fix: use pathspec exclusions in smartStage to prevent hanging on large repos (#1613)

smartStage() ran `git add -A` on the entire repo then unstaged exclusions,
causing indefinite hangs on repos with large untracked artifact trees (57GB+).
autoCommitDirtyState() bypassed smartStage() entirely via direct nativeAddAll().

Add nativeAddAllWithExclusions() using `git add -A -- ':!pattern'` syntax so
excluded paths are never hashed. Route autoCommitDirtyState() through it with
RUNTIME_EXCLUSION_PATHS.

Closes #1605

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/resources/extensions/gsd/auto-worktree.ts

@@ -37,13 +37,13 @@ import {
   resolveGitHeadPath,
   nudgeGitBranchCache,
 } from "./worktree.js";
-import { MergeConflictError, readIntegrationBranch } from "./git-service.js";
+import { MergeConflictError, readIntegrationBranch, RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
 import { parseRoadmap } from "./files.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import {
   nativeGetCurrentBranch,
   nativeWorkingTreeStatus,
-  nativeAddAll,
+  nativeAddAllWithExclusions,
   nativeCommit,
   nativeCheckoutBranch,
   nativeMergeSquash,
@@ -768,7 +768,7 @@ function autoCommitDirtyState(cwd: string): boolean {
   try {
     const status = nativeWorkingTreeStatus(cwd);
     if (!status) return false;
-    nativeAddAll(cwd);
+    nativeAddAllWithExclusions(cwd, RUNTIME_EXCLUSION_PATHS);
     const result = nativeCommit(
       cwd,
       "chore: auto-commit before milestone merge",

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

@@ -24,7 +24,7 @@ import {
   nativeDetectMainBranch,
   nativeBranchExists,
   nativeHasChanges,
-  nativeAddAll,
+  nativeAddAllWithExclusions,
   nativeResetPaths,
   nativeHasStagedChanges,
   nativeCommit,
@@ -385,7 +385,9 @@ export class GitServiceImpl {
       this._runtimeFilesCleanedUp = true;
     }
 
-    // Stage everything, then unstage excluded paths.
+    // Stage everything using pathspec exclusions so excluded paths are never
+    // hashed by git. The old approach of `git add -A` followed by unstaging
+    // hangs indefinitely on repos with large untracked artifact trees (#1605).
     //
     // Exclude only RUNTIME paths from staging — not the entire .gsd/ directory.
     // When .gsd/milestones/ files are already tracked in the index (projects
@@ -395,13 +397,9 @@ export class GitServiceImpl {
     // the second half of a milestone's artifacts are never committed (#1326).
     //
     // If .gsd/ IS in .gitignore (the default for external state projects),
-    // git add -A already skips it and the reset is a harmless no-op.
-    nativeAddAll(this.basePath);
-
-    const runtimeExclusions = [...RUNTIME_EXCLUSION_PATHS, ...extraExclusions];
-    for (const exclusion of runtimeExclusions) {
-      try { nativeResetPaths(this.basePath, [exclusion]); } catch { /* path not staged — ignore */ }
-    }
+    // git add -A already skips it and the exclusions are harmless no-ops.
+    const allExclusions = [...RUNTIME_EXCLUSION_PATHS, ...extraExclusions];
+    nativeAddAllWithExclusions(this.basePath, allExclusions);
   }
 
   /** Tracks whether runtime file cleanup has run this session. */

src/resources/extensions/gsd/native-git-bridge.ts

@@ -671,6 +671,43 @@ export function nativeAddAll(basePath: string): void {
   gitFileExec(basePath, ["add", "-A"]);
 }
 
+/**
+ * Stage all files with pathspec exclusions (git add -A -- ':!pattern' ...).
+ * Excluded paths are never hashed by git, preventing hangs on large
+ * untracked artifact trees (57GB+, 11K+ files). See #1605.
+ *
+ * Falls back to plain `git add -A` when no exclusions are provided.
+ * Always uses the CLI path (not libgit2) because libgit2's add_all
+ * does not support pathspec exclusion syntax.
+ *
+ * When excluded paths are already covered by .gitignore, git may exit
+ * with code 1 and an "ignored by .gitignore" warning. This is harmless
+ * (the staging succeeds for all non-ignored files) and is suppressed.
+ */
+export function nativeAddAllWithExclusions(basePath: string, exclusions: readonly string[]): void {
+  if (exclusions.length === 0) {
+    nativeAddAll(basePath);
+    return;
+  }
+  const pathspecs = exclusions.map(e => `:!${e}`);
+  try {
+    execFileSync("git", ["add", "-A", "--", ...pathspecs], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+      env: GIT_NO_PROMPT_ENV,
+    });
+  } catch (err: unknown) {
+    // git exits 1 when pathspec exclusions reference paths already covered
+    // by .gitignore. The staging itself succeeds — only suppress that case.
+    const stderr = (err as { stderr?: string })?.stderr ?? "";
+    if (stderr.includes("ignored by one of your .gitignore files")) {
+      return;
+    }
+    throw new GSDError(GSD_GIT_ERROR, `git add -A with exclusions failed in ${basePath}: ${getErrorMessage(err)}`);
+  }
+}
+
 /**
  * Stage specific files.
  * Native: libgit2 index add.