStringArrayColumn(raw: unknown): string[] {
+  if (Array.isArray(raw)) return raw.filter((entry): entry is string => typeof entry === "string");
+  if (typeof raw !== "string") return [];
+  const trimmed = raw.trim();
+  if (!trimmed) return [];
+  try {
+    const parsed = JSON.parse(trimmed);
+    if (Array.isArray(parsed)) return parsed.filter((entry): entry is string => typeof entry === "string");
+    if (typeof parsed === "string") return [parsed];
+  } catch {
+    return trimmed.split(",");
+  }
+  return [];
+}
+
+function normalizeRepoPath(file: string): string {
+  return file.trim().replace(/\\/g, "/").replace(/^\.\/+/, "");
+}
+
 // ─── ADR-011 Phase 2 escalation helpers ──────────────────────────────────
 
 /** Set pause-on-escalation state on a completed task. Mutually exclusive with awaiting_review. */
@@ -2073,6 +2118,9 @@ export function deleteMilestone(milestoneId: string): void {
     currentDb!.prepare(
       `DELETE FROM artifacts WHERE milestone_id = :mid`,
     ).run({ ":mid": milestoneId });
+    currentDb!.prepare(
+      `DELETE FROM milestone_commit_attributions WHERE milestone_id = :mid`,
+    ).run({ ":mid": milestoneId });
     currentDb!.prepare(
       `DELETE FROM milestone_leases WHERE milestone_id = :mid`,
     ).run({ ":mid": milestoneId });
@@ -2391,6 +2439,75 @@ export function upsertTurnGitTransaction(entry: {
   });
 }
 
+export function getMilestoneCommitAttributionShas(milestoneId: string): string[] {
+  if (!currentDb) return [];
+  const rows = currentDb.prepare(
+    `SELECT commit_sha
+     FROM milestone_commit_attributions
+     WHERE milestone_id = :mid
+     ORDER BY created_at, commit_sha`,
+  ).all({ ":mid": milestoneId }) as Array<Record<string, unknown>>;
+  return rows
+    .map((row) => typeof row["commit_sha"] === "string" ? row["commit_sha"] : "")
+    .filter(Boolean);
+}
+
+export function recordMilestoneCommitAttribution(entry: {
+  commitSha: string;
+  milestoneId: string;
+  sliceId?: string;
+  taskId?: string;
+  source: "recorded" | "backfill";
+  confidence: number;
+  files: string[];
+  createdAt: string;
+}): void {
+  if (!currentDb) return;
+  transaction(() => {
+    currentDb!.prepare(
+      `INSERT OR REPLACE INTO milestone_commit_attributions (
+        commit_sha, milestone_id, slice_id, task_id, source, confidence, files_json, created_at
+      ) VALUES (
+        :commit_sha, :milestone_id, :slice_id, :task_id, :source, :confidence, :files_json, :created_at
+      )`,
+    ).run({
+      ":commit_sha": entry.commitSha,
+      ":milestone_id": entry.milestoneId,
+      ":slice_id": entry.sliceId ?? null,
+      ":task_id": entry.taskId ?? null,
+      ":source": entry.source,
+      ":confidence": entry.confidence,
+      ":files_json": JSON.stringify(entry.files),
+      ":created_at": entry.createdAt,
+    });
+
+    currentDb!.prepare(
+      `INSERT OR IGNORE INTO audit_events (
+        event_id, trace_id, turn_id, caused_by, category, type, ts, payload_json
+      ) VALUES (
+        :event_id, :trace_id, :turn_id, :caused_by, :category, :type, :ts, :payload_json
+      )`,
+    ).run({
+      ":event_id": `milestone-commit-attribution:${entry.milestoneId}:${entry.commitSha}`,
+      ":trace_id": "milestone-commit-attribution",
+      ":turn_id": null,
+      ":caused_by": null,
+      ":category": "git",
+      ":type": "milestone-commit-attribution-recorded",
+      ":ts": entry.createdAt,
+      ":payload_json": JSON.stringify({
+        commitSha: entry.commitSha,
+        milestoneId: entry.milestoneId,
+        sliceId: entry.sliceId ?? null,
+        taskId: entry.taskId ?? null,
+        source: entry.source,
+        confidence: entry.confidence,
+        files: entry.files,
+      }),
+    });
+  });
+}
+
 export function insertAuditEvent(entry: {
   eventId: string;
   traceId: string;
@@ -2494,6 +2611,7 @@ export function clearEngineHierarchy(): void {
     currentDb!.exec("DELETE FROM slice_dependencies");
     currentDb!.exec("DELETE FROM assessments");
     currentDb!.exec("DELETE FROM replan_history");
+    currentDb!.exec("DELETE FROM milestone_commit_attributions");
     currentDb!.exec("DELETE FROM tasks");
     currentDb!.exec("DELETE FROM slices");
     currentDb!.exec("DELETE FROM milestone_leases");

package/src/resources/extensions/gsd/guided-flow.ts

@@ -2064,8 +2064,8 @@ export async function showSmartEntry(
   // standard wizard below.
   {
     const prefs = loadEffectiveGSDPreferences(basePath)?.preferences;
-    const { hasPendingDeepStage } = await import("./auto-dispatch.js");
-    if (hasPendingDeepStage(prefs, basePath)) {
+    const { shouldRunDeepProjectSetup } = await import("./auto-dispatch.js");
+    if (shouldRunDeepProjectSetup(state, prefs, basePath)) {
       await startDeepProjectSetupForeground(ctx, pi, basePath, stepMode);
       return;
     }