@opengsd/gsd-pi 1.1.1-dev.b2556262 → 1.2.0-dev.0b870afa

package/src/resources/extensions/gsd/doctor-format.ts

@@ -1,4 +1,9 @@
-import type { DoctorIssue, DoctorIssueCode, DoctorReport, DoctorSummary } from "./doctor-types.js";
+import type { DoctorIssue, DoctorIssueCode, DoctorReport, DoctorSummary, DoctorSeverity } from "./doctor-types.js";
+import { doctorFixHint } from "./guidance.js";
+
+function severityTag(severity: DoctorSeverity): string {
+  return severity === "error" ? "ERROR" : severity === "warning" ? "WARN" : "INFO";
+}
 
 function matchesScope(unitId: string, scope?: string): boolean {
   if (!scope) return true;
@@ -53,8 +58,9 @@ export function formatDoctorReport(
   if (scopedIssues.length > 0) {
     lines.push("Priority issues:");
     for (const issue of scopedIssues.slice(0, maxIssues)) {
-      const prefix = issue.severity === "error" ? "ERROR" : issue.severity === "warning" ? "WARN" : "INFO";
-      lines.push(`- [${prefix}] ${issue.unitId}: ${issue.message}${issue.file ? ` (${issue.file})` : ""}`);
+      lines.push(`- [${severityTag(issue.severity)}] ${issue.unitId}: ${issue.message}${issue.file ? ` (${issue.file})` : ""}`);
+      const hint = doctorFixHint(issue.code);
+      if (hint && issue.severity !== "info") lines.push(`  Fix: ${hint}`);
     }
     if (scopedIssues.length > maxIssues) {
       lines.push(`- ...and ${scopedIssues.length - maxIssues} more in scope`);
@@ -72,10 +78,9 @@ export function formatDoctorReport(
 
 export function formatDoctorIssuesForPrompt(issues: DoctorIssue[]): string {
   if (issues.length === 0) return "- No remaining issues in scope.";
-  return issues.map(issue => {
-    const prefix = issue.severity === "error" ? "ERROR" : issue.severity === "warning" ? "WARN" : "INFO";
-    return `- [${prefix}] ${issue.unitId} | ${issue.code} | ${issue.message}${issue.file ? ` | file: ${issue.file}` : ""} | fixable: ${issue.fixable ? "yes" : "no"}`;
-  }).join("\n");
+  return issues.map(issue =>
+    `- [${severityTag(issue.severity)}] ${issue.unitId} | ${issue.code} | ${issue.message}${issue.file ? ` | file: ${issue.file}` : ""} | fixable: ${issue.fixable ? "yes" : "no"}`
+  ).join("\n");
 }
 
 /**

package/src/resources/extensions/gsd/doctor-git-checks.ts

@@ -5,11 +5,10 @@ import { dirname, join } from "node:path";
 
 import type { DoctorIssue, DoctorIssueCode } from "./doctor-types.js";
 import { loadFile } from "./files.js";
-import { parseRoadmap as parseLegacyRoadmap } from "./parsers-legacy.js";
-import { isDbAvailable, getMilestone } from "./gsd-db.js";
 import { resolveMilestoneFile } from "./paths.js";
-import { deriveState, isMilestoneComplete } from "./state.js";
-import { createWorktree, listWorktrees, resolveGitDir, worktreesDir } from "./worktree-manager.js";
+import { isCompletedMilestoneTerminal } from "./milestone-closeout.js";
+import { deriveState } from "./state.js";
+import { allWorktreesDirs, createWorktree, listWorktrees, resolveGitDir } from "./worktree-manager.js";
 import { abortAndReset } from "./git-self-heal.js";
 import { RUNTIME_EXCLUSION_PATHS, resolveMilestoneIntegrationBranch, writeIntegrationBranch } from "./git-service.js";
 import { nativeIsRepo, nativeWorktreeList, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddTracked, nativeCommit } from "./native-git-bridge.js";
@@ -146,22 +145,6 @@ function getSnapshotDiffCheckFailure(basePath: string): string | null {
   return failures.length > 0 ? failures.join("\n") : null;
 }
 
-async function isCompletedMilestoneTerminal(basePath: string, milestoneId: string): Promise<boolean> {
-  const summaryPath = resolveMilestoneFile(basePath, milestoneId, "SUMMARY");
-  if (!summaryPath) return false;
-
-  if (isDbAvailable()) {
-    const milestone = getMilestone(milestoneId);
-    return !!milestone && milestone.status === "complete";
-  }
-
-  const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
-  const roadmapContent = roadmapPath ? await loadFile(roadmapPath) : null;
-  if (!roadmapContent) return false;
-  const roadmap = parseLegacyRoadmap(roadmapContent);
-  return isMilestoneComplete(roadmap);
-}
-
 export async function checkGitHealth(
   basePath: string,
   issues: DoctorIssue[],
@@ -496,8 +479,8 @@ export async function checkGitHealth(
   // that is no longer registered with git. These orphaned dirs cause
   // "already exists" errors when re-creating the same worktree name.
   try {
-    const wtDir = worktreesDir(basePath);
-    if (existsSync(wtDir)) {
+    for (const wtDir of allWorktreesDirs(basePath)) {
+      if (!existsSync(wtDir)) continue;
       // Resolve symlinks and normalize separators so that symlinked .gsd
       // paths (e.g. ~/.gsd/projects/<hash>/worktrees/…) match the paths
       // returned by `git worktree list`.

package/src/resources/extensions/gsd/doctor-proactive.ts

@@ -267,12 +267,18 @@ export async function preDispatchHealthGate(basePath: string): Promise<PreDispat
     // Non-fatal — dispatch continues without STATE.md if rebuild fails
   }
 
+  // #442 Phase 1.7: resolve repo-ness once per gate. ensureWorkspaceGitReady
+  // has already run, and nothing below initializes/deinitializes the repo, so
+  // the two downstream blocks (integration-branch check, stale-changes
+  // snapshot) can share one nativeIsRepo result instead of querying twice.
+  const isRepo = nativeIsRepo(basePath);
+
   // ── Integration branch existence check ──
   // If the active milestone's recorded integration branch no longer exists in
   // git, the merge-back at the end of the milestone will fail. Block dispatch
   // now to surface this before work is lost.
   try {
-    if (nativeIsRepo(basePath)) {
+    if (isRepo) {
       const state = await deriveState(basePath);
       if (state.activeMilestone) {
         const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git ?? {};
@@ -296,7 +302,7 @@ export async function preDispatchHealthGate(basePath: string): Promise<PreDispat
   // If the working tree is dirty and no commit has happened recently,
   // create a safety snapshot so work isn't lost if the next unit crashes.
   try {
-    if (nativeIsRepo(basePath)) {
+    if (isRepo) {
       const prefs = loadEffectiveGSDPreferences()?.preferences ?? {};
       // `git.snapshots: false` is the canonical toggle that disables WIP
       // snapshot commits — honour it before touching the threshold path (#4420).

package/src/resources/extensions/gsd/doctor-runtime-checks.ts

@@ -414,26 +414,31 @@ export async function checkRuntimeHealth(
         ".gsd/event-log.jsonl",
       ];
 
-      // If blanket .gsd/ or .gsd is present, all patterns are covered
+      // If blanket .gsd/ or .gsd is present, all .gsd/* patterns are covered —
+      // but NOT the .gsd-worktrees/ sibling, which always needs its own entry.
       const hasBlanketIgnore = existingLines.has(".gsd/") || existingLines.has(".gsd");
-
+      const missing: string[] = [];
+      if (!existingLines.has(".gsd-worktrees/") && !existingLines.has(".gsd-worktrees")) {
+        missing.push(".gsd-worktrees/");
+      }
       if (!hasBlanketIgnore) {
-        const missing = criticalPatterns.filter(p => !existingLines.has(p));
-        if (missing.length > 0) {
-          issues.push({
-            severity: "warning",
-            code: "gitignore_missing_patterns",
-            scope: "project",
-            unitId: "project",
-            message: `${missing.length} critical GSD runtime pattern(s) missing from .gitignore: ${missing.join(", ")}`,
-            file: ".gitignore",
-            fixable: true,
-          });
+        missing.push(...criticalPatterns.filter(p => !existingLines.has(p)));
+      }
 
-          if (shouldFix("gitignore_missing_patterns")) {
-            ensureGitignore(basePath, { manageGitignore });
-            fixesApplied.push("added missing GSD runtime patterns to .gitignore");
-          }
+      if (missing.length > 0) {
+        issues.push({
+          severity: "warning",
+          code: "gitignore_missing_patterns",
+          scope: "project",
+          unitId: "project",
+          message: `${missing.length} critical GSD runtime pattern(s) missing from .gitignore: ${missing.join(", ")}`,
+          file: ".gitignore",
+          fixable: true,
+        });
+
+        if (shouldFix("gitignore_missing_patterns")) {
+          ensureGitignore(basePath, { manageGitignore });
+          fixesApplied.push("added missing GSD runtime patterns to .gitignore");
         }
       }
     }

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

@@ -3,11 +3,13 @@ import { join } from "node:path";
 
 import { loadFile, parseSummary, saveFile, parseTaskPlanMustHaves, countMustHavesMentionedInSummary } from "./files.js";
 import { parseRoadmap as parseLegacyRoadmap, parsePlan as parseLegacyPlan } from "./parsers-legacy.js";
-import { isDbAvailable, openDatabase, getMilestoneSlices, getSliceTasks } from "./gsd-db.js";
+import { isDbAvailable, getMilestoneSlices, getSliceTasks } from "./gsd-db.js";
+import { openExistingWorkflowDatabase } from "./db-workspace.js";
 import { resolveMilestoneFile, resolveMilestonePath, resolveSliceFile, resolveSlicePath, resolveTaskFile, resolveTasksDir, milestonesDir, gsdRoot, relMilestoneFile, relSliceFile, relTaskFile, relSlicePath, relGsdRootFile, resolveGsdRootFile, relMilestonePath, resolveGsdPathContract } from "./paths.js";
 import { deriveState, isMilestoneComplete } from "./state.js";
 import { invalidateAllCaches } from "./cache.js";
 import { loadEffectiveGSDPreferences, type GSDPreferences } from "./preferences.js";
+import { collectPreferenceDiagnostics, formatPreferenceDiagnosticDetail } from "./preferences-diagnostics.js";
 import { isClosedStatus } from "./status-guards.js";
 
 import type { DoctorIssue, DoctorIssueCode, DoctorReport } from "./doctor-types.js";
@@ -314,10 +316,7 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
   // CLI doctor can run before any tool handler has opened the DB. Runtime
   // health checks need the existing project DB to surface DB-backed crash
   // locks, paused sessions, and coordination rows.
-  const dbPath = resolveGsdPathContract(basePath).projectDb;
-  if (existsSync(dbPath)) {
-    try { openDatabase(dbPath); } catch { /* surfaced later as db_unavailable */ }
-  }
+  openExistingWorkflowDatabase(basePath);
 
   // Issue codes that represent completion state transitions — creating summary
   // stubs, marking slices/milestones done in the roadmap. These belong to the
@@ -333,6 +332,17 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
   };
 
   const prefs = loadEffectiveGSDPreferences(basePath);
+  for (const diagnostic of collectPreferenceDiagnostics(basePath)) {
+    issues.push({
+      severity: diagnostic.severity,
+      code: "invalid_preferences",
+      scope: "project",
+      unitId: "project",
+      message: `GSD preferences ${diagnostic.kind}: ${formatPreferenceDiagnosticDetail(diagnostic)}`,
+      file: diagnostic.path,
+      fixable: false,
+    });
+  }
   if (prefs) {
     const prefIssues = validatePreferenceShape(prefs.preferences);
     for (const issue of prefIssues) {

package/src/resources/extensions/gsd/engine-hook-contract.ts

@@ -0,0 +1,79 @@
+// Project/App: gsd-pi
+// File Purpose: Typed contract for which tool lifecycle hooks fire under which
+// engine, plus the single seam for tool-name normalization.
+//
+// ── Why this contract exists ────────────────────────────────────────────────
+// External engines (claude-code-cli) pre-execute tools inside the vendor CLI
+// and hand the agent loop a `toolCall.externalResult`. The loop short-circuits
+// before `beforeToolCall`/`afterToolCall` ever run for those calls
+// (packages/pi-agent-core/src/agent-loop.ts, prepareToolCall: the
+// externalResult branch returns an "immediate" outcome before the
+// config.beforeToolCall invocation, and "immediate" outcomes skip
+// finalizeExecutedToolCall where config.afterToolCall lives).
+// `beforeToolCall`/`afterToolCall` are exactly what the extension runner maps
+// to the `tool_call`/`tool_result` extension events
+// (packages/gsd-agent-core/src/session/agent-session-extensions.ts,
+// installAgentToolHooks).
+//
+// `tool_execution_start` is emitted unconditionally before prepareToolCall
+// and `tool_execution_end` after every finalized outcome — immediate or
+// executed — so those two are the ONLY tool lifecycle hooks that fire for
+// every tool call on every engine.
+//
+// Consequence: any enforcement attached only to `tool_call` (blocking) or
+// `tool_result` (rewriting) is silently dead under external engines. Safety
+// enforcement must ride `tool_execution_start`/`tool_execution_end`, or
+// mirror across both with toolCallId dedup. See the per-registration contract
+// comments in bootstrap/register-hooks.ts for how each registered hook
+// honors (or knowingly violates) this contract.
+
+import { stripMcpToolPrefix } from "./mcp-tool-name.js";
+import { canonicalWorkflowSurfaceToolName } from "./workflow-tool-surface.js";
+
+/**
+ * Tool lifecycle hooks that fire for EVERY tool call on EVERY engine,
+ * including external engines (claude-code-cli) that pre-execute tools.
+ * Attach safety-critical enforcement and evidence collection here.
+ */
+export const UNIVERSAL_TOOL_HOOKS = ["tool_execution_start", "tool_execution_end"] as const;
+
+/**
+ * Tool lifecycle hooks that fire ONLY for natively executed tools. External
+ * engines pre-execute tools (externalResult), short-circuiting the agent
+ * loop's beforeToolCall/afterToolCall — so handlers on these events never run
+ * for those calls. Blocking guards attached only here are dead under external
+ * engines; they need a tool_execution_start mirror to be universal.
+ */
+export const NATIVE_ONLY_TOOL_HOOKS = ["tool_call", "tool_result"] as const;
+
+export type UniversalToolHook = (typeof UNIVERSAL_TOOL_HOOKS)[number];
+export type NativeOnlyToolHook = (typeof NATIVE_ONLY_TOOL_HOOKS)[number];
+
+// Non-tool lifecycle events (session_start, agent_end, message_update, ...)
+// are intentionally NOT classified here: they are emitted by the session
+// host / extension runner independent of tool execution, so the external
+// engine short-circuit above does not apply to them. Only classify events
+// whose engine behavior has been verified against the agent loop.
+
+/**
+ * Canonical tool name: strips the `mcp__<server>__` prefix when present,
+ * nothing else. Use for identity checks against host/native tool names and
+ * for any guard that must NOT conflate workflow aliases with their canonical
+ * tools (e.g. write gates, evidence keys).
+ *
+ * Malformed MCP names (empty server or empty tool segment, e.g.
+ * `mcp____tool` or `mcp__server__`) are returned unchanged.
+ */
+export function canonicalToolName(toolName: string): string {
+  return stripMcpToolPrefix(toolName);
+}
+
+/**
+ * Workflow-aware canonical tool name: strips the MCP prefix AND resolves
+ * workflow tool aliases to their canonical contract names. Use whenever the
+ * name is compared against the workflow tool surface (scoping, presentation,
+ * dispatch) — plain {@link canonicalToolName} would miss alias spellings.
+ */
+export function canonicalWorkflowToolName(toolName: string): string {
+  return canonicalWorkflowSurfaceToolName(toolName);
+}

package/src/resources/extensions/gsd/error-classifier.ts

@@ -10,6 +10,8 @@
  * @see https://github.com/open-gsd/gsd-pi/issues/2577
  */
 
+import { TOOL_SURFACE_NOT_READY } from "./tool-surface-readiness.js";
+
 // ── ErrorClass discriminated union ──────────────────────────────────────────
 
 export type ErrorClass =
@@ -58,7 +60,7 @@ const AFFORDABILITY_RE = /requires more credits|can only afford|insufficient cre
 // are emitted by SDK/harness transports for mid-stream disconnects.
 // These indicate transient network-level interruptions.
 // See: https://github.com/open-gsd/gsd-pi/issues/4558
-const NETWORK_RE = /network|ECONNRESET|ETIMEDOUT|ECONNREFUSED|socket hang up|web ?socket|fetch failed|connection.*reset|dns|unexpected eof|stream idle timeout|partial response received/i;
+const NETWORK_RE = /network|ECONNRESET|ETIMEDOUT|ECONNREFUSED|socket hang up|web ?socket|fetch failed|connection.*reset|dns|unexpected eof|stream idle timeout|partial response received|stream ended without finish_reason/i;
 // Context overflow errors (context window/length exceeded) should be treated as server-class
 // transient errors so auto-mode can retry with reduced budget or fall back to a larger-context model.
 // See: https://github.com/open-gsd/gsd-pi/issues/4528
@@ -70,6 +72,10 @@ const CONNECTION_RE = /terminated|connection.?(?:refused|error)|other side close
 const STREAM_RE = /in JSON at position \d+|Unexpected end of JSON|SyntaxError.*JSON/i;
 const RESET_DELAY_RE = /reset in (\d+)s/i;
 const TOOL_SCHEMA_RE = /schema overload|consecutive tool validation failures/i;
+// GSD tool-surface readiness abort (claude-code stream adapter): the workflow
+// MCP server had not registered the Unit's required tools at SDK init. The
+// server typically finishes connecting within seconds — same-model retry.
+const TOOL_SURFACE_NOT_READY_RE = new RegExp(TOOL_SURFACE_NOT_READY, "i");
 // Provider rejected the request shape for the selected model (400 bad request,
 // grammar limits, etc.). Not transient — try a different model/fallback.
 // Context-window 400s stay in SERVER_RE (checked earlier).
@@ -108,6 +114,11 @@ export function classifyError(errorMsg: string, retryAfterMs?: number): ErrorCla
     return { kind: "tool-schema", retryAfterMs: 0 };
   }
 
+  // Tool-surface readiness abort — transient; retry the same model shortly.
+  if (TOOL_SURFACE_NOT_READY_RE.test(errorMsg)) {
+    return { kind: "network", retryAfterMs: retryAfterMs ?? 3_000 };
+  }
+
   const isPermanent = PERMANENT_RE.test(errorMsg);
   const isRateLimit = RATE_LIMIT_RE.test(errorMsg) || AFFORDABILITY_RE.test(errorMsg);
   const isUnsupportedModel =

package/src/resources/extensions/gsd/exec-sandbox.ts

@@ -12,6 +12,7 @@ import { spawn } from "node:child_process";
 import { existsSync, mkdirSync, writeFileSync } from "node:fs";
 import { randomUUID } from "node:crypto";
 import { resolve } from "node:path";
+import { killProcessTree, SIGKILL_GRACE_MS, HARD_DEADLINE_MS } from "@gsd/pi-coding-agent";
 
 export interface ExecSandboxRequest {
   /** Interpreter to use. */
@@ -47,6 +48,17 @@ export interface ExecSandboxOptions {
   now?: () => Date;
   /** Optional override for id generation (tests). */
   generateId?: () => string;
+  /**
+   * Grace period (ms) between SIGTERM and SIGKILL on timeout.
+   * Defaults to SIGKILL_GRACE_MS. Exposed as a test seam.
+   */
+  kill_grace_ms?: number;
+  /**
+   * Delay (ms) after a kill is initiated before the hard-deadline force-resolves
+   * the promise (handles D-state / non-closing children).
+   * Defaults to SIGKILL_GRACE_MS + HARD_DEADLINE_MS. Exposed as a test seam.
+   */
+  force_resolve_delay_ms?: number;
 }
 
 export interface ExecSandboxResult {
@@ -55,6 +67,12 @@ export interface ExecSandboxResult {
   exit_code: number | null;
   signal: NodeJS.Signals | null;
   timed_out: boolean;
+  /**
+   * True when the result came from the hard-deadline force-resolve (a non-closing
+   * D-state child that never emitted 'close') rather than an observed process exit.
+   * In that case `signal` is the synthetic "SIGKILL" marker, not a delivered signal.
+   */
+  force_resolved: boolean;
   duration_ms: number;
   stdout_bytes: number;
   stderr_bytes: number;
@@ -68,6 +86,10 @@ export interface ExecSandboxResult {
 
 const ALWAYS_FORWARD_ENV = ["PATH", "HOME"] as const;
 
+// SIGKILL_GRACE_MS / HARD_DEADLINE_MS are imported from @gsd/pi-coding-agent
+// (shell.ts) — the single source of truth for the graceful-kill timing ladder —
+// so this sandbox can never drift from the canonical kill path it delegates to.
+
 export const EXEC_DEFAULTS = {
   clampTimeoutMs: 600_000,
   defaultTimeoutMs: 30_000,
@@ -180,6 +202,7 @@ export function runExecSandbox(
         exit_code: null,
         signal: null,
         timed_out: false,
+        force_resolved: false,
         duration_ms: duration,
         stdout_bytes: 0,
         stderr_bytes: Buffer.byteLength(`spawn error: ${message}\n`),
@@ -233,23 +256,39 @@ export function runExecSandbox(
       }
     });
 
+    const effectiveGraceMs = opts.kill_grace_ms ?? SIGKILL_GRACE_MS;
+    const effectiveForceResolveDelay = opts.force_resolve_delay_ms ?? (effectiveGraceMs + HARD_DEADLINE_MS);
+
     let timedOut = false;
+    let settled = false;
+    let forceResolveTimer: NodeJS.Timeout | undefined;
+
     const timer = setTimeout(() => {
       timedOut = true;
-      if (useProcessGroup && child.pid != null) {
-        try {
-          process.kill(-child.pid, "SIGKILL");
-        } catch {
-          child.kill("SIGKILL");
-        }
+      // killProcessTree handles both platforms and kills the whole tree: on Unix
+      // it signals the process group (SIGTERM -> grace -> SIGKILL); on Windows it
+      // force-kills the tree via taskkill /F /T. Using child.kill("SIGTERM") here
+      // would only terminate the direct child on Windows, orphaning grandchildren.
+      if (child.pid != null) {
+        killProcessTree(child.pid, { graceMs: effectiveGraceMs });
       } else {
-        child.kill("SIGKILL");
+        child.kill("SIGTERM");
       }
+      // Arm hard-deadline force-resolve in case child never closes (D-state).
+      // The "SIGKILL" here is a synthetic marker (the process may not have actually
+      // received it); force_resolved=true records that this was a deadline, not an exit.
+      forceResolveTimer = setTimeout(() => {
+        finalize(null, "SIGKILL", true);
+      }, effectiveForceResolveDelay);
+      forceResolveTimer.unref?.();
     }, timeoutMs);
     timer.unref?.();
 
-    const finalize = (exitCode: number | null, signal: NodeJS.Signals | null) => {
+    const finalize = (exitCode: number | null, signal: NodeJS.Signals | null, forceResolved = false) => {
+      if (settled) return;
+      settled = true;
       clearTimeout(timer);
+      clearTimeout(forceResolveTimer);
       const duration = Date.now() - started;
       const stdoutBuf = Buffer.concat(stdoutChunks);
       const stderrBuf = Buffer.concat(stderrChunks);
@@ -274,6 +313,7 @@ export function runExecSandbox(
         exit_code: exitCode,
         signal,
         timed_out: timedOut,
+        force_resolved: forceResolved,
         duration_ms: duration,
         stdout_bytes: stdoutBytes,
         stderr_bytes: stderrBytes,
@@ -324,6 +364,7 @@ function writeMeta(
     exit_code: result.exit_code,
     signal: result.signal,
     timed_out: result.timed_out,
+    force_resolved: result.force_resolved,
     duration_ms: result.duration_ms,
     stdout_bytes: result.stdout_bytes,
     stderr_bytes: result.stderr_bytes,
@@ -331,7 +372,6 @@ function writeMeta(
     stderr_truncated: result.stderr_truncated,
     stdout_path: result.stdout_path,
     stderr_path: result.stderr_path,
-    ...(request.metadata ? { metadata: request.metadata } : {}),
   };
   writeFileSync(path, `${JSON.stringify(meta, null, 2)}\n`);
 }

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

@@ -671,33 +671,54 @@ export function parseTaskPlanIO(content: string): { inputFiles: string[]; output
  */
 export type UatType = 'artifact-driven' | 'live-runtime' | 'human-experience' | 'mixed' | 'browser-executable' | 'runtime-executable';
 
+/** Canonical list of recognised UAT types — uat-policy.ts re-exports this as UAT_TYPES. */
+export const UAT_TYPE_KEYWORDS: readonly UatType[] = [
+  'artifact-driven',
+  'browser-executable',
+  'runtime-executable',
+  'live-runtime',
+  'mixed',
+  'human-experience',
+];
+
+/** Match a value against the recognised UAT type keywords (leading-keyword-only). */
+function matchUatTypeKeyword(value: string): UatType | undefined {
+  const normalized = value.trim().toLowerCase();
+  return UAT_TYPE_KEYWORDS.find(keyword => normalized.startsWith(keyword));
+}
+
 /**
  * Extract the UAT type from a UAT file's raw content.
  *
  * UAT files have no YAML frontmatter - pass raw file content directly.
  * Classification is leading-keyword-only: e.g. `mixed (artifact-driven + live-runtime)` → `'mixed'`.
  *
+ * The canonical form is a `- UAT mode: <type>` bullet under `## UAT Type`
+ * (case-insensitive prefix, `**bold**` tolerated). When no such line exists,
+ * a line that itself starts with a recognised keyword — e.g. a bare
+ * `browser-executable` under the heading — is accepted, so agent-authored
+ * format drift does not silently fall back to artifact-driven.
+ *
  * Returns `undefined` when:
  * - the `## UAT Type` section is absent
- * - no `UAT mode:` bullet is found in the section
- * - the value does not start with a recognised keyword
+ * - a `UAT mode:` line exists but its value starts with no recognised keyword
+ * - no line in the section starts with `UAT mode:` or a recognised keyword
  */
 export function extractUatType(content: string): UatType | undefined {
   const sectionText = extractSection(content, 'UAT Type');
   if (!sectionText) return undefined;
 
-  const bullets = parseBullets(sectionText);
-  const modeBullet = bullets.find(b => b.startsWith('UAT mode:'));
-  if (!modeBullet) return undefined;
+  const lines = parseBullets(sectionText).map(line => line.replace(/\*\*/g, ''));
 
-  const rawValue = modeBullet.slice('UAT mode:'.length).trim().toLowerCase();
+  for (const line of lines) {
+    const declared = /^uat mode:\s*(.*)$/i.exec(line);
+    if (declared) return matchUatTypeKeyword(declared[1]);
+  }
 
-  if (rawValue.startsWith('artifact-driven')) return 'artifact-driven';
-  if (rawValue.startsWith('browser-executable')) return 'browser-executable';
-  if (rawValue.startsWith('runtime-executable')) return 'runtime-executable';
-  if (rawValue.startsWith('live-runtime')) return 'live-runtime';
-  if (rawValue.startsWith('human-experience')) return 'human-experience';
-  if (rawValue.startsWith('mixed')) return 'mixed';
+  for (const line of lines) {
+    const matched = matchUatTypeKeyword(line);
+    if (matched) return matched;
+  }
 
   return undefined;
 }

package/src/resources/extensions/gsd/git-conflict-state.ts

@@ -64,7 +64,23 @@ export function gitDiffCheckFailures(basePath: string): string[] | null {
       .filter(Boolean)
       .join("\n")
       .trim();
-    failures.push(output || `git diff --check ${args.join(" ")} failed`);
+
+    // git diff --check exits non-zero for both whitespace errors and leftover
+    // conflict markers. Only conflict markers block the gate — whitespace errors
+    // in staged files (common in auto-generated code) must not be misread as an
+    // unresolved merge conflict. Filter to lines git explicitly labels as
+    // "leftover conflict marker".
+    if (!output) {
+      failures.push(`git diff --check ${args.join(" ")} failed`);
+      continue;
+    }
+    const conflictMarkerLines = output
+      .split("\n")
+      .filter((line) => /leftover conflict marker/i.test(line))
+      .join("\n");
+    if (conflictMarkerLines) {
+      failures.push(conflictMarkerLines);
+    }
   }
 
   return failures;

package/src/resources/extensions/gsd/git-service.ts

@@ -359,6 +359,7 @@ export interface PreMergeCheckResult {
  * This array must stay synchronized with it.
  */
 export const RUNTIME_EXCLUSION_PATHS: readonly string[] = [
+  ".gsd-worktrees/",
   ".gsd/activity/",
   ".gsd/audit/",
   ".gsd/forensics/",

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

@@ -25,6 +25,7 @@ import { GIT_NO_PROMPT_ENV } from "./git-constants.js";
  * but retained for backwards compatibility during migration.
  */
 const GSD_RUNTIME_PATTERNS = [
+  ".gsd-worktrees/",
   ".gsd/activity/",
   ".gsd/audit/",
   ".gsd/forensics/",
@@ -48,6 +49,8 @@ const GSD_RUNTIME_PATTERNS = [
 const BASELINE_PATTERNS = [
   // ── GSD state directory (symlink to external storage) ──
   ".gsd",
+  // Worktree container sibling — NOT covered by the ".gsd" pattern above.
+  ".gsd-worktrees/",
   ".gsd-id",
   ".mcp.json",
   ".bg-shell/",

package/src/resources/extensions/gsd/gsd-command-home.ts

@@ -66,7 +66,7 @@ function disabled(description: string, reason: string): string {
 
 export function buildGsdHomeModel(
   state: GSDState,
-  closeout?: Pick<CloseoutContext, "strandedQuick" | "unmergedMilestones">,
+  closeout?: Pick<CloseoutContext, "strandedQuick" | "unmergedMilestones" | "idleResidueHint">,
 ): GsdHomeModel {
   const blocked = isBlocked(state);
   const complete = state.phase === "complete";
@@ -74,10 +74,14 @@ export function buildGsdHomeModel(
   const workLabel = activeWorkLabel(state);
   const strandedQuick = closeout?.strandedQuick ?? null;
   const unmergedMilestone = closeout?.unmergedMilestones?.[0];
+  const idleResidueHint = closeout?.idleResidueHint ?? null;
+  const hasIdleResidue = Boolean(idleResidueHint);
   const nextReason = complete
     ? "all milestones are complete"
     : blocked
       ? "the active milestone is blocked"
+      : hasIdleResidue
+        ? "milestone git residue needs recovery"
       : !hasActiveWork
         ? "there is no active milestone"
         : "";
@@ -91,6 +95,8 @@ export function buildGsdHomeModel(
       ? "finish_milestone"
       : blocked
         ? "fix_recover"
+        : hasIdleResidue
+          ? "fix_recover"
         : canAdvance
           ? "continue_step"
           : complete && unmappedActive > 0
@@ -107,6 +113,8 @@ export function buildGsdHomeModel(
     ? [`Quick task Q${strandedQuick.taskNum} finished on ${strandedQuick.quickBranch} but is not merged to ${strandedQuick.originalBranch}.`]
     : unmergedMilestone
       ? [`${unmergedMilestone.milestoneId} is complete but not merged into ${unmergedMilestone.integrationBranch}.`]
+      : idleResidueHint
+        ? [idleResidueHint.message]
       : completionSummary;
 
   return {
@@ -181,10 +189,12 @@ export function buildGsdHomeModel(
         label: "Fix or recover",
         description: blocked
           ? "Review the blocker and recovery commands for the active milestone."
+          : hasIdleResidue
+            ? "Review stranded milestone worktrees/branches and run the suggested recovery command."
           : disabled("This becomes active when closeout, validation, or state recovery is needed.", "no blocker is active"),
-        enabled: blocked,
+        enabled: blocked || hasIdleResidue,
         recommended: recommended === "fix_recover",
-        disabledReason: blocked ? undefined : "no blocker is active",
+        disabledReason: blocked || hasIdleResidue ? undefined : "no blocker is active",
       },
       {
         id: "start_configure",