Fix leaked orphan worktree dirs failing execute node

Directories under .worktrees/ that survive with a dangling .git pointer
(present on disk, but their .git/worktrees/<name> admin entry is gone) are
invisible to `git worktree list`/`prune` yet collide with freshly generated
worktree names. The executor's conflict cleanup then fails with
"is not a working tree", failing the workflow graph at node 'execute' after
3 attempts.

- executor.ts: extend FN-4813 stale-conflict recovery to also treat
  "is not a working tree" and ENOENT (not just "validation failed, cannot
  remove working tree") as "no live worktree here" — prune the admin entry,
  force-remove the leftover dir, and proceed with fresh creation.
- worktree-pool.ts: reapOrphanWorktrees skipped any dir on mere .git-file
  presence, contradicting its own documented invariant. Resolve the .git
  pointer and only skip when the gitdir target exists; reap dangling
  pointers like any other orphan so they stop accumulating across runs.
- Tests for both the dangling (reaped) and valid (skipped) .git cases.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.changeset/fix-orphan-worktree-dir-cleanup.md

@@ -0,0 +1,10 @@
+---
+"@runfusion/fusion": patch
+---
+
+Fix worktree-creation failures (and the `Workflow graph terminated with failure at node 'execute'` they surface as) caused by leaked orphan worktree directories.
+
+A directory under `.worktrees/` that survives with a *dangling* `.git` pointer — present on disk, but the `.git/worktrees/<name>` admin entry it references is gone — is invisible to `git worktree list` and untouched by `git worktree prune`, yet collides with a freshly generated worktree name. When the executor then tries to clean up the "conflict", `git worktree remove --force` fails with `is not a working tree` and the whole `execute` node fails after 3 attempts.
+
+- **On-demand recovery (`executor.ts`):** the FN-4813 stale-conflict recovery now also treats `is not a working tree` and `ENOENT` (not just `validation failed, cannot remove working tree`) as "no live worktree at this path" — it prunes any admin entry, force-removes the leftover directory, and proceeds with fresh worktree creation instead of failing.
+- **Leak prevention (`worktree-pool.ts`):** `reapOrphanWorktrees` previously skipped any dir on the mere *presence* of a `.git` file ("may be partially registered"), contradicting its own documented invariant. It now resolves the `.git` pointer and only skips when the gitdir target actually exists; a dangling pointer is reaped like any other half-initialized orphan, so these directories no longer accumulate across runs.

packages/engine/src/__tests__/worktree-pool.test.ts

@@ -52,6 +52,7 @@ vi.mock("node:fs", () => ({
   existsSync: vi.fn().mockReturnValue(true),
   lstatSync: vi.fn().mockReturnValue({ isDirectory: () => true, isSymbolicLink: () => false }),
   readdirSync: vi.fn().mockReturnValue([]),
+  readFileSync: vi.fn().mockReturnValue(""),
   rmSync: vi.fn(),
 }));
 
@@ -73,13 +74,14 @@ import {
 import { BranchConflictError } from "../branch-conflicts.js";
 import * as branchConflictModule from "../branch-conflicts.js";
 import { execSync } from "node:child_process";
-import { existsSync, lstatSync, readdirSync, rmSync } from "node:fs";
+import { existsSync, lstatSync, readdirSync, readFileSync, rmSync } from "node:fs";
 import type { Task, Column } from "@fusion/core";
 
 const mockedExecSync = vi.mocked(execSync);
 const mockedExistsSync = vi.mocked(existsSync);
 const mockedLstatSync = vi.mocked(lstatSync);
 const mockedReaddirSync = vi.mocked(readdirSync);
+const mockedReadFileSync = vi.mocked(readFileSync);
 const mockedRmSync = vi.mocked(rmSync);
 const mockedPruneWorktreeAdminEntries = vi.mocked(worktreePrune.pruneWorktreeAdminEntries);
 const TEST_TASK_ID = "FN-test";
@@ -1109,5 +1111,50 @@ describe("reapOrphanWorktrees", () => {
     expect(mockedRmSync).toHaveBeenCalledWith("/root/.worktrees/half-built", { recursive: true, force: true });
     expect(mockedRmSync).not.toHaveBeenCalledWith("/root/.worktrees/.ai-merge", expect.anything());
   });
+
+  // FN-6782 follow-up: a directory whose `.git` points to a missing admin entry is leak
+  // residue (invisible to `git worktree list`/`prune`), not "partially registered". It
+  // must be reaped — otherwise it collides with freshly generated worktree names and
+  // breaks `execute`. Previously the reaper skipped on mere `.git` presence.
+  it("reaps a dir with a dangling .git pointer (admin gitdir missing)", async () => {
+    mockedReaddirSync.mockReturnValue([makeDirEntry("leaked-wt")] as any);
+    // `.git` is a link FILE (not a dir); the worktree dir itself is a dir.
+    mockedLstatSync.mockImplementation((p: any) =>
+      (String(p).endsWith("/.git")
+        ? { isDirectory: () => false, isSymbolicLink: () => false }
+        : { isDirectory: () => true, isSymbolicLink: () => false }) as any,
+    );
+    mockedReadFileSync.mockReturnValue("gitdir: /root/.git/worktrees/leaked-wt\n" as any);
+    mockedExistsSync.mockImplementation((p) => {
+      const s = String(p);
+      // .worktrees root exists; the .git link file exists; the gitdir target does NOT.
+      return s === "/root/.worktrees" || s === "/root/.worktrees/leaked-wt/.git";
+    });
+
+    const removed = await reapOrphanWorktrees("/root");
+
+    expect(removed).toBe(1);
+    expect(mockedRmSync).toHaveBeenCalledWith("/root/.worktrees/leaked-wt", { recursive: true, force: true });
+  });
+
+  it("skips a dir with a valid .git pointer (admin gitdir exists)", async () => {
+    mockedReaddirSync.mockReturnValue([makeDirEntry("live-wt")] as any);
+    mockedLstatSync.mockImplementation((p: any) =>
+      (String(p).endsWith("/.git")
+        ? { isDirectory: () => false, isSymbolicLink: () => false }
+        : { isDirectory: () => true, isSymbolicLink: () => false }) as any,
+    );
+    mockedReadFileSync.mockReturnValue("gitdir: /root/.git/worktrees/live-wt\n" as any);
+    mockedExistsSync.mockImplementation((p) => {
+      const s = String(p);
+      // The gitdir target exists too → treat as (maybe) registered, leave it alone.
+      return s === "/root/.worktrees" || s === "/root/.worktrees/live-wt/.git" || s === "/root/.git/worktrees/live-wt";
+    });
+
+    const removed = await reapOrphanWorktrees("/root");
+
+    expect(removed).toBe(0);
+    expect(mockedRmSync).not.toHaveBeenCalledWith("/root/.worktrees/live-wt", expect.anything());
+  });
 });
 

packages/engine/src/executor.ts

@@ -14247,14 +14247,24 @@ Backward compat fallback: if JSON is unavailable, you may still begin output wit
       return true;
     } catch (error: unknown) {
       const errorMessage = error instanceof Error ? error.message : String(error);
-      // FN-4811 follow-up (FN-4813): when `git worktree remove --force` fails with
-      // "fatal: validation failed, cannot remove working tree", the worktree directory
-      // doesn't exist on disk and the git admin entry (if any) is stale. Treat as
-      // already-cleaned: prune the stale admin entry, best-effort delete the branch, and
-      // return success so the caller can proceed with fresh worktree creation. Without
-      // this recovery, every `tryCreateWorktree` retry on a stale conflict path fails
-      // with "automatic cleanup failed".
-      if (/validation failed, cannot remove working tree/i.test(errorMessage)) {
+      // FN-4811 follow-up (FN-4813): when `git worktree remove --force` fails because the
+      // conflicting path isn't a recoverable git worktree, treat it as already-cleaned:
+      // prune any stale admin entry, force-remove the leftover directory, best-effort delete
+      // the branch, and return success so the caller can proceed with fresh worktree creation.
+      // Without this recovery, every `tryCreateWorktree` retry on such a path fails with
+      // "automatic cleanup failed".
+      //
+      // Three variants land here, all meaning "no live worktree to preserve at this path":
+      //   1. `validation failed, cannot remove working tree` — stale admin entry, dir missing.
+      //   2. `is not a working tree` — an orphan directory exists on disk but git never
+      //      registered it (e.g. a leaked worktree dir that outlived its admin entry). This
+      //      is the FN-6782 leak residue that collides with freshly generated worktree names.
+      //   3. `No such file or directory` / ENOENT — the path is already gone.
+      const staleConflictPath =
+        /validation failed, cannot remove working tree/i.test(errorMessage) ||
+        /is not a working tree/i.test(errorMessage) ||
+        /no such file or directory|ENOENT/i.test(errorMessage);
+      if (staleConflictPath) {
         try {
           await execAsync("git worktree prune", {
             cwd: this.rootDir,
@@ -14265,6 +14275,14 @@ Backward compat fallback: if JSON is unavailable, you may still begin output wit
           const pruneMsg = pruneErr instanceof Error ? pruneErr.message : String(pruneErr);
           executorLog.warn(`${taskId}: git worktree prune failed during stale-path cleanup of ${worktreePath}: ${pruneMsg}`);
         }
+        // An orphan directory ("is not a working tree") won't be removed by prune — git
+        // doesn't track it. Force-remove the leftover dir so the colliding name is free.
+        try {
+          await rm(worktreePath, { recursive: true, force: true });
+        } catch (rmErr: unknown) {
+          const rmMsg = rmErr instanceof Error ? rmErr.message : String(rmErr);
+          executorLog.warn(`${taskId}: failed to remove orphan worktree directory ${worktreePath}: ${rmMsg}`);
+        }
         try {
           await execAsync(`git branch -D "${branch}"`, { cwd: this.rootDir });
           this.store.clearStaleExecutionStartBranchReferences([branch], taskId);
@@ -14273,7 +14291,7 @@ Backward compat fallback: if JSON is unavailable, you may still begin output wit
         }
         await this.store.logEntry(
           taskId,
-          `Cleaned up stale conflicting worktree admin entry (validation failed — path likely missing on disk)`,
+          `Cleaned up stale conflicting worktree (no live worktree at path — pruned admin entry and removed orphan directory)`,
           worktreePath,
         );
         return true;

packages/engine/src/worktree-pool.ts

@@ -1,7 +1,7 @@
 import { exec } from "node:child_process";
 import { promisify } from "node:util";
-import { existsSync, lstatSync, readdirSync, rmSync, realpathSync } from "node:fs";
-import { basename, join, relative, resolve, isAbsolute } from "node:path";
+import { existsSync, lstatSync, readdirSync, readFileSync, rmSync, realpathSync } from "node:fs";
+import { basename, dirname, join, relative, resolve, isAbsolute } from "node:path";
 import type { ColumnId, SecretsStore, Settings, TaskStore, WorktrunkSettings } from "@fusion/core";
 import { assertCleanBranchAtBase, inspectBranchConflict } from "./branch-conflicts.js";
 import { worktreePoolLog } from "./logger.js";
@@ -848,6 +848,34 @@ export async function cleanupOrphanedWorktrees(
  * @param projectRoot - Absolute path to the project root (parent of `.worktrees/`)
  * @returns Number of orphan directories removed
  */
+/**
+ * Resolve a worktree's `.git` pointer to the gitdir admin path it references.
+ *
+ * Returns:
+ * - `"directory"` if `.git` is a real directory (a normal repo, not a worktree
+ *   link) — callers should treat that as "leave it alone".
+ * - an absolute path string for a `gitdir: <path>` link file (relative targets
+ *   are resolved against the worktree directory).
+ * - `null` if the pointer can't be read or parsed.
+ *
+ * Callers decide whether the target exists; a missing target means the link is
+ * dangling (leak residue) and the directory is safe to reap.
+ */
+function resolveGitdirPointer(dotGitPath: string): string | "directory" | null {
+  try {
+    if (lstatSync(dotGitPath).isDirectory()) {
+      return "directory";
+    }
+    const raw = readFileSync(dotGitPath, "utf8").trim();
+    const match = /^gitdir:\s*(.+)$/.exec(raw);
+    if (!match) return null;
+    const target = match[1].trim();
+    return isAbsolute(target) ? target : resolve(dirname(dotGitPath), target);
+  } catch {
+    return null;
+  }
+}
+
 export async function reapOrphanWorktrees(
   projectRoot: string,
   settings?: Pick<Settings, "worktreesDir">,
@@ -902,16 +930,29 @@ export async function reapOrphanWorktrees(
     // Belt-and-suspenders: skip if a .git file exists AND points to an existing gitdir.
     // This guards against races where git registered the worktree between our list
     // call and now, or against a broken repo whose porcelain is unreliable.
+    //
+    // FN-6782 follow-up: a *dangling* `.git` (file present, but the admin entry it
+    // points to is gone) is NOT "partially registered" — it is leak residue from a
+    // worktree whose admin entry was pruned while the directory survived. Such a dir
+    // is invisible to `git worktree list`/`prune` yet collides with freshly generated
+    // worktree names and breaks `execute` (cleanup can't `git worktree remove` a path
+    // git never registered). Only skip when the gitdir target actually exists; reap
+    // dangling pointers like any other half-initialized orphan.
     const dotGit = join(resolvedFull, ".git");
     if (existsSync(dotGit)) {
-      // If there's a .git file/dir, don't touch it — assertValidWorktreeSession
-      // will handle it on the next agent start.
-      worktreePoolLog.log(`reapOrphanWorktrees: skipping ${name} (has .git entry but not in registered list — may be partially registered)`);
-      continue;
+      const gitdirTarget = resolveGitdirPointer(dotGit);
+      if (gitdirTarget === "directory" || (gitdirTarget && existsSync(gitdirTarget))) {
+        // Valid registration (or a real .git dir) — leave it; assertValidWorktreeSession
+        // will handle it on the next agent start.
+        worktreePoolLog.log(`reapOrphanWorktrees: skipping ${name} (has .git entry but not in registered list — may be partially registered)`);
+        continue;
+      }
+      worktreePoolLog.log(`reapOrphanWorktrees: ${name} has a dangling .git pointer (admin entry missing) — treating as orphan`);
+      // fall through to removal
     }
 
-    // This directory is on disk but has no .git entry and is not a registered
-    // worktree — it is a half-initialized orphan.  Remove it.
+    // This directory is on disk but has no valid .git entry and is not a registered
+    // worktree — it is a half-initialized / leaked orphan.  Remove it.
     try {
       try {
         await cleanupSecretsEnvFile({