@opengsd/gsd-pi 1.3.0-dev.65546769 → 1.3.0-dev.738160b9

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/milestone-implementation-evidence.ts

@@ -19,6 +19,16 @@ import { resolveTasksDir } from "./paths.js";
 
 /** Large enough for unbounded milestone-history git log scans in big repos. */
 const GIT_LOG_MAX_BUFFER = 16 * 1024 * 1024;
+const LOG_FIELD_SEPARATOR = "\x1f";
+const LOG_RECORD_SEPARATOR = "\x1e";
+
+type CommitRecord = {
+  hash: string;
+  parents: string;
+  committedAt: string;
+  message: string;
+  files: string[];
+};
 
 /**
  * Check whether a milestone produced implementation artifacts (non-`.gsd/`
@@ -198,7 +208,7 @@ function getChangedFilesFromMilestoneTaggedCommits(
   // Primary: path-scoped log against .gsd/milestones/<id>. Fast and unbounded
   // by depth when .gsd/ is tracked in git.
   const scoped = scanGsdTaggedCommits(basePath, milestoneId, [
-    "log", "--format=%H%x1f%B%x1e", "HEAD", "--", `.gsd/milestones/${milestoneId}`,
+    "log", "--full-diff", "--name-only", "--format=%x1e%H%x1f%B%x1f", "HEAD", "--", `.gsd/milestones/${milestoneId}`,
   ]);
   if (!scoped.ok) return scoped;
   if (scoped.matched && classifyImplementationFiles(scoped.files) === "present") return scoped;
@@ -213,7 +223,7 @@ function getChangedFilesFromMilestoneTaggedCommits(
   // reintroducing the rolling-depth failure class removed in #4699 where
   // milestone evidence aged out behind unrelated activity.
   const unscoped = scanGsdTaggedCommits(basePath, milestoneId, [
-    "log", "--format=%H%x1f%B%x1e", "HEAD",
+    "log", "--name-only", "--format=%x1e%H%x1f%B%x1f", "HEAD",
   ]);
   if (!unscoped.ok) return scoped.matched ? scoped : unscoped;
   if (!unscoped.matched) return scoped;
@@ -299,8 +309,7 @@ function backfillChangedFilesFromUntaggedMilestoneCommits(
       if (record.parents.trim().split(/\s+/).filter(Boolean).length > 1) continue;
       if (commitMessageHasGsdTrailer(record.message)) continue;
 
-      const commitFiles = getChangedFilesForCommit(basePath, record.hash);
-      const implementationFiles = commitFiles.map(normalizeRepoPath).filter(isImplementationPath);
+      const implementationFiles = record.files.map(normalizeRepoPath).filter(isImplementationPath);
       if (implementationFiles.length === 0) continue;
       if (!implementationFiles.some((file) => hintSet.has(file))) continue;
 
@@ -323,25 +332,30 @@ function backfillChangedFilesFromUntaggedMilestoneCommits(
   }
 }
 
-function getCommitRecords(basePath: string): Array<{ hash: string; parents: string; committedAt: string; message: string }> {
-  const logOutput = execFileSync("git", ["log", "--format=%H%x1f%P%x1f%cI%x1f%B%x1e", "HEAD"], {
+function getCommitRecords(basePath: string): CommitRecord[] {
+  const logOutput = execFileSync("git", ["log", "--name-only", "--format=%x1e%H%x1f%P%x1f%cI%x1f%B%x1f", "HEAD"], {
     cwd: basePath,
     stdio: ["ignore", "pipe", "pipe"],
     encoding: "utf-8",
     maxBuffer: GIT_LOG_MAX_BUFFER,
   });
   return logOutput
-    .split("\x1e")
-    .map((record) => record.trim())
+    .split(LOG_RECORD_SEPARATOR)
     .filter(Boolean)
     .flatMap((record) => {
-      const parts = record.split("\x1f");
-      if (parts.length < 4) return [];
-      const [hash, parents, committedAt, ...messageParts] = parts;
-      return [{ hash: hash.trim(), parents: parents.trim(), committedAt: committedAt.trim(), message: messageParts.join("\x1f") }];
+      const parts = record.split(LOG_FIELD_SEPARATOR);
+      if (parts.length < 5) return [];
+      const [hash, parents, committedAt] = parts;
+      const files = parseNameOnlyFiles(parts.at(-1) ?? "");
+      const message = parts.slice(3, -1).join(LOG_FIELD_SEPARATOR);
+      return [{ hash: hash.trim(), parents: parents.trim(), committedAt: committedAt.trim(), message, files }];
     });
 }
 
+function parseNameOnlyFiles(rawFiles: string): string[] {
+  return rawFiles.split(/\r?\n/).map((file) => file.trim()).filter(Boolean);
+}
+
 function isFullCommitSha(value: string): boolean {
   return /^[0-9a-f]{40}$/i.test(value);
 }
@@ -359,23 +373,23 @@ function scanGsdTaggedCommits(
       maxBuffer: GIT_LOG_MAX_BUFFER,
     });
     const records = logOutput
-      .split("\x1e")
-      .map((record) => record.trim())
+      .split(LOG_RECORD_SEPARATOR)
       .filter(Boolean)
       .flatMap((record) => {
-        const sep = record.indexOf("\x1f");
-        if (sep === -1) return [];
-        const hash = record.slice(0, sep).trim();
-        const message = record.slice(sep + 1);
-        return [{ hash, message }];
+        const parts = record.split(LOG_FIELD_SEPARATOR);
+        if (parts.length < 3) return [];
+        const hash = parts[0].trim();
+        if (!hash) return [];
+        const files = parseNameOnlyFiles(parts.at(-1) ?? "");
+        const message = parts.slice(1, -1).join(LOG_FIELD_SEPARATOR);
+        return [{ message, files }];
       });
 
     const files = new Set<string>();
     let matched = false;
-    for (const { hash, message } of records) {
+    for (const { message, files: commitFiles } of records) {
       if (!commitMessageHasGsdTrailer(message)) continue;
 
-      const commitFiles = getChangedFilesForCommit(basePath, hash);
       if (!commitMatchesMilestone(basePath, message, milestoneId, commitFiles)) continue;
 
       matched = true;

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/quick.ts

@@ -10,8 +10,8 @@
  */
 
 import type { ExtensionAPI, ExtensionCommandContext } from "@gsd/pi-coding-agent";
-import { existsSync, mkdirSync, readFileSync, readdirSync, realpathSync, rmSync, writeFileSync } from "node:fs";
-import { isAbsolute, join, relative } from "node:path";
+import { existsSync, lstatSync, mkdirSync, readFileSync, readdirSync, realpathSync, rmSync, writeFileSync } from "node:fs";
+import { isAbsolute, join, relative, resolve } from "node:path";
 import { QUICK_BRANCH_RE } from "./branch-patterns.js";
 import { loadPrompt } from "./prompt-loader.js";
 import { gsdRoot } from "./paths.js";
@@ -31,6 +31,7 @@ interface QuickReturnState {
 }
 
 let pendingQuickReturn: QuickReturnState | null = null;
+const pendingQuickReturnMisses = new Map<string, string>();
 
 // ─── Quick Task Helpers ───────────────────────────────────────────────────────
 
@@ -189,12 +190,35 @@ export function buildQuickCommitInstruction(basePath: string, root: string): str
   ].join("\n");
 }
 
+function readHeadBranchName(basePath: string): string | null {
+  try {
+    const gitPath = join(basePath, ".git");
+    if (!existsSync(gitPath)) return null;
+
+    let headPath: string;
+    if (lstatSync(gitPath).isDirectory()) {
+      headPath = join(gitPath, "HEAD");
+    } else {
+      const gitFile = readFileSync(gitPath, "utf-8").trim();
+      if (!gitFile.startsWith("gitdir: ")) return null;
+      headPath = join(resolve(basePath, gitFile.slice("gitdir: ".length)), "HEAD");
+    }
+
+    const head = readFileSync(headPath, "utf-8").trim();
+    if (!head.startsWith("ref: refs/heads/")) return null;
+    return head.slice("ref: refs/heads/".length);
+  } catch {
+    return null;
+  }
+}
+
 function quickReturnStatePath(basePath: string): string {
   return join(gsdRoot(basePath), "runtime", "quick-return.json");
 }
 
 function persistPendingReturn(state: QuickReturnState): void {
   pendingQuickReturn = state;
+  pendingQuickReturnMisses.delete(state.basePath);
   mkdirSync(join(gsdRoot(state.basePath), "runtime"), { recursive: true });
   writeFileSync(quickReturnStatePath(state.basePath), JSON.stringify(state) + "\n", "utf-8");
 }
@@ -203,6 +227,13 @@ function readPendingReturn(basePath: string): QuickReturnState | null {
   if (pendingQuickReturn && pendingQuickReturn.basePath === basePath) {
     return pendingQuickReturn;
   }
+  if (pendingQuickReturnMisses.has(basePath)) {
+    const statePath = quickReturnStatePath(basePath);
+    if (!existsSync(statePath) && readHeadBranchName(basePath) === pendingQuickReturnMisses.get(basePath)) {
+      return null;
+    }
+    pendingQuickReturnMisses.delete(basePath);
+  }
 
   try {
     const raw = readFileSync(quickReturnStatePath(basePath), "utf-8");
@@ -216,6 +247,7 @@ function readPendingReturn(basePath: string): QuickReturnState | null {
       && typeof parsed.description === "string"
     ) {
       pendingQuickReturn = parsed as QuickReturnState;
+      pendingQuickReturnMisses.delete(basePath);
       return pendingQuickReturn;
     }
   } catch {
@@ -225,9 +257,14 @@ function readPendingReturn(basePath: string): QuickReturnState | null {
   const inferred = inferQuickReturnFromBranch(basePath);
   if (inferred) {
     pendingQuickReturn = inferred;
+    pendingQuickReturnMisses.delete(basePath);
     return inferred;
   }
 
+  const branchAtMiss = readHeadBranchName(basePath);
+  if (branchAtMiss) {
+    pendingQuickReturnMisses.set(basePath, branchAtMiss);
+  }
   return null;
 }
 
@@ -235,6 +272,10 @@ function clearPendingReturn(basePath: string): void {
   if (pendingQuickReturn?.basePath === basePath) {
     pendingQuickReturn = null;
   }
+  const branchAtMiss = readHeadBranchName(basePath);
+  if (branchAtMiss) {
+    pendingQuickReturnMisses.set(basePath, branchAtMiss);
+  }
   rmSync(quickReturnStatePath(basePath), { force: true });
 }
 

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 {

package/src/resources/extensions/gsd/safety/destructive-guard.ts

@@ -29,6 +29,13 @@ const DESTRUCTIVE_PATTERNS: readonly DestructivePattern[] = [
   { pattern: /\bkubectl\s+(delete|apply)\b/i, label: "kubectl mutation" },
 ];
 
+function stripQuotedAndComments(command: string): string {
+  return command
+    .replace(/"(?:[^"\\]|\\.)*"/g, '""')
+    .replace(/'(?:[^'\\]|\\.)*'/g, "''")
+    .replace(/(^|\s)#.*$/g, "$1");
+}
+
 // ─── Public API ─────────────────────────────────────────────────────────────
 
 export interface CommandClassification {
@@ -41,9 +48,10 @@ export interface CommandClassification {
  * Returns the list of matched destructive pattern labels.
  */
 export function classifyCommand(command: string): CommandClassification {
+  const commandToClassify = stripQuotedAndComments(command);
   const labels: string[] = [];
   for (const { pattern, label } of DESTRUCTIVE_PATTERNS) {
-    if (pattern.test(command)) {
+    if (pattern.test(commandToClassify)) {
       // Deduplicate labels (e.g., two force-push patterns)
       if (!labels.includes(label)) labels.push(label);
     }