@opengsd/gsd-pi 1.3.0-dev.eed73bea → 1.4.0

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

@@ -24,8 +24,9 @@ import { GIT_NO_PROMPT_ENV } from "./git-constants.js";
  * With external state (symlink), these are a no-op in most cases,
  * but retained for backwards compatibility during migration.
  */
-const GSD_RUNTIME_PATTERNS = [
+export const GSD_RUNTIME_PATTERNS = [
   ".gsd-worktrees/",
+  ".gsd-backups/",
   ".gsd/activity/",
   ".gsd/audit/",
   ".gsd/forensics/",
@@ -51,6 +52,8 @@ const BASELINE_PATTERNS = [
   ".gsd",
   // Worktree container sibling — NOT covered by the ".gsd" pattern above.
   ".gsd-worktrees/",
+  // Flat-phase migration snapshots — NOT covered by the ".gsd" pattern above.
+  ".gsd-backups/",
   ".gsd-id",
   ".mcp.json",
   ".bg-shell/",

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

@@ -360,24 +360,31 @@ function capExistingMilestonesContext(
   if (fullContext.length <= cap) return fullContext;
 
   const notice = `[Existing milestones context truncated to ${cap} chars. Read source paths in this prompt or the corresponding .gsd artifacts for full details.]`;
-  const compactSections = sections.map(compactSectionForQueueBudget);
-  const selected: string[] = [];
+  const noticeSuffix = `${QUEUE_CONTEXT_SECTION_SEPARATOR}${notice}`;
 
-  for (let i = 0; i < sections.length; i++) {
-    const withFullSection = [
-      ...selected,
-      sections[i],
-      ...compactSections.slice(i + 1),
-      notice,
-    ].join(QUEUE_CONTEXT_SECTION_SEPARATOR);
+  const selected: string[] = [];
+  for (const section of sections) {
+    const candidate = [...selected, section].join(QUEUE_CONTEXT_SECTION_SEPARATOR) + noticeSuffix;
+    if (candidate.length <= cap) {
+      selected.push(section);
+      continue;
+    }
+    break;
+  }
 
-    selected.push(withFullSection.length <= cap ? sections[i] : compactSections[i]);
+  if (selected.length === sections.length) {
+    return selected.join(QUEUE_CONTEXT_SECTION_SEPARATOR) + noticeSuffix;
   }
 
-  const capped = [...selected, notice].join(QUEUE_CONTEXT_SECTION_SEPARATOR);
-  if (capped.length <= cap) return capped;
+  const compactTail = sections.slice(selected.length).map(compactSectionForQueueBudget);
+  const hybrid = [...selected, ...compactTail].join(QUEUE_CONTEXT_SECTION_SEPARATOR) + noticeSuffix;
+  if (hybrid.length <= cap) return hybrid;
+
+  const compact = sections.map(compactSectionForQueueBudget);
+  const compactContext = compact.join(QUEUE_CONTEXT_SECTION_SEPARATOR) + noticeSuffix;
+  if (compactContext.length <= cap) return compactContext;
 
-  return `${capped.slice(0, Math.max(0, cap - notice.length - 2)).trimEnd()}\n\n${notice}`;
+  return `${compactContext.slice(0, Math.max(0, cap - notice.length - 2)).trimEnd()}\n\n${notice}`;
 }
 
 function compactSectionForQueueBudget(section: string): string {

package/src/resources/extensions/gsd/json-persistence.ts

@@ -62,6 +62,26 @@ export function saveJsonFile<T>(filePath: string, data: T): void {
   }
 }
 
+/**
+ * Save a JSON file atomically using compact serialization.
+ *
+ * Intended for machine-only ledgers where pretty-printing has no consumer.
+ * Keeps the same write-tmp-rename safety and non-fatal error behavior as
+ * saveJsonFile.
+ */
+export function saveJsonFileCompact<T>(filePath: string, data: T): void {
+  try {
+    mkdirSync(dirname(filePath), { recursive: true });
+    // Use randomized tmp suffix to prevent concurrent-write data loss
+    const tmp = `${filePath}.tmp.${randomBytes(4).toString("hex")}`;
+    writeFileSync(tmp, JSON.stringify(data) + "\n", "utf-8");
+    renameSync(tmp, filePath);
+    // No cleanup needed — renameSync atomically removes tmp on success
+  } catch {
+    // Non-fatal — don't let persistence failures break operation
+  }
+}
+
 /**
  * Write a JSON file atomically (write to .tmp, then rename).
  * Creates parent directories as needed. Non-fatal on error.

package/src/resources/extensions/gsd/knowledge-backfill.ts

@@ -35,8 +35,8 @@ interface SynthesizedRow {
  * - Idempotent (per-row): each migrated memory carries
  *   `structured_fields.sourceKnowledgeId = "<P|L>NNN"`. Rows whose ID is
  *   already present in the memory store are skipped.
- * - Best-effort: never throws. Logs and returns 0 on failure so a broken
- *   backfill cannot block agent startup.
+ * - Best-effort: never throws. Failed memory inserts are logged and skipped;
+ *   setup/read failures log and return 0 so backfill cannot block startup.
  * - Rules (K###) are intentionally skipped — they remain manually maintained
  *   in `KNOWLEDGE.md` per ADR-013.
  *
@@ -69,14 +69,20 @@ export function backfillKnowledgeToMemories(basePath: string): number {
       const matchPattern = `%"sourceKnowledgeId":"${synth.id}"%`;
       if (checkExisting.get({ ":pattern": matchPattern })) continue;
 
-      const id = createMemory({
-        category: synth.category,
-        content: synth.content,
-        scope: synth.scope,
-        confidence: 0.85,
-        structuredFields: synth.structuredFields,
-      });
-      if (id) written += 1;
+      try {
+        const id = createMemory({
+          category: synth.category,
+          content: synth.content,
+          scope: synth.scope,
+          confidence: 0.85,
+          structuredFields: synth.structuredFields,
+        });
+        if (id) written += 1;
+      } catch (rowErr) {
+        const message = rowErr instanceof Error ? rowErr.message : String(rowErr);
+        logWarning("knowledge-backfill", `KNOWLEDGE.md -> memories backfill skipped ${synth.id}: ${message}`);
+        continue;
+      }
     }
 
     return written;

package/src/resources/extensions/gsd/layout-policy.ts

@@ -47,8 +47,9 @@ export function dbPath(basePath: string): string {
  * Used by the renderer to derive the phase number from the DB's milestone_id.
  */
 export function milestoneIdToPhaseNum(milestoneId: string): number {
-  // No $ anchor: accepts bare (M012) and team-suffixed (M012-abc123) IDs.
+  // No $ anchor: accepts bare (M012), team-suffixed (M012-abc123), and legacy numeric IDs.
   const m = milestoneId.match(/^M0*(\d+)/i);
+  if (!m && /^\d+$/.test(milestoneId)) return Number.parseInt(milestoneId, 10);
   return m ? Number.parseInt(m[1]!, 10) : 1;
 }
 

package/src/resources/extensions/gsd/markdown-renderer.ts

@@ -632,16 +632,8 @@ export async function renderRoadmapCheckboxes(
   basePath: string,
   milestoneId: string,
 ): Promise<boolean> {
-  const slices = getMilestoneSlices(milestoneId);
-  if (slices.length === 0) {
-    process.stderr.write(
-      `markdown-renderer: no slices found for milestone ${milestoneId}\n`,
-    );
-    return false;
-  }
-
-  await renderRoadmapFromDb(basePath, milestoneId);
-  return true;
+  const rendered = await renderRoadmapFromDb(basePath, milestoneId);
+  return !("skipped" in rendered);
 }
 
 /**

package/src/resources/extensions/gsd/memory-backfill.ts

@@ -49,8 +49,8 @@ type DecisionContentFields = Pick<DecisionRow, "decision" | "choice" | "rational
  *   decision is checked individually; only decisions whose id is already
  *   present in the memory store are skipped. A user-authored memory with
  *   their own `sourceDecisionId` does NOT abort the backfill.
- * - Best-effort: never throws. Logs and returns 0 on failure so a broken
- *   backfill cannot block agent startup.
+ * - Best-effort: never throws. Failed memory inserts are logged and skipped;
+ *   setup/read failures log and return 0 so backfill cannot block startup.
  * - Full migration (ADR-013 Stage 2a): both active and superseded rows are
  *   migrated. `structured_fields.superseded_by` preserves the supersedes
  *   chain so the DECISIONS.md projection regen can source from memories
@@ -146,24 +146,30 @@ export function backfillDecisionsToMemories(): number {
       }
 
       const content = synthesizeDecisionMemoryContent(row);
-      const id = createMemory({
-        category: "architecture",
-        content,
-        scope: row.scope || "project",
-        confidence: 0.85,
-        structuredFields: {
-          sourceDecisionId: row.id,
-          when_context: row.when_context,
-          scope: row.scope,
-          decision: row.decision,
-          choice: row.choice,
-          rationale: row.rationale,
-          made_by: row.made_by,
-          revisable: row.revisable,
-          superseded_by: row.superseded_by,
-        },
-      });
-      if (id) written += 1;
+      try {
+        const id = createMemory({
+          category: "architecture",
+          content,
+          scope: row.scope || "project",
+          confidence: 0.85,
+          structuredFields: {
+            sourceDecisionId: row.id,
+            when_context: row.when_context,
+            scope: row.scope,
+            decision: row.decision,
+            choice: row.choice,
+            rationale: row.rationale,
+            made_by: row.made_by,
+            revisable: row.revisable,
+            superseded_by: row.superseded_by,
+          },
+        });
+        if (id) written += 1;
+      } catch (rowErr) {
+        const message = rowErr instanceof Error ? rowErr.message : String(rowErr);
+        logWarning("memory-backfill", `decisions->memories backfill skipped ${row.id}: ${message}`);
+        continue;
+      }
     }
 
     if (healed > 0) {

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

@@ -19,7 +19,7 @@ import { openSync, closeSync, unlinkSync, statSync, writeFileSync } from "node:f
 import type { ExtensionContext } from "@gsd/pi-coding-agent";
 import { gsdRoot } from "./paths.js";
 import { getAndClearSkills } from "./skill-telemetry.js";
-import { loadJsonFile, loadJsonFileOrNull, saveJsonFile } from "./json-persistence.js";
+import { loadJsonFile, loadJsonFileOrNull, saveJsonFileCompact } from "./json-persistence.js";
 import { parseUnitId } from "./unit-id.js";
 import { buildAuditEnvelope, emitUokAuditEvent } from "./uok/audit.js";
 import { isUnifiedAuditEnabled } from "./uok/audit-toggle.js";
@@ -873,7 +873,7 @@ export function pruneMetricsLedger(base: string, keepCount: number): number {
   if (!disk || disk.units.length <= keepCount) return 0;
   const removed = disk.units.length - keepCount;
   disk.units = keepNewestUnits(disk.units, keepCount);
-  saveJsonFile(metricsPath(base), disk);
+  saveJsonFileCompact(metricsPath(base), disk);
   // Keep the in-memory ledger in sync if it is loaded for this session.
   if (ledger) {
     ledger.units = keepNewestUnits(ledger.units, keepCount);
@@ -1041,7 +1041,7 @@ function saveLedger(base: string, data: MetricsLedger): void {
           : dataUnits;
       merged.sort(compareUnitsByTime);
       data.units = keepNewestUnits(merged);
-      saveJsonFile(path, data);
+      saveJsonFileCompact(path, data);
     } finally {
       releaseLock(lockPath);
     }
@@ -1053,6 +1053,6 @@ function saveLedger(base: string, data: MetricsLedger): void {
     // read-merge-write sequence without mutual exclusion.
     logWarning("fs", "saveLedger: lock not acquired — falling back to direct write (no merge)");
     data.units = keepNewestUnits(data.units);
-    saveJsonFile(path, data);
+    saveJsonFileCompact(path, data);
   }
 }

package/src/resources/extensions/gsd/migrate-external.ts

@@ -118,6 +118,7 @@ export function migrateToExternalState(basePath: string): MigrationResult {
 
     // Copy contents to external dir, skipping worktrees/
     const entries = readdirSync(migratingPath, { withFileTypes: true });
+    const copyFailures: string[] = [];
     for (const entry of entries) {
       if (entry.name === "worktrees") continue; // worktrees stay local
 
@@ -130,10 +131,15 @@ export function migrateToExternalState(basePath: string): MigrationResult {
         } else {
           cpSync(src, dst, { force: true });
         }
-      } catch {
-        // Non-fatal: continue with other files
+      } catch (copyErr) {
+        copyFailures.push(`${entry.name}: ${getErrorMessage(copyErr)}`);
       }
     }
+    if (copyFailures.length > 0) {
+      try { rmSync(localGsd, { force: true }); } catch { /* may not exist */ }
+      renameSync(migratingPath, localGsd);
+      return { migrated: false, error: `Migration copy failed: ${copyFailures.join("; ")}` };
+    }
 
     // Create symlink .gsd -> external path
     symlinkSync(externalPath, localGsd, "junction");

package/src/resources/extensions/gsd/migration-auto-check.ts

@@ -90,6 +90,28 @@ function scanHasExtraIdentities(a: HierarchyScan, b: HierarchyScan): boolean {
   );
 }
 
+function paddedMilestoneId(id: string): string | null {
+  return /^\d+$/.test(id) ? `M${id.padStart(3, "0")}` : null;
+}
+
+function replaceSetPrefix(values: Set<string>, from: string, to: string): void {
+  for (const value of [...values]) {
+    if (value !== from && !value.startsWith(`${from}/`)) continue;
+    values.delete(value);
+    values.add(`${to}${value.slice(from.length)}`);
+  }
+}
+
+function alignNumericMarkdownIdsWithDb(markdownScan: HierarchyScan, dbScan: HierarchyScan): void {
+  for (const dbId of dbScan.milestones) {
+    const paddedId = paddedMilestoneId(dbId);
+    if (!paddedId || dbScan.milestones.has(paddedId) || !markdownScan.milestones.has(paddedId)) continue;
+    replaceSetPrefix(markdownScan.milestones, paddedId, dbId);
+    replaceSetPrefix(markdownScan.slices, paddedId, dbId);
+    replaceSetPrefix(markdownScan.tasks, paddedId, dbId);
+  }
+}
+
 /**
  * True when the DB holds any milestone/slice/task identity the markdown lacks —
  * i.e. a `/gsd recover --confirm` (markdown → DB) would DELETE authoritative DB
@@ -185,6 +207,7 @@ export async function checkMarkdownHierarchyAgainstDb(
 
   const dbScan = scanDbHierarchy();
   const beforeDb = dbScan.counts;
+  alignNumericMarkdownIdsWithDb(markdownScan, dbScan);
 
   // Discussion-phase scratch: a milestone dir with no ROADMAP and no DB row is
   // a pre-registration discussion artifact (CONTEXT/CONTEXT-DRAFT only — the

package/src/resources/extensions/gsd/milestone-ids.ts

@@ -141,7 +141,8 @@ export function clearReservedMilestoneIds(): void {
 
 // ─── Discovery ──────────────────────────────────────────────────────────────
 
-function scanMilestoneIdsFromDir(dir: string): string[] {
+function scanMilestoneIdsFromDir(basePath: string, dir: string): string[] {
+  const legacyNumericIds = idsWithLegacyNumericDirs(basePath);
   return readdirSync(dir, { withFileTypes: true })
     .filter((d) => d.isDirectory())
     .map((d) => {
@@ -149,6 +150,12 @@ function scanMilestoneIdsFromDir(dir: string): string[] {
       if (MILESTONE_ID_RE.test(d.name)) {
         return d.name;
       }
+      // Legacy recovery/imports may contain bare numeric milestone directories
+      // (for example `milestones/15/15-ROADMAP.md`). The DB can preserve that
+      // id, and rebuild renders it, so drift scans must see it too.
+      if (/^\d+$/.test(d.name)) {
+        return d.name;
+      }
       // Legacy layout: M001-abcdef-slug descriptor directories
       const legacyMatch = d.name.match(/^(M\d{3}(?:-[a-z0-9]{6})?)-/);
       if (legacyMatch) {
@@ -162,6 +169,10 @@ function scanMilestoneIdsFromDir(dir: string): string[] {
         if (MILESTONE_ID_RE.test(fromSlug)) {
           return fromSlug;
         }
+        const numericId = String(phaseNum);
+        if (legacyNumericIds.has(numericId)) {
+          return numericId;
+        }
         return `M${String(phaseNum).padStart(3, "0")}`;
       }
       return null;
@@ -169,6 +180,24 @@ function scanMilestoneIdsFromDir(dir: string): string[] {
     .filter((id): id is string => id !== null);
 }
 
+function idsWithLegacyNumericDirs(basePath: string): Set<string> {
+  const legacyDir = join(gsdProjectionRoot(basePath), "milestones");
+  const ids = new Set<string>();
+  try {
+    for (const entry of readdirSync(legacyDir, { withFileTypes: true })) {
+      if (entry.isDirectory() && /^\d+$/.test(entry.name)) ids.add(entry.name);
+    }
+  } catch (err) {
+    // A missing legacy directory is the common, benign case (nothing to
+    // consult). Only surface a real failure when the directory exists but
+    // could not be read.
+    if (existsSync(legacyDir)) {
+      logWarning("engine", `idsWithLegacyNumericDirs: ${legacyDir} exists but readdirSync failed — ${getErrorMessage(err)}`);
+    }
+  }
+  return ids;
+}
+
 /** Scan the milestones directory and return IDs sorted by queue order (or numeric fallback). */
 export function findMilestoneIds(basePath: string): string[] {
   const root = gsdProjectionRoot(basePath);
@@ -181,7 +210,7 @@ export function findMilestoneIds(basePath: string): string[] {
   const ids = new Set<string>();
   for (const dir of dirs) {
     try {
-      for (const id of scanMilestoneIdsFromDir(dir)) ids.add(id);
+      for (const id of scanMilestoneIdsFromDir(basePath, dir)) ids.add(id);
     } catch (err) {
       if (existsSync(dir)) {
         logWarning("engine", `findMilestoneIds: ${dir} exists but readdirSync failed — ${getErrorMessage(err)}`);

package/src/resources/extensions/gsd/orphan-stash-audit.ts

@@ -33,16 +33,87 @@ function _isAlreadyRestoredApplyError(err: unknown): boolean {
 
 export { _isAlreadyRestoredApplyError };
 
+function gitOutput(basePath: string, args: string[]): string {
+  return execFileSync("git", args, {
+    cwd: basePath,
+    stdio: ["ignore", "pipe", "pipe"],
+    encoding: "utf-8",
+    env: GIT_NO_PROMPT_ENV,
+  });
+}
+
+function listStashUntrackedPaths(basePath: string, stashRef: string): string[] | null {
+  try {
+    return gitOutput(basePath, ["ls-tree", "-r", "-z", "--name-only", `${stashRef}^3`]).split("\0").filter(Boolean);
+  } catch {
+    return null;
+  }
+}
+
+function listStashTrackedPaths(basePath: string, stashRef: string): string[] | null {
+  try {
+    return gitOutput(basePath, ["diff", "--name-only", "-z", `${stashRef}^1`, stashRef]).split("\0").filter(Boolean);
+  } catch {
+    return null;
+  }
+}
+
+interface PorcelainEntry {
+  code: string;
+  path: string;
+}
+
+function readWorkingTreeStatus(basePath: string): PorcelainEntry[] | null {
+  try {
+    return gitOutput(basePath, ["status", "--porcelain", "-z", "--untracked-files=all"])
+      .split("\0")
+      .filter(Boolean)
+      .map((entry) => ({ code: entry.slice(0, 2), path: entry.slice(3) }));
+  } catch {
+    return null;
+  }
+}
+
+function isAlreadyRestoredUntrackedStatus(basePath: string, stashRef: string, statusEntries: PorcelainEntry[]): boolean {
+  if (statusEntries.length === 0 || statusEntries.some((entry) => entry.code !== "??")) return false;
+  const stashTrackedPaths = listStashTrackedPaths(basePath, stashRef);
+  if (!stashTrackedPaths || stashTrackedPaths.length > 0) return false;
+  const stashUntrackedPaths = listStashUntrackedPaths(basePath, stashRef);
+  if (!stashUntrackedPaths || stashUntrackedPaths.length === 0) return false;
+  const stashUntrackedPathSet = new Set(stashUntrackedPaths);
+  const workingTreeUntrackedPathSet = new Set(statusEntries.map((entry) => entry.path));
+  // "Already restored" requires the working tree's untracked paths to match the
+  // stash's untracked paths exactly, in BOTH directions:
+  //   1. every current untracked path comes from the stash (no unexplained user
+  //      work that an apply would clobber), AND
+  //   2. every stash untracked path is already present in the working tree.
+  // Without (2), a partial restore (where only some stash files were recovered)
+  // would be misread as fully restored: the audit would no-op without applying
+  // or warning, leaving the remaining pre-merge files missing.
+  return (
+    statusEntries.every((entry) => stashUntrackedPathSet.has(entry.path)) &&
+    stashUntrackedPaths.every((path) => workingTreeUntrackedPathSet.has(path))
+  );
+}
+
+function manualApplyWarning(stashRef: string, milestoneId: string, reason: string): string {
+  return (
+    `Pre-merge stash ${stashRef} for milestone ${milestoneId} not auto-applied: ${reason}; ` +
+    `run \`git stash apply ${stashRef}\` manually to restore your pre-merge changes.`
+  );
+}
+
 /**
  * Audit `git stash list` for orphaned `gsd-preflight-stash:M00x:*` entries.
  *
  * The matching merge code in `phases.ts` previously skipped the postflight
  * pop whenever `mergeAndExit` threw, leaking the user's pre-merge working
- * tree into the stash list. For every preflight-stash entry whose milestone
- * is now complete (per the supplied callback), `git stash apply` is invoked —
+ * tree into the stash list. Completed-milestone stashes are only auto-applied
+ * when the working tree is clean and the stash does not modify tracked files.
+ * Dirty trees and tracked-file stashes are left untouched with a manual
+ * recovery warning. When auto-apply is safe, `git stash apply` is invoked —
  * NOT `pop`. The stash entry stays in the list so the user retains a backup
- * if the apply produces unexpected merge results. Idempotent across repeated
- * startup runs.
+ * if the apply produces unexpected merge results.
  *
  * Failures are best-effort: a list error (no repo, git unavailable) returns
  * an empty result. An apply error becomes a warning the user sees alongside
@@ -56,16 +127,7 @@ export function auditOrphanedPreflightStashes(
 
   let listOutput: string;
   try {
-    listOutput = execFileSync(
-      "git",
-      ["stash", "list", "--format=%gd%x00%s"],
-      {
-        cwd: basePath,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: GIT_NO_PROMPT_ENV,
-      },
-    );
+    listOutput = gitOutput(basePath, ["stash", "list", "--format=%gd%x00%s"]);
   } catch {
     return result;
   }
@@ -93,13 +155,39 @@ export function auditOrphanedPreflightStashes(
     }
     if (!complete) continue;
 
+    const statusEntries = readWorkingTreeStatus(basePath);
+    if (!statusEntries) {
+      result.warnings.push(
+        manualApplyWarning(ref, milestoneId, "could not verify working tree status"),
+      );
+      continue;
+    }
+    if (statusEntries.length > 0) {
+      if (isAlreadyRestoredUntrackedStatus(basePath, ref, statusEntries)) continue;
+      result.warnings.push(manualApplyWarning(ref, milestoneId, "working tree not clean"));
+      continue;
+    }
+
+    const trackedPaths = listStashTrackedPaths(basePath, ref);
+    if (trackedPaths === null) {
+      result.warnings.push(
+        manualApplyWarning(ref, milestoneId, "could not inspect tracked paths in stash"),
+      );
+      continue;
+    }
+    if (trackedPaths.length > 0) {
+      // A retained tracked-file stash has no durable marker showing whether a
+      // clean tree needs first recovery or would be re-mutated by an old backup.
+      const preview = trackedPaths.slice(0, 5).join(", ");
+      const suffix = trackedPaths.length > 5 ? `, and ${trackedPaths.length - 5} more` : "";
+      result.warnings.push(
+        manualApplyWarning(ref, milestoneId, `stash modifies tracked files (${preview}${suffix})`),
+      );
+      continue;
+    }
+
     try {
-      execFileSync("git", ["stash", "apply", "--quiet", ref], {
-        cwd: basePath,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: GIT_NO_PROMPT_ENV,
-      });
+      gitOutput(basePath, ["stash", "apply", "--quiet", ref]);
       result.applied.push({ milestoneId, stashRef: ref });
     } catch (err) {
       // Idempotent steady state: stash was already applied in a prior audit

package/src/resources/extensions/gsd/prompts/code-review.md

@@ -16,18 +16,20 @@ You are running the GSD **code-review** workflow — review source files changed
 
 1. **Determine the file set.** Use the explicit `--files` list if provided. Otherwise derive the changed source files from the active slice's recent commits / SUMMARY, or fall back to the git diff against the base branch. Exclude `.gsd/`, lockfiles, generated/vendored code, and docs unless `--files` names them.
 
-2. **Review each file** at the requested depth:
+2. **Gather diff-first context.** Run `git diff` for the file set (or the relevant commit range) and use that as the primary review evidence. Use `read` only when the diff is insufficient — new/untracked files, truncated hunks, or missing surrounding context needed for a finding. Do **not** read every changed file when the diff already covers the edits. If the Tool Call Loop Guard blocks a tool, stop calling tools for the rest of this turn and continue in text.
+
+3. **Review at the requested depth:**
    - **quick** — bugs, security, and correctness only.
    - **standard** (default) — quick + maintainability, error handling, edge cases.
    - **deep** — standard + performance, concurrency, API design, test coverage gaps.
 
    Ground every finding in the actual code with file path + line reference. Categorize each by severity (critical / warning / nit) and type (bug, security, quality, performance).
 
-3. **Write the review.** Produce `.gsd/reviews/{{reviewId}}-REVIEW.md` with the findings table and per-finding detail (location, issue, suggested fix).
+4. **Write the review.** Produce `.gsd/reviews/{{reviewId}}-REVIEW.md` with the findings table and per-finding detail (location, issue, suggested fix).
 
-4. **Present results.** Summarize counts by severity and list the critical findings first.
+5. **Present results.** Summarize counts by severity and list the critical findings first.
 
-5. **Fix mode** (only when `--fix` is set): for each finding that is safely auto-fixable (deterministic, no behavior change beyond the fix), apply it. After each fix batch, run the project's tests. Commit atomically with the finding IDs referenced in the message. Do not auto-apply findings that are ambiguous or that change public behavior — surface those for a human decision instead.
+6. **Fix mode** (only when `--fix` is set): for each finding that is safely auto-fixable (deterministic, no behavior change beyond the fix), apply it. After each fix batch, run the project's tests. Commit atomically with the finding IDs referenced in the message. Do not auto-apply findings that are ambiguous or that change public behavior — surface those for a human decision instead.
 
 ## Success criteria
 

package/src/resources/extensions/gsd/prompts/plan-milestone.md

@@ -104,8 +104,8 @@ If the preference is off, ignore this section and plan every slice fully.
 
 If the roadmap has one slice, also plan S01 and its tasks inline:
 
-1. After `gsd_plan_milestone` returns, call `gsd_plan_slice` for S01 with full task breakdown.
-2. Use inlined **Slice Plan** and **Task Plan** templates for tool parameters.
+1. After `gsd_plan_milestone` returns, call `gsd_plan_slice` for S01 with slice metadata only; omit `tasks`.
+2. Then call `gsd_plan_task` once per S01 task. Use inlined **Slice Plan** and **Task Plan** templates for tool parameters.
 3. Keep simple slices lean. Omit Proof Level, Integration Closure, and Observability if all would be "none"; executable verification commands are enough.
 
 Do **not** write plan files manually; use DB-backed tools so state stays consistent.

package/src/resources/extensions/gsd/prompts/plan-slice.md

@@ -45,8 +45,8 @@ If slice research is inlined, trust its architectural findings, but verify every
 6. Include Threat Surface (Q3), Requirement Impact (Q4), proof level, observability, integration closure, Failure Modes (Q5), Load Profile (Q6), and Negative Tests (Q7) only where applicable.
 7. Right-size tasks. Simple slices can be one task; split only when context, ownership, or verification boundaries justify it.
 8. Task `verify` commands must be safe, simple commands. Do not use shell pipes, redirects, semicolons, backticks, command substitution, output trimming, or grep regex alternation with `|`. If multiple checks are needed, create a small test file and run it with `node --test` or a package test script, or use separate simple commands joined only with `&&`. For absence checks, verify a pattern does not exist with `! grep -q 'pattern' file` or `! rg -q 'pattern' file`; do not use `grep -c` or `rg -c` to assert zero matches because count commands exit 1 when they find zero matches, and the verification gate treats that as failure.
-9. Each task needs the exact `gsd_plan_slice.tasks[]` shape: `taskId`, `title`, `description`, `estimate`, `files`, `verify`, `inputs`, `expectedOutput`, and optional `observabilityImpact`. `description` should contain the Why / Do / Done-when narrative. `files`, `inputs`, and `expectedOutput` must be JSON arrays of strings, even when there is only one path (for example, `"inputs": ["src/index.ts"]`, never `"inputs": "src/index.ts"`). Use paths relative to `{{workingDirectory}}`; do not put absolute paths to the original checkout or any directory outside `{{workingDirectory}}` in `files`, `inputs`, `expectedOutput`, or verification commands. **`expectedOutput` must only list files the task actually creates or overwrites on disk.** Do NOT include files the task merely reads, verifies, tests, or describes — those belong in `inputs`, `verify`, `description`, or slice success criteria. If a task is a pure verification or test task that produces no new files, `expectedOutput` must be `[]`; if it writes a test-result log or assertion output file, list only that concrete file path. A file that does not yet exist on disk and is needed as an `input` must be produced by an earlier task's `expectedOutput` — if no prior task creates it, add a task before this one that does. Never list GSD planning artifacts — anything under `.gsd/`, `.planning/`, or `.audits/`, or artifact names like `M001-CONTEXT.md` / `S01-PLAN.md` — in `inputs`, `files`, or `expectedOutput`: their content is preloaded as context, and they are written by workflow tools, not by tasks.
-10. Persist with `gsd_plan_slice` using `milestoneId`, `sliceId`, `goal`, optional `successCriteria`/`proofLevel`/`integrationClosure`/`observabilityImpact`, and `tasks`. `gsd_plan_slice` handles task persistence transactionally and renders `{{outputPath}}` plus task plans; do not call `gsd_plan_task`. The DB-backed tool is the canonical write path. Do **not** rely on direct `PLAN.md` writes as the source of truth.
+9. Each task persisted with `gsd_plan_task` needs the exact shape: `milestoneId`, `sliceId`, `taskId`, `title`, `description`, `estimate`, `files`, `verify`, `inputs`, `expectedOutput`, and optional `observabilityImpact`. `description` should contain the Why / Do / Done-when narrative. Any npm package name in a task description's install/add instructions (`npm install`, `yarn add`, `pnpm add`) or in `require('...')` or `import ... from '...'` code examples is subject to pre-execution registry validation; reference only packages that exist on the public npm registry, and remove or correct any package name that is not real. `files`, `inputs`, and `expectedOutput` must be JSON arrays of strings, even when there is only one path (for example, `"inputs": ["src/index.ts"]`, never `"inputs": "src/index.ts"`). Use paths relative to `{{workingDirectory}}`; do not put absolute paths to the original checkout or any directory outside `{{workingDirectory}}` in `files`, `inputs`, `expectedOutput`, or verification commands. **`expectedOutput` must only list files the task actually creates or overwrites on disk.** Do NOT include files the task merely reads, verifies, tests, or describes — those belong in `inputs`, `verify`, `description`, or slice success criteria. If a task is a pure verification or test task that produces no new files, `expectedOutput` must be `[]`; if it writes a test-result log or assertion output file, list only that concrete file path. A file that does not yet exist on disk and is needed as an `input` must be produced by an earlier task's `expectedOutput` — if no prior task creates it, add a task before this one that does. Never list GSD planning artifacts — anything under `.gsd/`, `.planning/`, or `.audits/`, or artifact names like `M001-CONTEXT.md` / `S01-PLAN.md` — in `inputs`, `files`, or `expectedOutput`: their content is preloaded as context, and they are written by workflow tools, not by tasks.
+10. Persist incrementally through DB-backed tools. First call `gsd_plan_slice` with `milestoneId`, `sliceId`, `goal`, and optional `successCriteria`/`proofLevel`/`integrationClosure`/`observabilityImpact`; omit `tasks` for this metadata call. Then call `gsd_plan_task` once per task, using the task shape above. Each successful tool call saves progress and re-renders `{{outputPath}}` from DB. The DB-backed tools are the canonical write path. Do **not** rely on direct `PLAN.md` writes as the source of truth.
 11. Self-audit before finishing: goal/demo closure, requirement coverage, deliverable coverage audit (cross-check every file listed in CONTEXT.md `## Scope` / `### In Scope` against task `files` or `expectedOutput`), locked decisions, concrete paths, dependency order, wiring, scope size, proof truthfulness, feature completeness, and quality gates. Quality gates: non-trivial slices/tasks include specific Q3-Q7 coverage where applicable.
 12. If planning creates structural decisions, call `gsd_decision_save` for each; the tool persists the decision and regenerates `.gsd/DECISIONS.md`.
 13. {{commitInstruction}}
@@ -55,6 +55,6 @@ The slice directory already exists. Do not mkdir.
 
 **Autonomous execution:** no human is available. Do not call `ask_user_questions` or `secure_env_collect`; make reasonable assumptions and document them.
 
-**You MUST call `gsd_plan_slice` to persist planning state before finishing, unless the stale-path safety rule above stops the unit before safe planning can occur.**
+**You MUST call `gsd_plan_slice` and then `gsd_plan_task` once for each planned task before finishing, unless the stale-path safety rule above stops the unit before safe planning can occur.**
 
 When done, say: "Slice {{sliceId}} planned." Say this exactly once — if you already said it in a prior message, do not repeat it.

package/src/resources/extensions/gsd/root-write-leak-guard.ts

@@ -5,8 +5,18 @@ import { execFileSync } from "node:child_process";
 import { createHash } from "node:crypto";
 import { existsSync, readFileSync, statSync } from "node:fs";
 import { join } from "node:path";
+import { GSD_RUNTIME_PATTERNS } from "./gitignore.js";
 
 const MAX_SYNC_FINGERPRINT_BYTES = 1_500_000_000;
+const ROOT_RUNTIME_PATH_PREFIXES = Array.from(
+  new Set(
+    GSD_RUNTIME_PATTERNS.map((pattern) => {
+      const path = pattern.replace(/\/+$/, "");
+      const slash = path.indexOf("/");
+      return slash === -1 ? path : path.slice(0, slash);
+    }),
+  ),
+);
 
 export interface RootDirtyEntry {
   path: string;
@@ -25,7 +35,9 @@ export interface RootWriteLeak {
 export type RootDirtySnapshot = Map<string, RootDirtyEntry>;
 
 function isRootRuntimePath(path: string): boolean {
-  return path === ".gsd" || path.startsWith(".gsd/");
+  return ROOT_RUNTIME_PATH_PREFIXES.some(
+    (prefix) => path === prefix || path.startsWith(`${prefix}/`),
+  );
 }
 
 function fileFingerprint(rootPath: string, relPath: string): string {