@opengsd/gsd-pi 1.4.0 → 1.5.0-dev.4fb2d460

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

@@ -39,7 +39,7 @@ import {
   type SkillDiscoveryMode,
   formatSkillRef,
 } from "./preferences-types.js";
-import { validatePreferences } from "./preferences-validation.js";
+import { crossAxisPreferenceWarnings, validatePreferences } from "./preferences-validation.js";
 import { gsdHome } from "./gsd-home.js";
 
 // ─── Re-exports: types ──────────────────────────────────────────────────────
@@ -270,6 +270,12 @@ export function normalizePreferencesShape(
 const EFFECTIVE_PREFERENCES_CACHE_MAX = 64;
 const effectivePreferencesCache = new Map<string, LoadedGSDPreferences | null>();
 
+type EffectivePreferencesLoadOptions = {
+  availableModelIds?: string[];
+  preferredModelId?: string;
+  skipProfileDefaults?: boolean;
+};
+
 export function clearGSDPreferencesCache(): void {
   effectivePreferencesCache.clear();
 }
@@ -301,7 +307,7 @@ function preferencesFileSignature(path: string): string {
 
 function effectivePreferencesCacheKey(
   basePath?: string,
-  opts?: { availableModelIds?: string[]; preferredModelId?: string },
+  opts?: EffectivePreferencesLoadOptions,
 ): string {
   return JSON.stringify({
     basePath: basePath ?? null,
@@ -309,6 +315,7 @@ function effectivePreferencesCacheKey(
     project: projectPreferencesCandidatePaths(basePath).map(preferencesFileSignature),
     availableModelIds: opts?.availableModelIds ?? null,
     preferredModelId: opts?.preferredModelId ?? null,
+    skipProfileDefaults: opts?.skipProfileDefaults === true,
   });
 }
 
@@ -338,7 +345,7 @@ export function loadProjectGSDPreferences(basePath?: string): LoadedGSDPreferenc
 
 export function loadEffectiveGSDPreferences(
   basePath?: string,
-  opts?: { availableModelIds?: string[]; preferredModelId?: string },
+  opts?: EffectivePreferencesLoadOptions,
 ): LoadedGSDPreferences | null {
   const cacheKey = effectivePreferencesCacheKey(basePath, opts);
   if (effectivePreferencesCache.has(cacheKey)) {
@@ -384,7 +391,7 @@ export function loadEffectiveGSDPreferences(
   } else {
     profileForDefaults = DEFAULT_TOKEN_PROFILE;
   }
-  if (profileForDefaults) {
+  if (profileForDefaults && !opts?.skipProfileDefaults) {
     const profileDefaults = _resolveProfileDefaults(
       profileForDefaults,
       opts?.availableModelIds,
@@ -409,11 +416,38 @@ export function loadEffectiveGSDPreferences(
   }
 
   result = stripInheritedPlanningDepth(result, projectHasPlanningDepth);
+  result = appendCrossAxisPreferenceWarnings(result);
 
   cacheEffectivePreferences(cacheKey, result);
   return result;
 }
 
+function appendCrossAxisPreferenceWarnings(loaded: LoadedGSDPreferences): LoadedGSDPreferences {
+  const crossWarnings = crossAxisPreferenceWarnings(loaded.preferences);
+  const existingMessages = new Set([
+    ...(loaded.warnings ?? []),
+    ...(loaded.diagnostics ?? []).map((diagnostic) => diagnostic.message),
+  ]);
+  const newWarnings = crossWarnings.filter((message) => !existingMessages.has(message));
+  if (newWarnings.length === 0) return loaded;
+
+  return {
+    ...loaded,
+    warnings: [...(loaded.warnings ?? []), ...newWarnings],
+    diagnostics: [
+      ...(loaded.diagnostics ?? []),
+      ...newWarnings.map((message): PreferenceDiagnostic => ({
+        path: loaded.path,
+        scope: loaded.scope,
+        severity: "warning",
+        kind: "validation",
+        message,
+        sanitized: true,
+      })),
+    ],
+  };
+}
+
 function withoutProfilePhaseDefaults(defaults: Partial<GSDPreferences>): Partial<GSDPreferences> {
   if (defaults.phases === undefined) return defaults;
   const { phases: _phases, ...rest } = defaults;
@@ -999,6 +1033,26 @@ export function renderPreferencesForSystemPrompt(
   return lines.join("\n");
 }
 
+/**
+ * Render a compact response-language directive for injection into dispatched
+ * prompt *content* (discuss/QA and auto-execution unit prompts).
+ *
+ * The main session's system prompt already carries the full GSD Skill
+ * Preferences block (including language) via `before_agent_start`, but
+ * discuss/QA turns and auto-execution units are dispatched as separate
+ * turns/sessions whose prompts are assembled here — without that block — so the
+ * configured language never reaches them (#1210). Injecting this directive into
+ * the dispatched prompt content makes the `language` preference effective across
+ * both guided and auto workflows.
+ *
+ * Returns "" when no language is configured.
+ */
+export function renderLanguageDirectiveForPrompt(preferences: GSDPreferences | undefined): string {
+  if (!preferences?.language) return "";
+  const safeLang = preferences.language.replace(/[\r\n]/g, " ").slice(0, 50);
+  return `## Response Language\n\nAlways respond in ${safeLang} — questions, explanations, and summaries.`;
+}
+
 // ─── Hook Resolution ──────────────────────────────────────────────────────────
 
 /**

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

@@ -32,6 +32,8 @@ Before planning, validate roadmap assumptions against code and dependency summar
 
 If slice research is inlined, trust its architectural findings, but verify every concrete file path you place in task `inputs` or `expectedOutput` against the current tree or prior/same-task outputs. Explore enough code to confirm paths, boundaries, and verification. Executors later get only task plans, slice excerpt, and prior summaries, so put required paths, steps, inputs, and outputs in task plans.
 
+{{repoRegistry}}
+
 {{executorContextConstraints}}
 
 ## Planning Rules
@@ -45,8 +47,8 @@ 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 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.
+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`. In a parent workspace (when a Declared Repositories block is present above), also set `targetRepositories` to the repository id(s) the task touches. `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` (and `targetRepositories` in a parent workspace, to set the slice-wide default); 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}}

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

@@ -38,7 +38,7 @@ If a `GSD Skill Preferences` block appears below, treat it as durable guidance f
 
 ### Naming Convention
 
-Directories use bare IDs. Files use ID-SUFFIX format. Milestones: `M001/` or `M{seq}-{rand6}/` when `unique_milestone_ids: true`; files like `M001-CONTEXT.md`, `M001-ROADMAP.md`, `M001-RESEARCH.md`. Slices: `S01/` with `S01-PLAN.md`, `S01-RESEARCH.md`, `S01-SUMMARY.md`, `S01-UAT.md`. Tasks: `T01-PLAN.md`, `T01-SUMMARY.md`. Titles live inside content, not names.
+GSD projects use a flat-phase layout. Phase directories are `{MM}-{slug}` where `{MM}` is the zero-padded phase number and `{slug}` is derived from the phase title (e.g. `47-real-time-runtime-hardening`). Phase-level files are `{MM}-SUFFIX.md` (e.g. `47-CONTEXT.md`, `47-RESEARCH.md`, `47-ROADMAP.md`, `47-VALIDATION.md`, `47-SUMMARY.md`). Slice/plan files live directly in the phase directory as `{MM}-{SS}-SUFFIX.md` (e.g. `47-01-PLAN.md`, `47-01-SUMMARY.md`, `47-01-UAT.md`). Task plan content lives inside the slice plan file (`{MM}-{SS}-PLAN.md`) as checkboxes; there is no `tasks/` subdirectory and no `tasks/T##-PLAN.md`. Titles live inside content, not names. Prefer GSD-provided layout-aware paths/resolvers over hardcoding artifact paths, since phase slugs are title-derived.
 
 ### Directory Structure
 
@@ -46,13 +46,13 @@ Directories use bare IDs. Files use ID-SUFFIX format. Milestones: `M001/` or `M{
 .gsd/
   PROJECT.md, REQUIREMENTS.md, DECISIONS.md, KNOWLEDGE.md, CODEBASE.md, OVERRIDES.md, QUEUE.md, STATE.md
   runtime/, activity/, worktrees/
-  milestones/M001/
-    M001-CONTEXT.md, M001-RESEARCH.md, M001-ROADMAP.md, M001-SUMMARY.md
-    slices/S01/
-      S01-CONTEXT.md, S01-RESEARCH.md, S01-PLAN.md, S01-SUMMARY.md, S01-UAT.md
-      tasks/T01-PLAN.md, tasks/T01-SUMMARY.md
+  phases/{MM}-{slug}/
+    {MM}-CONTEXT.md, {MM}-RESEARCH.md, {MM}-ROADMAP.md, {MM}-VALIDATION.md, {MM}-SUMMARY.md
+    {MM}-{SS}-PLAN.md, {MM}-{SS}-SUMMARY.md, {MM}-{SS}-UAT.md
 ```
 
+Task plan content is embedded in `{MM}-{SS}-PLAN.md`; do not expect `tasks/T##-PLAN.md`.
+
 `runtime/`, `activity/`, `worktrees/`, and `STATE.md` are system-managed. `PROJECT.md` is current state; `REQUIREMENTS.md` is the active capability contract; `DECISIONS.md` and `KNOWLEDGE.md` are append-only; `CODEBASE.md` is an auto-refreshed codebase map.
 
 ### Isolation Model

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

@@ -15,7 +15,7 @@ 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";
-import { GitServiceImpl, runGit } from "./git-service.js";
+import { GitServiceImpl, runGit, taskBranchArgs } from "./git-service.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { nativeBranchExists, nativeDetectMainBranch, nativeDiffNumstat } from "./native-git-bridge.js";
 import { nativeHasStagedChanges } from "./native-git-bridge.js";
@@ -365,6 +365,7 @@ export async function handleQuick(
   const git = new GitServiceImpl(basePath, gitPrefs);
   const branchName = `gsd/quick/${taskNum}-${slug}`;
   let originalBranch = git.getCurrentBranch();
+  let returnBranch = originalBranch;
 
   const { getIsolationMode } = await import("./preferences.js");
   const usesBranch = getIsolationMode() !== "none" && isGitOpsEnabled();
@@ -381,7 +382,14 @@ export async function handleQuick(
           }
         } catch { /* nothing to commit — fine */ }
 
-        runGit(basePath, ["checkout", "-b", branchName]);
+        const branchArgs = taskBranchArgs(basePath, branchName, current, git.getMainBranch());
+        const startPoint = branchArgs[3];
+        // When the quick branch is redirected off a stale task branch, the
+        // squash-merge on closeout must return to the same base — merging a
+        // base-branch-rooted quick branch back into the stale task branch
+        // would drag the base's newer history into it.
+        if (startPoint) returnBranch = startPoint;
+        runGit(basePath, branchArgs);
         branchCreated = true;
       }
     } catch (err) {
@@ -395,7 +403,7 @@ export async function handleQuick(
   if (actualBranch === branchName && originalBranch !== branchName) {
     persistPendingReturn({
       basePath,
-      originalBranch,
+      originalBranch: returnBranch,
       quickBranch: branchName,
       taskNum,
       slug,

package/src/resources/extensions/gsd/redact-secrets.ts

@@ -0,0 +1,40 @@
+// redact-secrets.ts
+// Best-effort redaction of secret-shaped substrings before persisting free text
+// (exec-sandbox output, activity-log session entries) to disk under .gsd/, which
+// the secret scanner skips. Patterns mirror scripts/secret-scan.mjs.
+
+const PLACEHOLDER = "«redacted»";
+
+// Each secret shape. Global flag so replace() catches every occurrence in a line.
+// Order is not significant — matches are replaced independently.
+const PATTERNS: RegExp[] = [
+  /AKIA[0-9A-Z]{16}/g, // AWS access key id
+  /(api[_-]?key|apikey|api[_-]?secret)[ \t]*[:=][ \t]*['"][0-9a-zA-Z_./-]{20,}['"]/gi,
+  /(secret|token|password|passwd|pwd|credential)[ \t]*[:=][ \t]*['"][^\s'"]{8,}['"]/gi,
+  /(authorization|bearer)[ \t]*[:=][ \t]*['"][^\s'"]{8,}['"]/gi,
+  /Bearer[ \t]+[0-9a-zA-Z._-]{8,}/g, // Authorization: Bearer <token> (unquoted)
+  /-----BEGIN\s+(RSA|DSA|EC|OPENSSH|PGP)\s+PRIVATE\s+KEY-----[\s\S]*?-----END\s+(RSA|DSA|EC|OPENSSH|PGP)\s+PRIVATE\s+KEY-----/g,
+  /(mysql|postgres|postgresql|mongodb|redis|amqp|mssql):\/\/[^\s'"]{8,}/gi,
+  /gh[pousr]_[0-9a-zA-Z]{36,}/g, // GitHub token
+  /glpat-[0-9a-zA-Z-]{20,}/g, // GitLab token
+  /xox[baprs]-[0-9a-zA-Z-]{10,}/g, // Slack token
+  /hooks\.slack\.com\/services\/T[0-9A-Z]{8,}\/B[0-9A-Z]{8,}\/[0-9a-zA-Z]{20,}/g,
+  /AIza[0-9A-Za-z_-]{35}/g, // Google API key
+  /[sr]k_(live|test)_[0-9a-zA-Z]{20,}/g, // Stripe key
+  /sk-(ant-)?[0-9a-zA-Z_-]{20,}/g, // OpenAI / Anthropic style key
+  /npm_[0-9a-zA-Z]{36,}/g, // npm token
+  /(secret|key|token|password)[ \t]*[:=][ \t]*['"]?[0-9a-f]{32,}['"]?/gi, // hex secret
+];
+
+/**
+ * Replace secret-shaped substrings in `text` with a placeholder, preserving the
+ * surrounding content. Pure and safe to call per log line. The placeholder
+ * contains no quote/brace/backslash, so redacting a JSON string keeps it valid.
+ */
+export function redactSecrets(text: string): string {
+  let out = text;
+  for (const pattern of PATTERNS) {
+    out = out.replace(pattern, PLACEHOLDER);
+  }
+  return out;
+}

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

@@ -355,6 +355,23 @@ export function externalProjectsRoot(): string {
   return join(base, "projects");
 }
 
+/**
+ * Check whether this project already has authoritative external state.
+ *
+ * Used by legacy `.gsd/` migration to avoid re-copying a re-materialized local
+ * directory over newer state when an already-migrated symlink was replaced.
+ */
+export function externalStateAlreadyExistsForProject(basePath: string): boolean {
+  const base = process.env.GSD_STATE_DIR || gsdHome();
+  const computedPath = join(base, "projects", repoIdentity(basePath));
+  if (hasProjectState(computedPath)) return true;
+
+  const markerId = readGsdIdMarker(resolveGitRoot(basePath));
+  if (!markerId) return false;
+
+  return hasProjectState(join(base, "projects", markerId));
+}
+
 // ─── Numbered Variant Cleanup ────────────────────────────────────────────────
 
 /**

package/src/resources/extensions/gsd/repository-registry.ts

@@ -23,6 +23,12 @@ export interface RepositoryRegistry {
 }
 
 export function defaultRepositoryTargets(registry: RepositoryRegistry): string[] {
+  // In parent mode, default to the declared child repositories so work is
+  // attributed to the repo it touches — not silently to the root "project".
+  if (registry.mode === "parent") {
+    return registry.repositories.filter((repo) => repo.id !== "project").map((repo) => repo.id);
+  }
+
   const project = registry.byId.get("project");
   if (project) return [project.id];
   const first = registry.repositories[0];
@@ -78,7 +84,7 @@ export function createRepositoryRegistry(
 ): RepositoryRegistry {
   const contract = resolveGsdPathContract(basePath);
   const projectRoot = contract.isWorktree
-    ? resolveGitWorkingTreeRoot(contract.workRoot) ?? contract.projectRoot
+    ? resolveGitWorkingTreeRoot(contract.workRoot) ?? contract.workRoot
     : contract.projectRoot;
   const mode = workspacePrefs?.mode ?? "project";
   const repoMap = new Map<string, RegisteredRepository>();

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

@@ -65,11 +65,12 @@ export function captureRootDirtySnapshot(rootPath: string): RootDirtySnapshot {
   for (const line of status.split("\n")) {
     if (!line.trim()) continue;
     const code = line.slice(0, 2);
+    if (code !== "??") continue;
     const path = line.slice(3).replace(/^"|"$/g, "");
     if (!path || isRootRuntimePath(path)) continue;
     snapshot.set(path, {
       path,
-      status: code.trim() || code,
+      status: code,
       fingerprint: fileFingerprint(rootPath, path),
     });
   }
@@ -87,7 +88,7 @@ export function detectRootWriteLeak(input: {
   const leaked: RootDirtyEntry[] = [];
   for (const entry of after.values()) {
     const prior = input.before?.get(entry.path);
-    if (!prior || prior.status !== entry.status || prior.fingerprint !== entry.fingerprint) {
+    if (!prior || prior.fingerprint !== entry.fingerprint) {
       leaked.push(entry);
     }
   }

package/src/resources/extensions/gsd/safe-fs.ts

@@ -1,4 +1,4 @@
-import { existsSync, mkdirSync, cpSync, type CopySyncOptions } from "node:fs"
+import { existsSync, mkdirSync, cpSync, statSync, type CopySyncOptions } from "node:fs"
 import { dirname } from "node:path"
 import { logWarning } from "./workflow-logger.js"
 
@@ -39,7 +39,27 @@ export function safeCopyRecursive(src: string, dst: string, opts?: Omit<CopySync
   if (!existsSync(src)) return false
   try {
     mkdirSync(dirname(dst), { recursive: true })
-    cpSync(src, dst, { ...opts, recursive: true })
+    const userFilter = opts?.filter
+    cpSync(src, dst, {
+      ...opts,
+      recursive: true,
+      filter: (srcPath, dstPath) => {
+        if (existsSync(dstPath)) {
+          try {
+            const srcStat = statSync(srcPath)
+            const dstStat = statSync(dstPath)
+            if (srcStat.isDirectory() !== dstStat.isDirectory()) {
+              logWarning("fs", `recursive copy skipped type collision: ${srcPath} → ${dstPath}`)
+              return false
+            }
+          } catch (err) {
+            logWarning("fs", `recursive copy skipped unreadable path: ${srcPath} → ${dstPath}: ${(err as Error).message}`)
+            return false
+          }
+        }
+        return userFilter ? userFilter(srcPath, dstPath) : true
+      },
+    })
     return true
   } catch (err) {
     logWarning("fs", `recursive copy failed: ${src} → ${dst}: ${(err as Error).message}`)

package/src/resources/extensions/gsd/skill-discovery.ts

@@ -9,8 +9,8 @@
  */
 
 import { existsSync, readdirSync, readFileSync, type Dirent } from "node:fs";
-import { homedir } from "node:os";
 import { join } from "node:path";
+import { getSkillDirectories } from "@gsd/pi-coding-agent";
 import { gsdHome } from "./gsd-home.js";
 import { getInstalledSkills, normalizeSkillName } from "./skills.js";
 
@@ -20,28 +20,47 @@ export interface DiscoveredSkill {
   location: string;
 }
 
-/** Snapshot of normalized skill names at auto-mode start */
-let baselineSkills: Set<string> | null = null;
+/**
+ * Snapshot state. `searchDirs` is captured at snapshot time so every detection
+ * pass during the session scans the same project + user dirs (the bug fix:
+ * previously only user dirs were scanned, so skills installed into the project
+ * mid-session were silently missed).
+ */
+interface SkillSnapshotState {
+  baselineNames: Set<string>;
+  searchDirs: string[];
+}
+
+let snapshot: SkillSnapshotState | null = null;
 
 /**
  * Snapshot the current installed skill catalog. Call at auto-mode start.
+ * `cwd` is the project base path; skills dropped into `<cwd>/.agents/skills/`,
+ * `<cwd>/.claude/skills/`, or `<cwd>/.gsd/skills/` mid-session are detected.
  */
-export function snapshotSkills(): void {
-  baselineSkills = snapshotCurrentSkillNames();
+export function snapshotSkills(options?: { cwd?: string }): void {
+  const searchDirs = getSkillDirectories({
+    cwd: options?.cwd ?? process.cwd(),
+    gsdHome: gsdHome(),
+  }).map((entry) => entry.path);
+  snapshot = {
+    baselineNames: snapshotCurrentSkillNames(searchDirs),
+    searchDirs,
+  };
 }
 
 /**
  * Clear the snapshot. Call when auto-mode stops.
  */
 export function clearSkillSnapshot(): void {
-  baselineSkills = null;
+  snapshot = null;
 }
 
 /**
  * Check if a snapshot is active (auto-mode is running with discovery).
  */
 export function hasSkillSnapshot(): boolean {
-  return baselineSkills !== null;
+  return snapshot !== null;
 }
 
 /**
@@ -49,12 +68,12 @@ export function hasSkillSnapshot(): boolean {
  * Returns skill metadata for any new skills found in the loader catalog or on disk.
  */
 export function detectNewSkills(): DiscoveredSkill[] {
-  if (!baselineSkills) return [];
+  if (!snapshot) return [];
 
   const newSkills: DiscoveredSkill[] = [];
-  for (const skill of getCurrentSkillsForDiscovery()) {
+  for (const skill of getCurrentSkillsForDiscovery(snapshot.searchDirs)) {
     const normalized = normalizeSkillName(skill.name);
-    if (baselineSkills.has(normalized)) continue;
+    if (snapshot.baselineNames.has(normalized)) continue;
     newSkills.push(skill);
   }
 
@@ -84,7 +103,13 @@ export async function refreshCatalogForNewSkills(options?: {
     }
   }
 
-  snapshotSkills();
+  // Re-snapshot, preserving the search dirs captured at auto-mode start.
+  if (snapshot) {
+    snapshot = {
+      baselineNames: snapshotCurrentSkillNames(),
+      searchDirs: snapshot.searchDirs,
+    };
+  }
   const names = newSkills.map((skill) => skill.name).join(", ");
   options?.notify?.(`GSD: loaded new skills: ${names}`, "info");
   return newSkills;
@@ -132,19 +157,18 @@ function escapeXml(value: string): string {
   });
 }
 
-function skillSearchDirs(): string[] {
-  return [
-    join(gsdHome(), "agent", "skills"),
-    join(homedir(), ".agents", "skills"),
-    join(homedir(), ".claude", "skills"),
-  ];
+function snapshotCurrentSkillNames(searchDirsOverride?: string[]): Set<string> {
+  // Uses explicit dirs, the snapshot's search dirs when active, or user-only dirs
+  // (no project context) when called before a snapshot is taken.
+  const searchDirs = searchDirsOverride ?? snapshot?.searchDirs ?? defaultSearchDirs();
+  return new Set(getCurrentSkillsForDiscovery(searchDirs).map(skill => normalizeSkillName(skill.name)));
 }
 
-function snapshotCurrentSkillNames(): Set<string> {
-  return new Set(getCurrentSkillsForDiscovery().map(skill => normalizeSkillName(skill.name)));
+function defaultSearchDirs(): string[] {
+  return getSkillDirectories({ cwd: process.cwd(), gsdHome: gsdHome() }).map((entry) => entry.path);
 }
 
-function getCurrentSkillsForDiscovery(): DiscoveredSkill[] {
+function getCurrentSkillsForDiscovery(searchDirs: string[]): DiscoveredSkill[] {
   const skills = new Map<string, DiscoveredSkill>();
   for (const skill of getInstalledSkills()) {
     const normalized = normalizeSkillName(skill.name);
@@ -155,7 +179,7 @@ function getCurrentSkillsForDiscovery(): DiscoveredSkill[] {
     });
   }
 
-  for (const skill of getDiskSkills()) {
+  for (const skill of getDiskSkills(searchDirs)) {
     const normalized = normalizeSkillName(skill.name);
     if (!skills.has(normalized)) skills.set(normalized, skill);
   }
@@ -163,9 +187,9 @@ function getCurrentSkillsForDiscovery(): DiscoveredSkill[] {
   return [...skills.values()];
 }
 
-function getDiskSkills(): DiscoveredSkill[] {
+function getDiskSkills(searchDirs: string[]): DiscoveredSkill[] {
   const skills = new Map<string, DiscoveredSkill>();
-  for (const dir of skillSearchDirs()) {
+  for (const dir of searchDirs) {
     if (!existsSync(dir)) continue;
     let entries: Dirent[];
     try {

package/src/resources/extensions/gsd/skills/gsd-headless/SKILL.md

@@ -211,17 +211,15 @@ All state lives in `.gsd/` as markdown files (version-controllable):
 
 ```
 .gsd/
-  milestones/M001/
-    M001-CONTEXT.md      # Requirements, scope, decisions
-    M001-ROADMAP.md      # Slices with tasks, dependencies, checkboxes
-    M001-SUMMARY.md      # Completion summary
-    slices/S01/
-      S01-PLAN.md        # Task list
-      S01-SUMMARY.md     # Slice summary with frontmatter
-      tasks/T01-PLAN.md  # Individual task spec
+  phases/01-foundation/
+    01-CONTEXT.md        # Requirements, scope, decisions
+    01-ROADMAP.md        # Slices with tasks, dependencies, checkboxes
+    01-SUMMARY.md        # Completion summary
+    01-01-PLAN.md        # First slice task list
+    01-01-SUMMARY.md     # First slice summary with frontmatter
 ```
 
-State is derived from files on disk — checkboxes in ROADMAP.md are the source of truth for completion.
+Runtime state is stored in the project-root database; markdown files are reviewable projections written under `.gsd/phases/`. Legacy projects may still resolve to `.gsd/milestones/<MID>/` until migrated.
 
 ## All Headless Commands
 

package/src/resources/extensions/gsd/skills/gsd-headless/references/commands.md

@@ -22,6 +22,7 @@ All commands can be run via `gsd headless [command]`.
 | `status` | Progress dashboard (TUI overlay — useful interactively, not for parsing) |
 | `visualize` | Workflow visualizer (deps, metrics, timeline) |
 | `history` | Execution history (supports --cost, --phase, --model, limit) |
+| `codebase` | Manage `.gsd/CODEBASE.md`; parent workspaces include declared child repositories under repo-labeled sections |
 
 ## Unit Control
 

package/src/resources/extensions/gsd/slice-parallel-orchestrator.ts

@@ -30,7 +30,9 @@ import { isAbsolute, join, dirname, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 import { gsdRoot } from "./paths.js";
 import { createWorktree, worktreePath, removeWorktree } from "./worktree-manager.js";
-import { autoWorktreeBranch, runWorktreePostCreateHook, syncGsdStateToWorktreeByScope } from "./auto-worktree.js";
+import { autoWorktreeBranch } from "./auto-worktree-branch-lifecycle.js";
+import { syncGsdStateToWorktreeByScope } from "./auto-worktree-sync.js";
+import { runWorktreePostCreateHook } from "./worktree-post-create-hook.js";
 import { createWorkspace, scopeMilestone } from "./workspace.js";
 import {
   writeSessionStatus,