Fix worktree pruning: lock worktrees + disable agent auto-gc

Root cause: concurrent agents' git commits trigger gc --auto, which
calls git worktree prune, deleting metadata for other agents' worktrees.

Fix (belt and suspenders):
1. Lock worktrees immediately after creation — locked worktrees survive
   gc prune. Unlock before removal.
2. Disable auto-gc in agent environment via GIT_CONFIG env vars — prevents
   agent git commands from triggering gc entirely.
3. Verify worktree metadata directory (not just .git file) in getDiff.

Removes old .git file backup approach (addressed symptom not cause).

Closes #136

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

Author: unknown

src/runners/claude-code.ts

@@ -1,6 +1,4 @@
 import { spawn } from "node:child_process";
-import { readFile, writeFile } from "node:fs/promises";
-import { join } from "node:path";
 import type { AgentResult } from "../types.js";
 import { getDiff, getDiffStats } from "../utils/git.js";
 import type { Runner, RunnerOptions } from "./base.js";
@@ -22,15 +20,6 @@ export const claudeCodeRunner: Runner = {
   async run(id: number, opts: RunnerOptions): Promise<AgentResult> {
     const start = Date.now();
 
-    // Backup the .git pointer file — agents sometimes delete it during long runs
-    const gitFilePath = join(opts.worktreePath, ".git");
-    let gitFileBackup: string | null = null;
-    try {
-      gitFileBackup = await readFile(gitFilePath, "utf-8");
-    } catch {
-      // Not a worktree or .git is a directory — skip backup
-    }
-
     return new Promise((resolve) => {
       let output = "";
       let error = "";
@@ -57,7 +46,15 @@ export const claudeCodeRunner: Runner = {
       const child = spawn("claude", args, {
         cwd: opts.worktreePath,
         stdio: ["ignore", "pipe", "pipe"],
-        env: { ...process.env },
+        env: {
+          ...process.env,
+          // Disable git auto-gc to prevent worktree pruning during parallel agent runs.
+          // When gc --auto triggers, it calls "git worktree prune" which can delete
+          // metadata for other concurrent agents' worktrees.
+          GIT_CONFIG_COUNT: "1",
+          GIT_CONFIG_KEY_0: "gc.auto",
+          GIT_CONFIG_VALUE_0: "0",
+        },
       });
 
       child.stdout.on("data", (data: Buffer) => {
@@ -97,15 +94,6 @@ export const claudeCodeRunner: Runner = {
         if (settled) return;
         settled = true;
 
-        // Restore .git file if the agent deleted it during execution
-        if (gitFileBackup) {
-          try {
-            await readFile(gitFilePath, "utf-8");
-          } catch {
-            await writeFile(gitFilePath, gitFileBackup).catch(() => {});
-          }
-        }
-
         const duration = Date.now() - start;
         const diff = await getDiff(opts.worktreePath);
         const stats = await getDiffStats(opts.worktreePath);

src/utils/git.ts

@@ -1,6 +1,6 @@
 import { execFile } from "node:child_process";
 import { randomUUID } from "node:crypto";
-import { access, mkdtemp, rm } from "node:fs/promises";
+import { access, mkdtemp, readFile, rm } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { promisify } from "node:util";
@@ -31,6 +31,13 @@ export async function createWorktree(id: number): Promise<string> {
     cwd: repoRoot,
   });
 
+  // Lock the worktree to prevent git gc --auto from pruning it while agents run.
+  // Without this, concurrent agents' git commits can trigger gc which prunes
+  // other worktrees' metadata from .git/worktrees/.
+  await exec("git", ["worktree", "lock", "--reason", "thinktank agent in use", dir], {
+    cwd: repoRoot,
+  });
+
   // Symlink node_modules from the main repo so tests and tools work in worktrees.
   // Git worktrees don't include gitignored directories like node_modules.
   const mainNodeModules = join(repoRoot, "node_modules");
@@ -49,6 +56,9 @@ export async function createWorktree(id: number): Promise<string> {
 export async function removeWorktree(worktreePath: string): Promise<void> {
   const repoRoot = await getMainRepoRoot();
 
+  // Unlock the worktree before removal (it was locked during creation)
+  await exec("git", ["worktree", "unlock", worktreePath], { cwd: repoRoot }).catch(() => {});
+
   // Remove node_modules symlink/junction BEFORE removing worktree.
   // On Windows, rm -rf follows junctions and deletes the target.
   try {
@@ -77,9 +87,14 @@ export async function removeWorktree(worktreePath: string): Promise<void> {
 export async function getDiff(worktreePath: string): Promise<string> {
   const absPath = resolve(worktreePath);
   try {
-    // Verify worktree is still a git repo before running git commands
+    // Verify worktree .git file AND its metadata directory still exist.
+    // git gc --auto can prune .git/worktrees/NAME/ even if the .git pointer file remains.
     await access(join(absPath, ".git"));
-    await exec("git", ["rev-parse", "--git-dir"], { cwd: absPath });
+    const gitContent = await readFile(join(absPath, ".git"), "utf-8");
+    const gitdirMatch = gitContent.match(/gitdir:\s*(.+)/);
+    if (gitdirMatch?.[1]) {
+      await access(gitdirMatch[1].trim());
+    }
 
     await exec("git", ["add", "-A"], { cwd: absPath });
     await exec("git", ["reset", "HEAD", "--", "node_modules"], { cwd: absPath }).catch(() => {});
@@ -99,6 +114,11 @@ export async function getDiffStats(
   const absPath = resolve(worktreePath);
   try {
     await access(join(absPath, ".git"));
+    const gitContent = await readFile(join(absPath, ".git"), "utf-8");
+    const gitdirMatch = gitContent.match(/gitdir:\s*(.+)/);
+    if (gitdirMatch?.[1]) {
+      await access(gitdirMatch[1].trim());
+    }
     await exec("git", ["add", "-A"], { cwd: absPath });
     await exec("git", ["reset", "HEAD", "--", "node_modules"], { cwd: absPath }).catch(() => {});
     const { stdout } = await exec("git", ["diff", "--cached", "--stat", "HEAD"], {