diff --git a/gitnexus/src/mcp/local/local-backend.ts b/gitnexus/src/mcp/local/local-backend.ts
index 720e73eaa..4cff47a28 100644
--- a/gitnexus/src/mcp/local/local-backend.ts
+++ b/gitnexus/src/mcp/local/local-backend.ts
@@ -248,6 +248,29 @@ function tryRealpath(p: string): string {
  */
 export function resolveWorktreeCwd(repoPath: string, launchCwd: string): string {
   try {
+    // Verify repoPath is a git root before comparing against its canonical
+    // root. If getGitRoot returns a different path, repoPath is an arbitrary
+    // subdirectory — skip both the linked-worktree guard and auto-detection
+    // and fall through to the repoPath fallback.
+    const repoGitRoot = getGitRoot(repoPath);
+    const repoCanonical =
+      repoGitRoot && tryRealpath(repoGitRoot) === tryRealpath(repoPath)
+        ? getCanonicalRepoRoot(repoPath)
+        : null;
+
+    // Early exit: if repoPath is a linked worktree (differs from its canonical
+    // main-checkout root), return it unchanged. Do NOT override it with the
+    // server's launch directory — that would silently replace the explicitly-
+    // resolved worktree index with the main checkout.
+    //
+    // getCanonicalRepoRoot returns the main-checkout path for both the checkout
+    // and all linked worktrees:
+    //   repoPath === canonical → main checkout (auto-detect may fire below)
+    //   repoPath !== canonical → linked worktree (return as-is)
+    if (repoCanonical && tryRealpath(repoPath) !== tryRealpath(repoCanonical)) {
+      return repoPath;
+    }
+
     const launchGitRoot = getGitRoot(launchCwd);
     if (launchGitRoot) {
       // Normalise via realpathSync before comparing so macOS /var → /private/var
@@ -256,8 +279,12 @@ export function resolveWorktreeCwd(repoPath: string, launchCwd: string): string
       const realRepo = tryRealpath(repoPath);
       if (realLaunch !== realRepo) {
         const launchCanonical = getCanonicalRepoRoot(launchCwd);
-        const repoCanonical = getCanonicalRepoRoot(repoPath);
-        if (launchCanonical && repoCanonical && launchCanonical === repoCanonical) {
+        // Use tryRealpath on both canonical values for cross-platform safety.
+        if (
+          launchCanonical &&
+          repoCanonical &&
+          tryRealpath(launchCanonical) === tryRealpath(repoCanonical)
+        ) {
           return launchGitRoot;
         }
       }
diff --git a/gitnexus/test/unit/detect-changes-worktree.test.ts b/gitnexus/test/unit/detect-changes-worktree.test.ts
index 02e440100..925731118 100644
--- a/gitnexus/test/unit/detect-changes-worktree.test.ts
+++ b/gitnexus/test/unit/detect-changes-worktree.test.ts
@@ -189,6 +189,81 @@ describe('resolveWorktreeCwd — auto-detection helper', () => {
       rmSync(repoB, { recursive: true, force: true });
     }
   });
+
+  it('returns worktreeDir unchanged when repoPath IS a linked worktree and launchCwd is the main checkout', () => {
+    // Regression for: detect_changes returns no changes when the MCP server
+    // runs from the main checkout but the resolved repo index is a separately-
+    // indexed linked worktree (issue #1659 / dpearson2699 report).
+    //
+    // Before the fix, resolveWorktreeCwd would detect that launchCwd (main
+    // checkout) and repoPath (worktree) share the same canonical root and
+    // wrongly override repoPath with the main-checkout path, causing git diff
+    // to run from the wrong directory and return 0 changes.
+    const repoDir = mkdtempSync(path.join(os.tmpdir(), 'gitnexus-rwc-idx-wt-'));
+    try {
+      execSync('git init -q', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git config user.email "test@example.com"', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git config user.name "Test"', { cwd: repoDir, stdio: 'ignore' });
+      writeFileSync(path.join(repoDir, 'x.ts'), 'export const x = 1;\n');
+      execSync('git add x.ts', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git commit -q -m "initial"', { cwd: repoDir, stdio: 'ignore' });
+
+      const worktreeDir = path.join(repoDir, 'wt-indexed');
+      execSync(`git worktree add -q -b indexed "${worktreeDir}"`, {
+        cwd: repoDir,
+        stdio: 'ignore',
+      });
+
+      // Simulate: repo registry entry points to the worktree (repoPath = worktreeDir)
+      // but the MCP server was launched from the main checkout (launchCwd = repoDir).
+      // resolveWorktreeCwd must NOT override the correct worktree path with repoDir.
+      const result = resolveWorktreeCwd(worktreeDir, repoDir);
+      expect(realpathSync.native(result)).toBe(realpathSync.native(worktreeDir));
+      expect(realpathSync.native(result)).not.toBe(realpathSync.native(repoDir));
+    } finally {
+      try {
+        execSync('git worktree remove -f wt-indexed', { cwd: repoDir, stdio: 'ignore' });
+      } catch {
+        // ignore
+      }
+      rmSync(repoDir, { recursive: true, force: true });
+    }
+  });
+
+  it('returns worktreeA unchanged when both repoPath and launchCwd are different linked worktrees of the same repo', () => {
+    // Covers: repoPath = wt-A (indexed), launchCwd = wt-B (server launched from another worktree).
+    // The guard fires on repoPath being a linked worktree regardless of what launchCwd is,
+    // so wt-A must be returned unchanged — not wt-B, not the main checkout.
+    const repoDir = mkdtempSync(path.join(os.tmpdir(), 'gitnexus-rwc-two-wt-'));
+    try {
+      execSync('git init -q', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git config user.email "test@example.com"', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git config user.name "Test"', { cwd: repoDir, stdio: 'ignore' });
+      writeFileSync(path.join(repoDir, 'x.ts'), 'export const x = 1;\n');
+      execSync('git add x.ts', { cwd: repoDir, stdio: 'ignore' });
+      execSync('git commit -q -m "initial"', { cwd: repoDir, stdio: 'ignore' });
+
+      const worktreeA = path.join(repoDir, 'wt-a');
+      const worktreeB = path.join(repoDir, 'wt-b');
+      execSync(`git worktree add -q -b branch-a "${worktreeA}"`, { cwd: repoDir, stdio: 'ignore' });
+      execSync(`git worktree add -q -b branch-b "${worktreeB}"`, { cwd: repoDir, stdio: 'ignore' });
+
+      // repoPath = wt-A (the indexed worktree), launchCwd = wt-B (where the server runs).
+      // resolveWorktreeCwd must return wt-A — the indexed path — unchanged.
+      const result = resolveWorktreeCwd(worktreeA, worktreeB);
+      expect(realpathSync.native(result)).toBe(realpathSync.native(worktreeA));
+      expect(realpathSync.native(result)).not.toBe(realpathSync.native(worktreeB));
+      expect(realpathSync.native(result)).not.toBe(realpathSync.native(repoDir));
+    } finally {
+      try {
+        execSync('git worktree remove -f wt-a', { cwd: repoDir, stdio: 'ignore' });
+        execSync('git worktree remove -f wt-b', { cwd: repoDir, stdio: 'ignore' });
+      } catch {
+        // ignore
+      }
+      rmSync(repoDir, { recursive: true, force: true });
+    }
+  });
 });
 
 // ── Guard logic via real path arithmetic ─────────────────────────────────────