diff --git a/src/resources/extensions/gsd/doctor.ts b/src/resources/extensions/gsd/doctor.ts
index 5a16fec93..a70a5af9c 100644
--- a/src/resources/extensions/gsd/doctor.ts
+++ b/src/resources/extensions/gsd/doctor.ts
@@ -5,7 +5,7 @@ import { loadFile, parsePlan, parseRoadmap, parseSummary, saveFile, parseTaskPla
 import { resolveMilestoneFile, resolveMilestonePath, resolveSliceFile, resolveSlicePath, resolveTaskFile, resolveTaskFiles, resolveTasksDir, milestonesDir, gsdRoot, relMilestoneFile, relSliceFile, relTaskFile, relSlicePath, relGsdRootFile, resolveGsdRootFile } from "./paths.js";
 import { deriveState, isMilestoneComplete } from "./state.js";
 import { loadEffectiveGSDPreferences, type GSDPreferences } from "./preferences.js";
-import { listWorktrees } from "./worktree-manager.js";
+import { listWorktrees, resolveGitDir } from "./worktree-manager.js";
 import { abortAndReset } from "./git-self-heal.js";
 import { RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
 import { nativeIsRepo, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached } from "./native-git-bridge.js";
@@ -480,7 +480,7 @@ async function checkGitHealth(
     return; // Not a git repo — skip all git health checks
   }
 
-  const gitDir = join(basePath, ".git");
+  const gitDir = resolveGitDir(basePath);
 
   // ── Orphaned auto-worktrees ──────────────────────────────────────────
   try {
diff --git a/src/resources/extensions/gsd/tests/worktree-bugfix.test.ts b/src/resources/extensions/gsd/tests/worktree-bugfix.test.ts
new file mode 100644
index 000000000..72899a1ce
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/worktree-bugfix.test.ts
@@ -0,0 +1,113 @@
+/**
+ * Tests for worktree edge-case bugfixes:
+ *
+ *   1. resolveGitDir() follows gitdir: pointer in worktrees
+ *   2. captureIntegrationBranch() is a no-op in worktrees
+ *   3. detectWorktreeName() correctly identifies worktree paths
+ */
+
+import {
+  mkdtempSync, mkdirSync, writeFileSync, rmSync,
+  existsSync, readFileSync,
+} from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+import { execSync } from "node:child_process";
+import { describe, it, after } from "node:test";
+
+import { resolveGitDir } from "../worktree-manager.ts";
+import { detectWorktreeName, captureIntegrationBranch } from "../worktree.ts";
+import { createTestContext } from "./test-helpers.ts";
+
+const { assertEq, assertTrue, report } = createTestContext();
+
+// ─── Helpers ──────────────────────────────────────────────────────────────
+
+function initRepo(dir: string): void {
+  execSync("git init && git commit --allow-empty -m init", { cwd: dir, stdio: "ignore" });
+}
+
+// ─── Tests ────────────────────────────────────────────────────────────────
+
+describe("worktree-bugfix", () => {
+  const dirs: string[] = [];
+  after(() => {
+    for (const d of dirs) rmSync(d, { recursive: true, force: true });
+    report();
+  });
+
+  it("resolveGitDir returns .git directory in normal repo", () => {
+    const repo = mkdtempSync(join(tmpdir(), "gsd-wt-fix-"));
+    dirs.push(repo);
+    initRepo(repo);
+    const gitDir = resolveGitDir(repo);
+    assertTrue(gitDir.endsWith(".git"), "ends with .git");
+    assertTrue(existsSync(gitDir), ".git dir exists");
+  });
+
+  it("resolveGitDir follows gitdir: pointer in worktree", () => {
+    const repo = mkdtempSync(join(tmpdir(), "gsd-wt-fix-"));
+    dirs.push(repo);
+    initRepo(repo);
+
+    // Simulate a worktree .git file (git worktree add creates these)
+    const wtDir = mkdtempSync(join(tmpdir(), "gsd-wt-fix-wt-"));
+    dirs.push(wtDir);
+    const realGitDir = join(repo, ".git", "worktrees", "test-wt");
+    mkdirSync(realGitDir, { recursive: true });
+    writeFileSync(join(wtDir, ".git"), `gitdir: ${realGitDir}\n`);
+
+    const resolved = resolveGitDir(wtDir);
+    assertEq(resolved, realGitDir, "resolves to real git dir");
+  });
+
+  it("resolveGitDir returns default when .git doesn't exist", () => {
+    const noGit = mkdtempSync(join(tmpdir(), "gsd-wt-fix-"));
+    dirs.push(noGit);
+    const gitDir = resolveGitDir(noGit);
+    assertTrue(gitDir.endsWith(".git"), "returns default .git path");
+  });
+
+  it("detectWorktreeName returns name for worktree path", () => {
+    assertEq(
+      detectWorktreeName("/project/.gsd/worktrees/M005"),
+      "M005",
+      "detects worktree name",
+    );
+  });
+
+  it("detectWorktreeName returns null for normal repo", () => {
+    assertEq(
+      detectWorktreeName("/project"),
+      null,
+      "null for non-worktree path",
+    );
+  });
+
+  it("captureIntegrationBranch is a no-op when in a worktree", () => {
+    const repo = mkdtempSync(join(tmpdir(), "gsd-wt-fix-"));
+    dirs.push(repo);
+    initRepo(repo);
+
+    // Create a fake worktree path structure
+    const wtPath = join(repo, ".gsd", "worktrees", "M005");
+    mkdirSync(wtPath, { recursive: true });
+    mkdirSync(join(wtPath, ".gsd", "milestones", "M005"), { recursive: true });
+    // Initialize git in the worktree so getService doesn't fail
+    execSync("git init && git commit --allow-empty -m init", { cwd: wtPath, stdio: "ignore" });
+
+    // captureIntegrationBranch should be a no-op — no META.json written
+    const metaPath = join(wtPath, ".gsd", "milestones", "M005", "M005-META.json");
+    captureIntegrationBranch(wtPath, "M005");
+    assertTrue(!existsSync(metaPath), "no META.json written in worktree");
+  });
+
+  it("detectWorktreeName prevents pull in worktree context", () => {
+    // Verifies the guard pattern: if detectWorktreeName returns non-null,
+    // the caller should skip pull/fetch operations
+    const inWorktree = detectWorktreeName("/project/.gsd/worktrees/M006");
+    const inNormal = detectWorktreeName("/project");
+    assertTrue(inWorktree !== null, "worktree detected → skip pull");
+    assertTrue(inNormal === null, "normal repo → allow pull");
+  });
+});
diff --git a/src/resources/extensions/gsd/worktree-manager.ts b/src/resources/extensions/gsd/worktree-manager.ts
index 0a7a36746..aa846b5ec 100644
--- a/src/resources/extensions/gsd/worktree-manager.ts
+++ b/src/resources/extensions/gsd/worktree-manager.ts
@@ -15,7 +15,7 @@
  *   4. remove()  — git worktree remove + branch cleanup
  */
 
-import { existsSync, mkdirSync, realpathSync } from "node:fs";
+import { existsSync, mkdirSync, readFileSync, realpathSync } from "node:fs";
 import { join, resolve, sep } from "node:path";
 import {
   nativeBranchDelete,
@@ -74,6 +74,34 @@ export function getMainBranch(basePath: string): string {
   return nativeDetectMainBranch(basePath);
 }
 
+// ─── resolveGitDir ─────────────────────────────────────────────────────────
+
+/**
+ * Resolve the actual git directory for a given repository path.
+ *
+ * In a normal repo, .git is a directory → returns `<basePath>/.git`.
+ * In a worktree, .git is a file containing `gitdir: <path>` → resolves
+ * and returns that path.
+ *
+ * This is critical for operations that reference git metadata files like
+ * MERGE_HEAD, SQUASH_MSG, etc. — these live in the git directory, not
+ * in the working tree root. Without this, worktree merges fail because
+ * they look for MERGE_HEAD in the wrong location.
+ */
+export function resolveGitDir(basePath: string): string {
+  const gitPath = join(basePath, ".git");
+  if (!existsSync(gitPath)) return join(basePath, ".git");
+  try {
+    const content = readFileSync(gitPath, "utf-8").trim();
+    if (content.startsWith("gitdir: ")) {
+      return resolve(basePath, content.slice(8));
+    }
+  } catch {
+    // Not a file or unreadable — fall through to default
+  }
+  return join(basePath, ".git");
+}
+
 export function worktreesDir(basePath: string): string {
   return join(basePath, ".gsd", "worktrees");
 }
diff --git a/src/resources/extensions/gsd/worktree.ts b/src/resources/extensions/gsd/worktree.ts
index 59c4e9543..a74b673f1 100644
--- a/src/resources/extensions/gsd/worktree.ts
+++ b/src/resources/extensions/gsd/worktree.ts
@@ -55,6 +55,9 @@ export function setActiveMilestoneId(basePath: string, milestoneId: string | nul
  * if on a GSD slice branch.
  */
 export function captureIntegrationBranch(basePath: string, milestoneId: string, options?: { commitDocs?: boolean }): void {
+  // In a worktree, the base branch is implicit (worktree/<name>).
+  // Writing it to META.json would leave stale metadata after merge back to main.
+  if (detectWorktreeName(basePath)) return;
   const svc = getService(basePath);
   const current = svc.getCurrentBranch();
   writeIntegrationBranch(basePath, milestoneId, current, options);