fix: exclude .claude from git tracking in worktrees

src/main/worktree/worktree-manager.test.ts

@@ -5,6 +5,7 @@ import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import {
   createWorktree,
+  excludeClaudeDir,
   generateWorktreePath,
   listWorktrees,
   removeWorktree,
@@ -189,4 +190,87 @@ describe("worktree operations", () => {
       expect(worktrees).toHaveLength(2);
     });
   });
+
+  describe("excludeClaudeDir", () => {
+    it("excludes .claude from git tracking in worktree after symlink", () => {
+      // Track .claude in the main repo
+      const claudeDir = path.join(repoDir, ".claude");
+      fs.mkdirSync(claudeDir);
+      fs.writeFileSync(path.join(claudeDir, "settings.local.json"), '{"permissions":{}}');
+      execFileSync("git", ["add", ".claude"], { cwd: repoDir });
+      execFileSync("git", ["commit", "-m", "add .claude"], { cwd: repoDir });
+
+      const worktreePath = createWorktree(repoDir, "exclude-test");
+
+      // The common git dir's info/exclude should contain .claude
+      const commonDir = execFileSync("git", ["rev-parse", "--git-common-dir"], {
+        cwd: worktreePath,
+        encoding: "utf8",
+      }).trim();
+      const resolvedCommonDir = path.isAbsolute(commonDir) ? commonDir : path.resolve(worktreePath, commonDir);
+      const excludeFile = path.join(resolvedCommonDir, "info", "exclude");
+
+      expect(fs.existsSync(excludeFile)).toBe(true);
+      const excludeContent = fs.readFileSync(excludeFile, "utf8");
+      expect(excludeContent).toContain(".claude");
+
+      // git status should not show .claude as untracked or modified
+      const status = execFileSync("git", ["status", "--porcelain"], {
+        cwd: worktreePath,
+        encoding: "utf8",
+      });
+      expect(status).not.toMatch(/\?\? .*\.claude/);
+      expect(status).not.toMatch(/ M .*\.claude/);
+    });
+
+    it("git operations work after symlinking .claude", () => {
+      // Track .claude in the main repo
+      const claudeDir = path.join(repoDir, ".claude");
+      fs.mkdirSync(claudeDir);
+      fs.mkdirSync(path.join(claudeDir, "commands"));
+      fs.writeFileSync(path.join(claudeDir, "commands", "test.md"), "test command");
+      execFileSync("git", ["add", ".claude"], { cwd: repoDir });
+      execFileSync("git", ["commit", "-m", "add .claude"], { cwd: repoDir });
+
+      const worktreePath = createWorktree(repoDir, "merge-test");
+
+      // Make a commit on main that we'll merge into the worktree
+      fs.writeFileSync(path.join(repoDir, "new-file.txt"), "new content");
+      execFileSync("git", ["add", "new-file.txt"], { cwd: repoDir });
+      execFileSync("git", ["commit", "-m", "add new file"], { cwd: repoDir });
+
+      // Merge main into the worktree — should not fail with "beyond a symbolic link"
+      expect(() => {
+        execFileSync("git", ["merge", "main"], {
+          cwd: worktreePath,
+          encoding: "utf8",
+          stdio: "pipe",
+        });
+      }).not.toThrow();
+
+      expect(fs.existsSync(path.join(worktreePath, "new-file.txt"))).toBe(true);
+    });
+
+    it("does not duplicate .claude entry in exclude file", () => {
+      const claudeDir = path.join(repoDir, ".claude");
+      fs.mkdirSync(claudeDir);
+      fs.writeFileSync(path.join(claudeDir, "settings.local.json"), "{}");
+
+      const worktreePath = createWorktree(repoDir, "no-dup-test");
+
+      // Call excludeClaudeDir a second time
+      excludeClaudeDir(worktreePath);
+
+      const commonDir = execFileSync("git", ["rev-parse", "--git-common-dir"], {
+        cwd: worktreePath,
+        encoding: "utf8",
+      }).trim();
+      const resolvedCommonDir = path.isAbsolute(commonDir) ? commonDir : path.resolve(worktreePath, commonDir);
+      const excludeContent = fs.readFileSync(path.join(resolvedCommonDir, "info", "exclude"), "utf8");
+
+      // Should appear exactly once
+      const matches = excludeContent.match(/^\.claude$/gm);
+      expect(matches).toHaveLength(1);
+    });
+  });
 });

src/main/worktree/worktree-manager.ts

@@ -58,6 +58,50 @@ export function symlinkClaudeDir(repoPath: string, worktreePath: string): void {
   }
 
   fs.symlinkSync(sourceClaudeDir, targetClaudeDir);
+  excludeClaudeDir(worktreePath);
+
+  // Remove .claude from the worktree's index so git doesn't see
+  // tracked-file deletions after replacing the directory with a symlink.
+  // This only affects the worktree's index, not the main repo.
+  try {
+    execFileSync("git", ["rm", "--cached", "-r", "--quiet", ".claude"], {
+      cwd: worktreePath,
+      stdio: "pipe",
+    });
+  } catch {
+    // .claude may not be tracked — ignore
+  }
+}
+
+/** Add .claude to the worktree's git exclude file so git ignores the symlink.
+ *  Git worktrees read info/exclude from the common git dir (the main repo's .git/). */
+export function excludeClaudeDir(worktreePath: string): void {
+  let commonDir: string;
+  try {
+    commonDir = execFileSync("git", ["rev-parse", "--git-common-dir"], {
+      cwd: worktreePath,
+      encoding: "utf8",
+      stdio: "pipe",
+    }).trim();
+  } catch {
+    return;
+  }
+
+  // Resolve relative paths (git may return a relative path)
+  if (!path.isAbsolute(commonDir)) {
+    commonDir = path.resolve(worktreePath, commonDir);
+  }
+
+  const infoDir = path.join(commonDir, "info");
+  fs.mkdirSync(infoDir, { recursive: true });
+
+  const excludeFile = path.join(infoDir, "exclude");
+  const existingContent = fs.existsSync(excludeFile) ? fs.readFileSync(excludeFile, "utf8") : "";
+
+  if (existingContent.split("\n").some((line) => line.trim() === ".claude")) return;
+
+  const separator = existingContent.length > 0 && !existingContent.endsWith("\n") ? "\n" : "";
+  fs.appendFileSync(excludeFile, `${separator}.claude\n`);
 }
 
 export function removeWorktree(worktreePath: string, branchName: string, repoPath: string): void {