cherry-pick(doctor): self-heal symlinked .sf staging to prevent silent data loss

Cherry-pick of gsd-build/gsd-2 9340f1e9b (#4423) — doctor self-heal
detection for symlinked staging directories that can cause silent
data loss. Skips native-git-bridge.ts and git-service test (drifted).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/resources/extensions/sf/doctor-runtime-checks.ts

@@ -8,7 +8,7 @@ import { deriveState } from "./state.js";
 import { saveFile } from "./files.js";
 import { nativeIsRepo, nativeForEachRef, nativeUpdateRef } from "./native-git-bridge.js";
 import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.js";
-import { ensureGitignore } from "./gitignore.js";
+import { ensureGitignore, isGsdGitignored } from "./gitignore.js";
 import { readAllSessionStatuses, isSessionStale, removeSessionStatus } from "./session-status-io.js";
 import { recoverFailedMigration } from "./migrate-external.js";
 
@@ -383,6 +383,27 @@ export async function checkRuntimeHealth(
             fixable: false,
           });
         }
+
+        // ── Symlinked .gsd without .gitignore entry (#4423) ──
+        // When `.gsd` is a symlink AND not gitignored, `git add -A -- :!.gsd/...`
+        // pathspecs fail with "beyond a symbolic link". Without self-heal this
+        // silently drops new user files during auto-commit.
+        if (nativeIsRepo(basePath) && !isGsdGitignored(basePath)) {
+          issues.push({
+            severity: "warning",
+            code: "symlinked_gsd_unignored",
+            scope: "project",
+            unitId: "project",
+            message: ".gsd is a symlink to external state but is not listed in .gitignore. This causes git pathspec exclusions to fail and can lead to silently dropped new files during auto-commit. Add `.gsd` to .gitignore.",
+            file: ".gitignore",
+            fixable: true,
+          });
+
+          if (shouldFix("symlinked_gsd_unignored")) {
+            const modified = ensureGitignore(basePath);
+            if (modified) fixesApplied.push("added .gsd to .gitignore (symlinked external state)");
+          }
+        }
       }
     }
   } catch {

src/resources/extensions/sf/doctor-types.ts

@@ -23,6 +23,7 @@ export type DoctorIssueCode =
   | "state_file_stale"
   | "state_file_missing"
   | "gitignore_missing_patterns"
+  | "symlinked_gsd_unignored"
   | "unresolvable_dependency"
   | "failed_migration"
   | "broken_symlink"

src/resources/extensions/sf/tests/integration/doctor-runtime.test.ts

@@ -9,7 +9,7 @@ import assert from 'node:assert/strict';
  *   state_file_stale, gitignore_missing_patterns
  */
 
-import { mkdtempSync, mkdirSync, writeFileSync, rmSync, existsSync, readFileSync, realpathSync } from "node:fs";
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync, existsSync, readFileSync, realpathSync, symlinkSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 import { execSync } from "node:child_process";
@@ -252,6 +252,37 @@ node_modules/
     } else {
     }
 
+    // ─── Test 8b: Symlinked .gsd without .gitignore entry (#4423) ─────
+    if (process.platform !== "win32") {
+    test('symlinked_gsd_unignored', async () => {
+      const dir = createGitProject();
+      cleanups.push(dir);
+
+      // Create .gsd as a symlink to an external directory (standard external
+      // state layout), and write a .gitignore that does NOT list .gsd.
+      const externalGsd = mkdtempSync(join(tmpdir(), "gsd-external-doctor-"));
+      cleanups.push(externalGsd);
+      writeFileSync(join(externalGsd, "STATE.md"), "# State\n");
+      symlinkSync(externalGsd, join(dir, ".gsd"));
+
+      writeFileSync(join(dir, ".gitignore"), "node_modules/\n");
+
+      const detect = await runGSDDoctor(dir);
+      const symlinkIssues = detect.issues.filter(i => i.code === "symlinked_gsd_unignored");
+      assert.ok(symlinkIssues.length > 0, "detects symlinked .gsd without gitignore entry");
+
+      const fixed = await runGSDDoctor(dir, { fix: true });
+      assert.ok(
+        fixed.fixesApplied.some(f => f.includes(".gitignore")),
+        "fix updates .gitignore",
+      );
+
+      const content = readFileSync(join(dir, ".gitignore"), "utf-8");
+      assert.ok(/^\.gsd\/?$/m.test(content), "gitignore now has .gsd entry");
+    });
+    } else {
+    }
+
     // ─── Test 9: Orphaned completed-units detection & fix ─────────────
     test('orphaned_completed_units', async () => {
       const dir = createMinimalProject();