gsd-pi 2.58.0 → 2.59.0-dev.3de3832

package/src/resources/extensions/gsd/prompts/rethink.md

@@ -80,4 +80,4 @@ If a proposed order would violate constraints, explain the issue and suggest alt
 - Do NOT park completed milestones — it would corrupt dependency satisfaction
 - Park is preferred over discard when a milestone has any completed work
 - Always persist queue order changes to `.gsd/QUEUE-ORDER.json`
-- After changes, run `git add .gsd/ && git commit -m "docs(gsd): rethink milestone plan"` to persist (rethink runs interactively outside auto-mode, so no system auto-commit)
+- {{commitInstruction}}

package/src/resources/extensions/gsd/prompts/triage-captures.md

@@ -54,6 +54,7 @@ For each capture, classify it as one of:
    - Add `**Resolution:** <brief description of what will happen>`
    - Add `**Rationale:** <why this classification>`
    - Add `**Resolved:** <current ISO timestamp>`
+   - Add `**Milestone:** <current milestone ID>` (e.g., `**Milestone:** M003`)
 
 4. **Summarize** what was triaged: how many captures, what classifications were assigned, and what actions are pending (e.g., "2 quick-tasks ready for execution, 1 deferred to S03").
 

package/src/resources/extensions/gsd/repo-identity.ts

@@ -8,7 +8,7 @@
 
 import { createHash } from "node:crypto";
 import { execFileSync } from "node:child_process";
-import { existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, realpathSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
+import { cpSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, realpathSync, renameSync, rmSync, symlinkSync, unlinkSync, writeFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { basename, dirname, join, resolve } from "node:path";
 
@@ -276,9 +276,14 @@ export function validateProjectId(id: string): boolean {
  * If `GSD_PROJECT_ID` is set, returns it directly (validation is expected
  * to have already happened at startup via `validateProjectId`).
  *
- * Otherwise returns SHA-256 of `${remoteUrl}\n${resolvedRoot}`, truncated
- * to 12 hex chars. Deterministic: same repo always produces the same hash
- * regardless of which worktree the caller is inside.
+ * For repos with a remote URL, returns SHA-256 of the remote URL only —
+ * this makes the identity stable across directory moves/renames (#2750).
+ *
+ * For local-only repos (no remote), includes the git root in the hash.
+ * Local repos use a `.gsd-id` marker file for recovery after moves.
+ *
+ * Deterministic: same repo always produces the same hash regardless of
+ * which worktree the caller is inside.
  */
 export function repoIdentity(basePath: string): string {
   const projectId = process.env.GSD_PROJECT_ID;
@@ -286,8 +291,14 @@ export function repoIdentity(basePath: string): string {
     return projectId;
   }
   const remoteUrl = getRemoteUrl(basePath);
+  if (remoteUrl) {
+    // Remote URL alone uniquely identifies the repo — path is redundant.
+    // This makes moves transparent for repos with remotes (#2750).
+    return createHash("sha256").update(remoteUrl).digest("hex").slice(0, 12);
+  }
+  // Local-only repo: include git root since there's no remote to anchor identity.
   const root = resolveGitRoot(basePath);
-  const input = `${remoteUrl}\n${root}`;
+  const input = `\n${root}`;
   return createHash("sha256").update(input).digest("hex").slice(0, 12);
 }
 
@@ -351,21 +362,148 @@ export function cleanNumberedGsdVariants(projectPath: string): string[] {
   return removed;
 }
 
+// ─── .gsd-id Marker ─────────────────────────────────────────────────────────
+
+/**
+ * Write a `.gsd-id` marker file in the project root.
+ *
+ * This file records the identity hash used for the external state directory.
+ * For local-only repos (no remote), this marker survives directory moves and
+ * enables automatic recovery of orphaned state (#2750).
+ *
+ * The marker is gitignored by ensureGitignore(). Non-fatal: failure to write
+ * the marker must never block project setup.
+ */
+function writeGsdIdMarker(projectPath: string, identity: string): void {
+  try {
+    const markerPath = join(projectPath, ".gsd-id");
+    // Only write if content differs to avoid unnecessary disk writes.
+    if (existsSync(markerPath)) {
+      try {
+        if (readFileSync(markerPath, "utf-8").trim() === identity) return;
+      } catch { /* fall through and overwrite */ }
+    }
+    writeFileSync(markerPath, identity + "\n", "utf-8");
+  } catch {
+    // Non-fatal — marker write failure should not block project setup
+  }
+}
+
+/**
+ * Read the `.gsd-id` marker from the project root.
+ * Returns the identity hash, or null if the marker doesn't exist or is unreadable.
+ */
+function readGsdIdMarker(projectPath: string): string | null {
+  try {
+    const markerPath = join(projectPath, ".gsd-id");
+    if (!existsSync(markerPath)) return null;
+    const content = readFileSync(markerPath, "utf-8").trim();
+    return /^[a-zA-Z0-9_-]+$/.test(content) ? content : null;
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Check whether an external state directory has meaningful content.
+ * Returns true if the directory contains any files or subdirectories
+ * beyond just repo-meta.json.
+ */
+function hasProjectState(externalPath: string): boolean {
+  try {
+    if (!existsSync(externalPath)) return false;
+    const entries = readdirSync(externalPath);
+    return entries.some(e => e !== "repo-meta.json");
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Resolve the external state directory, with recovery for relocated projects.
+ *
+ * For local-only repos where the computed identity produces an empty state dir,
+ * checks the `.gsd-id` marker for the original identity hash and recovers
+ * the old state directory if it still exists and contains data (#2750).
+ *
+ * Returns the resolved external path (may differ from the computed identity).
+ */
+function resolveExternalPathWithRecovery(projectPath: string): string {
+  const computedPath = externalGsdRoot(projectPath);
+  const computedId = repoIdentity(projectPath);
+
+  // Check if computed path already has state — fast path, no recovery needed.
+  if (hasProjectState(computedPath)) {
+    return computedPath;
+  }
+
+  // Check for .gsd-id marker from a previous location.
+  const markerId = readGsdIdMarker(projectPath);
+  if (markerId && markerId !== computedId) {
+    // The marker points to a different identity — the repo was likely moved.
+    const base = process.env.GSD_STATE_DIR || gsdHome;
+    const markerPath = join(base, "projects", markerId);
+    if (hasProjectState(markerPath)) {
+      // Recover: use the old state directory and update the marker to the new identity.
+      // Move the state from the old hash dir to the new one so future lookups work
+      // without the marker.
+      try {
+        mkdirSync(computedPath, { recursive: true });
+        const entries = readdirSync(markerPath);
+        for (const entry of entries) {
+          try {
+            const src = join(markerPath, entry);
+            const dst = join(computedPath, entry);
+            // Use rename for same-filesystem (fast) or fall back to copy.
+            try {
+              renameSync(src, dst);
+            } catch {
+              cpSync(src, dst, { recursive: true, force: true });
+            }
+          } catch { /* continue with remaining entries */ }
+        }
+        // Clean up old directory after successful migration.
+        try { rmSync(markerPath, { recursive: true, force: true }); } catch { /* non-fatal */ }
+      } catch {
+        // If migration fails, just point at the old directory.
+        return markerPath;
+      }
+    }
+  }
+
+  return computedPath;
+}
+
 // ─── Symlink Management ─────────────────────────────────────────────────────
 
 /**
  * Ensure the `<project>/.gsd` symlink points to the external state directory.
  *
  * 1. Clean up any macOS numbered collision variants (`.gsd 2`, `.gsd 3`, etc.)
- * 2. mkdir -p the external dir
- * 3. If `<project>/.gsd` doesn't exist → create symlink
- * 4. If `<project>/.gsd` is already the correct symlink → no-op
- * 5. If `<project>/.gsd` is a real directory → return as-is (migration handles later)
+ * 2. Resolve external dir (with relocation recovery via `.gsd-id` marker)
+ * 3. mkdir -p the external dir
+ * 4. If `<project>/.gsd` doesn't exist → create symlink
+ * 5. If `<project>/.gsd` is already the correct symlink → no-op
+ * 6. If `<project>/.gsd` is a real directory → return as-is (migration handles later)
+ * 7. Write `.gsd-id` marker for future relocation recovery
  *
  * Returns the resolved external path.
  */
 export function ensureGsdSymlink(projectPath: string): string {
-  const externalPath = externalGsdRoot(projectPath);
+  const result = ensureGsdSymlinkCore(projectPath);
+
+  // Write .gsd-id marker so future relocations can recover this state (#2750).
+  // Only write for the project root (not subdirectories or worktrees that
+  // delegate to a parent .gsd).
+  if (!isInsideWorktree(projectPath)) {
+    writeGsdIdMarker(projectPath, repoIdentity(projectPath));
+  }
+
+  return result;
+}
+
+function ensureGsdSymlinkCore(projectPath: string): string {
+  const externalPath = resolveExternalPathWithRecovery(projectPath);
   const localGsd = join(projectPath, ".gsd");
   const inWorktree = isInsideWorktree(projectPath);
 
@@ -418,12 +556,28 @@ export function ensureGsdSymlink(projectPath: string): string {
 
   const replaceWithSymlink = (): string => {
     rmSync(localGsd, { recursive: true, force: true });
+    // Defensive: remove any residual entry (e.g. dangling symlink) before creating.
+    try { unlinkSync(localGsd); } catch { /* already gone */ }
     symlinkSync(externalPath, localGsd, "junction");
     return externalPath;
   };
 
+  // Check for dangling symlinks (e.g. after relocation recovery removed the old
+  // state dir). existsSync follows symlinks, so it returns false for dangling ones.
+  // lstatSync does NOT follow, so we can detect the dangling symlink and replace it.
   if (!existsSync(localGsd)) {
-    // Nothing exists yet — create symlink
+    try {
+      const stat = lstatSync(localGsd);
+      if (stat.isSymbolicLink()) {
+        // Dangling symlink — replace with correct one (#2750).
+        return replaceWithSymlink();
+      }
+    } catch {
+      // lstat also failed — nothing exists at this path
+    }
+    // Nothing exists yet — create symlink.
+    // Defensive: remove any residual entry to avoid EEXIST race (#2750).
+    try { unlinkSync(localGsd); } catch { /* nothing to remove */ }
     symlinkSync(externalPath, localGsd, "junction");
     return externalPath;
   }
@@ -442,6 +596,27 @@ export function ensureGsdSymlink(projectPath: string): string {
       if (inWorktree) {
         return replaceWithSymlink();
       }
+      // After identity hash change (e.g. upgrade from path-based to remote-only
+      // hash, or relocation recovery), migrate data from old target to new path
+      // and update the symlink (#2750).
+      if (!hasProjectState(externalPath) && hasProjectState(target)) {
+        try {
+          mkdirSync(externalPath, { recursive: true });
+          const oldEntries = readdirSync(target);
+          for (const entry of oldEntries) {
+            try {
+              const src = join(target, entry);
+              const dst = join(externalPath, entry);
+              try { renameSync(src, dst); } catch { cpSync(src, dst, { recursive: true, force: true }); }
+            } catch { /* continue */ }
+          }
+          try { rmSync(target, { recursive: true, force: true }); } catch { /* non-fatal */ }
+          return replaceWithSymlink();
+        } catch {
+          // Migration failed — preserve old symlink
+          return target;
+        }
+      }
       // Outside worktrees, preserve custom overrides or legacy symlinks.
       return target;
     }

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

@@ -19,6 +19,7 @@ import { isParked, getParkedReason } from "./milestone-actions.js";
 import { getMilestoneSlices, isDbAvailable } from "./gsd-db.js";
 import { buildExistingMilestonesContext } from "./guided-flow-queue.js";
 import { loadPrompt } from "./prompt-loader.js";
+import { isGsdGitignored } from "./gitignore.js";
 
 // ─── Entry Point ──────────────────────────────────────────────────────────────
 
@@ -53,9 +54,14 @@ export async function handleRethink(
   const rethinkData = buildRethinkData(basePath, milestoneIds, state, queueOrder);
   const existingMilestonesContext = await buildExistingMilestonesContext(basePath, milestoneIds, state);
 
+  const commitInstruction = isGsdGitignored(basePath)
+    ? "Do not commit planning artifacts — .gsd/ is gitignored in this project."
+    : 'After changes, run `git add .gsd/ && git commit -m "docs(gsd): rethink milestone plan"` to persist (rethink runs interactively outside auto-mode, so no system auto-commit)';
+
   const content = loadPrompt("rethink", {
     rethinkData,
     existingMilestonesContext,
+    commitInstruction,
   });
 
   pi.sendMessage(

package/src/resources/extensions/gsd/roadmap-slices.ts

@@ -219,13 +219,14 @@ export function parseRoadmapSlices(content: string): RoadmapSliceEntry[] {
 function parseProseSliceHeaders(content: string): RoadmapSliceEntry[] {
   const slices: RoadmapSliceEntry[] = [];
   // Match H1-H4 headers containing S<digits> with optional "Slice" prefix, bold markers,
-  // and optional checkmark completion marker before the slice ID.
+  // numeric prefixes (e.g., "1.", "(1)"), bracketed IDs (e.g., "[S01]"),
+  // optional checkmark completion marker, and optional leading indentation.
   // Separator after the ID is flexible: colon, dash, em/en dash, dot, or just whitespace.
-  const headerPattern = /^#{1,4}\s+\*{0,2}(?:\u2713\s+)?(?:Slice\s+)?(S\d+)\*{0,2}[:\s.\u2014\u2013-]*\s*(.+)/gm;
+  const headerPattern = /^\s*#{1,4}\s+\*{0,2}(?:\u2713\s+)?(?:\d+[.)]\s+)?(?:\(\d+\)\s+)?(?:Slice\s+)?\[?(S\d+)\]?\*{0,2}[:\s.\u2014\u2013-]*\s*(.+)/gm;
   let match: RegExpExecArray | null;
 
   // Check for checkmark before the slice ID (e.g., "## checkmark S01: Title")
-  const prefixCheckPattern = /^#{1,4}\s+\*{0,2}\u2713\s+/;
+  const prefixCheckPattern = /^\s*#{1,4}\s+\*{0,2}\u2713\s+/;
 
   while ((match = headerPattern.exec(content)) !== null) {
     const id = match[1]!;
@@ -251,7 +252,7 @@ function parseProseSliceHeaders(content: string): RoadmapSliceEntry[] {
 
     // Try to extract depends from prose: "Depends on: S01" or "**Depends on:** S01, S02"
     const afterHeader = content.slice(match.index + match[0].length);
-    const nextHeader = afterHeader.search(/^#{1,4}\s/m);
+    const nextHeader = afterHeader.search(/^\s*#{1,4}\s/m);
     const section = nextHeader !== -1 ? afterHeader.slice(0, nextHeader) : afterHeader.slice(0, 500);
 
     const depsMatch = section.match(/\*{0,2}Depends\s+on:?\*{0,2}\s*(.+)/i);

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

@@ -36,22 +36,24 @@ import {
 
 import { findMilestoneIds } from './milestone-ids.js';
 import { loadQueueOrder, sortByQueueOrder } from './queue-order.js';
-import { isClosedStatus } from './status-guards.js';
 import { nativeBatchParseGsdFiles, type BatchParsedFile } from './native-parser-bridge.js';
 
 import { join, resolve } from 'path';
-import { existsSync, readdirSync } from 'node:fs';
+import { existsSync, readdirSync, readFileSync } from 'node:fs';
 import { debugCount, debugTime } from './debug-logger.js';
 import { extractVerdict } from './verdict-parser.js';
+import { logWarning, logError } from './workflow-logger.js';
 
 import {
   isDbAvailable,
   getAllMilestones,
+  getMilestone,
   getMilestoneSlices,
   getSliceTasks,
   getReplanHistory,
   getSlice,
   insertMilestone,
+  insertSlice,
   updateTaskStatus,
   getPendingSliceGateCount,
   type MilestoneRow,
@@ -64,8 +66,29 @@ import {
  * files like CONTEXT, CONTEXT-DRAFT, ROADMAP, or SUMMARY).  These appear when
  * a milestone is created but never initialised.  Treating them as active causes
  * auto-mode to stall or falsely declare completion.
+ *
+ * However, a milestone is NOT a ghost if:
+ * - It has a DB row with a meaningful status (queued, active, etc.) — the DB
+ *   knows about it even if content files haven't been created yet.
+ * - It has a worktree directory — a worktree proves the milestone was
+ *   legitimately created and is expected to be populated.
+ *
+ * Fixes #2921: queued milestones with worktrees were incorrectly classified
+ * as ghosts, causing auto-mode to skip them entirely.
  */
 export function isGhostMilestone(basePath: string, mid: string): boolean {
+  // If the milestone has a DB row, it's a known milestone — not a ghost.
+  if (isDbAvailable()) {
+    const dbRow = getMilestone(mid);
+    if (dbRow) return false;
+  }
+
+  // If a worktree exists for this milestone, it was legitimately created.
+  const root = gsdRoot(basePath);
+  const wtPath = join(root, 'worktrees', mid);
+  if (existsSync(wtPath)) return false;
+
+  // Fall back to content-file check: no substantive files means ghost.
   const context   = resolveMilestoneFile(basePath, mid, "CONTEXT");
   const draft     = resolveMilestoneFile(basePath, mid, "CONTEXT-DRAFT");
   const roadmap   = resolveMilestoneFile(basePath, mid, "ROADMAP");
@@ -209,10 +232,10 @@ export async function deriveState(basePath: string): Promise<GSDState> {
   if (isDbAvailable()) {
     let dbMilestones = getAllMilestones();
 
-    // Disk→DB reconciliation (#2631): when the milestones table is empty
-    // (e.g. failed initial migration per #2529), the reconciliation code
-    // inside deriveStateFromDb is unreachable. Populate from disk here so
-    // the DB path activates correctly.
+    // Disk→DB reconciliation when DB is empty but disk has milestones (#2631).
+    // deriveStateFromDb() does its own reconciliation, but deriveState() skips
+    // it entirely when the DB is empty. Sync here so the DB path is used when
+    // disk milestones exist but haven't been migrated yet.
     if (dbMilestones.length === 0) {
       const diskIds = findMilestoneIds(basePath);
       let synced = false;
@@ -231,7 +254,7 @@ export async function deriveState(basePath: string): Promise<GSDState> {
       stopDbTimer({ phase: result.phase, milestone: result.activeMilestone?.id });
       _telemetry.dbDeriveCount++;
     } else {
-      // DB open but empty hierarchy tables — pre-migration project, use filesystem
+      // DB open but no milestones on disk either — use filesystem path
       result = await _deriveStateImpl(basePath);
       _telemetry.markdownDeriveCount++;
     }
@@ -268,6 +291,13 @@ function extractContextTitle(content: string | null, fallback: string): string {
 
 // ─── DB-backed State Derivation ────────────────────────────────────────────
 
+/**
+ * Helper: check if a DB status counts as "done" (handles K002 ambiguity).
+ */
+function isStatusDone(status: string): boolean {
+  return status === 'complete' || status === 'done';
+}
+
 /**
  * Derive GSD state from the milestones/slices/tasks DB tables.
  * Flag files (PARKED, VALIDATION, CONTINUE, REPLAN, REPLAN-TRIGGER, CONTEXT-DRAFT)
@@ -298,6 +328,36 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   }
   if (synced) allMilestones = getAllMilestones();
 
+  // Disk→DB slice reconciliation (#2533): slices defined in ROADMAP.md but
+  // missing from the DB cause permanent "No slice eligible" blocks because
+  // the dependency resolver only sees DB rows. Parse each milestone's roadmap
+  // and insert any missing slices, checking SUMMARY files to set correct status.
+  // insertSlice uses INSERT OR IGNORE, so existing rows are never overwritten.
+  for (const mid of diskIds) {
+    if (isGhostMilestone(basePath, mid)) continue;
+    const roadmapPath = resolveMilestoneFile(basePath, mid, "ROADMAP");
+    if (!roadmapPath) continue;
+
+    const dbSlices = getMilestoneSlices(mid);
+    const dbSliceIds = new Set(dbSlices.map(s => s.id));
+
+    let roadmapContent: string;
+    try { roadmapContent = readFileSync(roadmapPath, "utf-8"); }
+    catch { continue; }
+
+    const parsed = parseRoadmap(roadmapContent);
+    for (const s of parsed.slices) {
+      if (dbSliceIds.has(s.id)) continue;
+      const summaryPath = resolveSliceFile(basePath, mid, s.id, "SUMMARY");
+      const sliceStatus = (s.done || summaryPath) ? "complete" : "pending";
+      insertSlice({
+        id: s.id, milestoneId: mid, title: s.title,
+        status: sliceStatus, risk: s.risk,
+        depends: s.depends, demo: s.demo,
+      });
+    }
+  }
+
   // Reconcile: discover milestones that exist on disk but are missing from
   // the DB. This happens when milestones were created before the DB migration
   // or were manually added to the filesystem. Without this, disk-only
@@ -357,7 +417,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
       continue;
     }
 
-    if (isClosedStatus(m.status)) {
+    if (isStatusDone(m.status)) {
       completeMilestoneIds.add(m.id);
       continue;
     }
@@ -371,7 +431,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
 
     // Check roadmap: all slices done means milestone is complete
     const slices = getMilestoneSlices(m.id);
-    if (slices.length > 0 && slices.every(s => isClosedStatus(s.status))) {
+    if (slices.length > 0 && slices.every(s => isStatusDone(s.status))) {
       // All slices done but no summary — still counts as complete for dep resolution
       // if a summary file exists
       // Note: without summary file, the milestone is in validating/completing state, not complete
@@ -393,7 +453,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
 
     // Ghost milestone check: no slices in DB AND no substantive files on disk
     const slices = getMilestoneSlices(m.id);
-    if (slices.length === 0 && !isClosedStatus(m.status)) {
+    if (slices.length === 0 && !isStatusDone(m.status)) {
       // Check disk for ghost detection
       if (isGhostMilestone(basePath, m.id)) continue;
     }
@@ -416,7 +476,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
     }
 
     // Not complete — determine if it should be active
-    const allSlicesDone = slices.length > 0 && slices.every(s => isClosedStatus(s.status));
+    const allSlicesDone = slices.length > 0 && slices.every(s => isStatusDone(s.status));
 
     // Get title — prefer DB, fall back to context file extraction
     let title = stripMilestonePrefix(m.title) || m.id;
@@ -526,7 +586,8 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
       ? `All milestones complete. ${activeReqs} active requirement${activeReqs === 1 ? '' : 's'} in REQUIREMENTS.md ${activeReqs === 1 ? 'has' : 'have'} not been mapped to a milestone.`
       : 'All milestones complete.';
     return {
-      activeMilestone: lastEntry ? { id: lastEntry.id, title: lastEntry.title } : null,
+      activeMilestone: null,
+      lastCompletedMilestone: lastEntry ? { id: lastEntry.id, title: lastEntry.title } : null,
       activeSlice: null, activeTask: null,
       phase: 'complete',
       recentDecisions: [], blockers: [],
@@ -568,10 +629,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   }
 
   // ── All slices done → validating/completing ─────────────────────────
-  // Guard: [].every() === true (vacuous truth). Without the length check,
-  // an empty slice array causes a premature phase transition to
-  // validating-milestone. See: https://github.com/gsd-build/gsd-2/issues/2667
-  const allSlicesDone = activeMilestoneSlices.length > 0 && activeMilestoneSlices.every(s => isClosedStatus(s.status));
+  const allSlicesDone = activeMilestoneSlices.every(s => isStatusDone(s.status));
   if (allSlicesDone) {
     const validationFile = resolveMilestoneFile(basePath, activeMilestone.id, "VALIDATION");
     const validationContent = validationFile ? await loadFile(validationFile) : null;
@@ -604,19 +662,19 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
 
   // ── Find active slice (first incomplete with deps satisfied) ─────────
   const sliceProgress = {
-    done: activeMilestoneSlices.filter(s => isClosedStatus(s.status)).length,
+    done: activeMilestoneSlices.filter(s => isStatusDone(s.status)).length,
     total: activeMilestoneSlices.length,
   };
 
   const doneSliceIds = new Set(
-    activeMilestoneSlices.filter(s => isClosedStatus(s.status)).map(s => s.id)
+    activeMilestoneSlices.filter(s => isStatusDone(s.status)).map(s => s.id)
   );
 
   let activeSlice: ActiveRef | null = null;
   let activeSliceRow: SliceRow | null = null;
 
   for (const s of activeMilestoneSlices) {
-    if (isClosedStatus(s.status)) continue;
+    if (isStatusDone(s.status)) continue;
     if (s.depends.every(dep => doneSliceIds.has(dep))) {
       activeSlice = { id: s.id, title: s.title };
       activeSliceRow = s;
@@ -659,20 +717,16 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   // causing the dispatcher to re-dispatch the same completed task forever.
   let reconciled = false;
   for (const t of tasks) {
-    if (isClosedStatus(t.status)) continue;
+    if (isStatusDone(t.status)) continue;
     const summaryPath = resolveTaskFile(basePath, activeMilestone.id, activeSlice.id, t.id, "SUMMARY");
     if (summaryPath && existsSync(summaryPath)) {
       try {
         updateTaskStatus(activeMilestone.id, activeSlice.id, t.id, "complete");
-        process.stderr.write(
-          `gsd-reconcile: task ${activeMilestone.id}/${activeSlice.id}/${t.id} had SUMMARY on disk but DB status was "${t.status}" — updated to "complete" (#2514)\n`,
-        );
+        logWarning("reconcile", `task ${activeMilestone.id}/${activeSlice.id}/${t.id} status reconciled from "${t.status}" to "complete" (#2514)`, { mid: activeMilestone.id, sid: activeSlice.id, tid: t.id });
         reconciled = true;
       } catch (e) {
         // DB write failed — continue with stale status rather than crash
-        process.stderr.write(
-          `gsd-reconcile: failed to update task ${t.id}: ${(e as Error).message}\n`,
-        );
+        logError("reconcile", `failed to update task ${t.id}`, { tid: t.id, error: (e as Error).message });
       }
     }
   }
@@ -682,11 +736,11 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   }
 
   const taskProgress = {
-    done: tasks.filter(t => isClosedStatus(t.status)).length,
+    done: tasks.filter(t => isStatusDone(t.status)).length,
     total: tasks.length,
   };
 
-  const activeTaskRow = tasks.find(t => !isClosedStatus(t.status));
+  const activeTaskRow = tasks.find(t => !isStatusDone(t.status));
 
   if (!activeTaskRow && tasks.length > 0) {
     // All tasks done but slice not marked complete → summarizing
@@ -747,7 +801,7 @@ export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   }
 
   // ── Blocker detection: check completed tasks for blocker_discovered ──
-  const completedTasks = tasks.filter(t => isClosedStatus(t.status));
+  const completedTasks = tasks.filter(t => isStatusDone(t.status));
   let blockerTaskId: string | null = null;
   for (const ct of completedTasks) {
     if (ct.blocker_discovered) {
@@ -1327,9 +1381,7 @@ export async function _deriveStateImpl(basePath: string): Promise<GSDState> {
     const summaryPath = resolveTaskFile(basePath, activeMilestone.id, activeSlice.id, t.id, "SUMMARY");
     if (summaryPath && existsSync(summaryPath)) {
       t.done = true;
-      process.stderr.write(
-        `gsd-reconcile: task ${activeMilestone.id}/${activeSlice.id}/${t.id} has SUMMARY on disk but plan shows incomplete — marking done (#2514)\n`,
-      );
+      logWarning("reconcile", `task ${activeMilestone.id}/${activeSlice.id}/${t.id} reconciled via SUMMARY on disk (#2514)`, { mid: activeMilestone.id, sid: activeSlice.id, tid: t.id });
     }
   }
 

package/src/resources/extensions/gsd/tests/auto-loop.test.ts

@@ -317,6 +317,35 @@ test("auto/resolve.ts one-shot pattern: _currentResolve is nulled before calling
   );
 });
 
+test("auto/phases.ts: selectAndApplyModel called exactly once and before updateProgressWidget (#2907)", () => {
+  const src = readFileSync(
+    resolve(import.meta.dirname, "..", "auto", "phases.ts"),
+    "utf-8",
+  );
+  // Extract the runUnitPhase function body
+  const fnStart = src.indexOf("export async function runUnitPhase");
+  assert.ok(fnStart > 0, "runUnitPhase should exist in phases.ts");
+  const fnBody = src.slice(fnStart, fnStart + 8000);
+
+  // selectAndApplyModel must appear exactly once
+  const allOccurrences = [...fnBody.matchAll(/selectAndApplyModel\(/g)];
+  assert.equal(
+    allOccurrences.length,
+    1,
+    `selectAndApplyModel should be called exactly once in runUnitPhase, found ${allOccurrences.length} calls`,
+  );
+
+  // selectAndApplyModel must appear BEFORE updateProgressWidget
+  const modelIdx = fnBody.indexOf("selectAndApplyModel(");
+  const widgetIdx = fnBody.indexOf("updateProgressWidget(");
+  assert.ok(modelIdx > 0, "selectAndApplyModel should exist in runUnitPhase");
+  assert.ok(widgetIdx > 0, "updateProgressWidget should exist in runUnitPhase");
+  assert.ok(
+    modelIdx < widgetIdx,
+    "selectAndApplyModel must be called BEFORE updateProgressWidget (#2899/#2907)",
+  );
+});
+
 // ─── autoLoop tests (T02) ─────────────────────────────────────────────────
 
 /**