fix(gsd): snapshot new untracked files before dispatch

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

@@ -10,7 +10,7 @@ import { deriveState, isMilestoneComplete } from "./state.js";
 import { listWorktrees, resolveGitDir, worktreesDir } 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";
+import { nativeIsRepo, nativeWorktreeList, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddAllWithExclusions, nativeCommit } from "./native-git-bridge.js";
 import { getAllWorktreeHealth } from "./worktree-health.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 
@@ -386,19 +386,19 @@ export async function checkGitHealth(
             code: "stale_uncommitted_changes",
             scope: "project",
             unitId: "project",
-            message: `Uncommitted changes detected with no commit in ${mins} minute${mins === 1 ? "" : "s"} (threshold: ${thresholdMinutes}m). Snapshotting tracked files.`,
+            message: `Uncommitted changes detected with no commit in ${mins} minute${mins === 1 ? "" : "s"} (threshold: ${thresholdMinutes}m). Snapshotting uncommitted changes.`,
             fixable: true,
           });
 
           if (shouldFix("stale_uncommitted_changes")) {
             try {
-              nativeAddTracked(basePath);
+              nativeAddAllWithExclusions(basePath, RUNTIME_EXCLUSION_PATHS);
               const commitMsg = `gsd snapshot: uncommitted changes after ${mins}m inactivity`;
               const result = nativeCommit(basePath, commitMsg);
               if (result) {
                 fixesApplied.push(`created gsd snapshot after ${mins}m of uncommitted changes`);
               } else {
-                fixesApplied.push("gsd snapshot skipped — nothing to commit after staging tracked files");
+                fixesApplied.push("gsd snapshot skipped — nothing to commit after staging changes");
               }
             } catch {
               fixesApplied.push("failed to create gsd snapshot commit");

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

@@ -21,8 +21,8 @@ import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.j
 import { abortAndReset } from "./git-self-heal.js";
 import { rebuildState } from "./doctor.js";
 import { deriveState } from "./state.js";
-import { resolveMilestoneIntegrationBranch } from "./git-service.js";
-import { nativeIsRepo, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddTracked, nativeCommit } from "./native-git-bridge.js";
+import { RUNTIME_EXCLUSION_PATHS, resolveMilestoneIntegrationBranch } from "./git-service.js";
+import { nativeIsRepo, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddAllWithExclusions, nativeCommit } from "./native-git-bridge.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { runEnvironmentChecks } from "./doctor-environment.js";
 
@@ -312,7 +312,7 @@ export async function preDispatchHealthGate(basePath: string): Promise<PreDispat
         if (minutesSinceCommit >= thresholdMinutes) {
           const mins = Math.floor(minutesSinceCommit);
           try {
-            nativeAddTracked(basePath);
+            nativeAddAllWithExclusions(basePath, RUNTIME_EXCLUSION_PATHS);
             const commitMsg = `gsd snapshot: pre-dispatch, uncommitted changes after ${mins}m inactivity`;
             const result = nativeCommit(basePath, commitMsg);
             if (result) {

src/resources/extensions/gsd/tests/integration/doctor-git.test.ts

@@ -661,9 +661,10 @@ describe('doctor-git', async () => {
         env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
       });
 
-      // Modify an already-tracked file (nativeAddTracked uses git add -u,
-      // which only stages tracked files — new untracked files are not staged)
+      // Modify a tracked file and create a new untracked file. The snapshot
+      // must preserve both, not just tracked changes.
       writeFileSync(join(dir, "README.md"), "# test\nmodified content\n");
+      writeFileSync(join(dir, "new-untracked.ts"), "export const preserved = true;\n");
 
       const detect = await runGSDDoctor(dir);
       const staleIssues = detect.issues.filter(i => i.code === "stale_uncommitted_changes");
@@ -681,6 +682,12 @@ describe('doctor-git', async () => {
       // Verify the snapshot commit was created with the gsd snapshot tag
       const log = run("git log -1 --oneline", dir);
       assert.ok(log.includes("gsd snapshot"), "commit is tagged with gsd snapshot");
+
+      const files = run("git show --name-only --format= HEAD", dir);
+      assert.ok(files.includes("README.md"), "snapshot keeps tracked modifications");
+      assert.ok(files.includes("new-untracked.ts"), "snapshot also includes new untracked files");
+      const status = run("git status --short", dir);
+      assert.ok(!status.includes("new-untracked.ts"), "snapshot does not leave the new source file untracked");
     });
 
     // ─── Test: stale_uncommitted_changes NOT flagged when recent commit ──

src/resources/extensions/gsd/tests/integration/doctor-proactive.test.ts

@@ -219,6 +219,39 @@ describe('doctor-proactive', async () => {
       assert.ok(result.fixesApplied.some((f: string) => f.includes("STATE.md")), "reports STATE.md status as info");
     });
 
+    test('health gate: pre-dispatch snapshot includes new untracked files', async () => {
+      const dir = createRepoWithActiveMilestone();
+      cleanups.push(dir);
+
+      const pastDate = new Date(Date.now() - 45 * 60 * 1000).toISOString();
+      run(`git commit --amend --no-edit --date="${pastDate}"`, dir);
+      execSync(`git commit --amend --no-edit`, {
+        cwd: dir,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+        env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
+      });
+
+      writeFileSync(join(dir, "README.md"), "# test\nmodified content\n");
+      writeFileSync(join(dir, "new-untracked.ts"), "export const preserved = true;\n");
+
+      const result = await preDispatchHealthGate(dir);
+      assert.ok(result.proceed, "dispatch still proceeds after snapshotting");
+      assert.ok(
+        result.fixesApplied.some((f: string) => f.includes("gsd snapshot")),
+        "pre-dispatch gate creates a snapshot commit",
+      );
+
+      const log = run("git log -1 --oneline", dir);
+      assert.ok(log.includes("gsd snapshot"), "snapshot commit is created");
+
+      const files = run("git show --name-only --format= HEAD", dir);
+      assert.ok(files.includes("README.md"), "snapshot keeps tracked modifications");
+      assert.ok(files.includes("new-untracked.ts"), "snapshot also includes new untracked files");
+      const status = run("git status --short", dir);
+      assert.ok(!status.includes("new-untracked.ts"), "snapshot does not leave the new source file untracked");
+    });
+
     test('health gate: stale crash lock auto-cleared', async () => {
       const dir = realpathSync(mkdtempSync(join(tmpdir(), "doc-proactive-")));
       cleanups.push(dir);