fix(vscode): keep Agent Manager .kilo out of git in subdirectory workspaces

.changeset/disable-kilo-folder-creation.md

@@ -0,0 +1,5 @@
+---
+"kilo-code": patch
+---
+
+Keep the Agent Manager `.kilo` directory out of git in subdirectory workspaces and avoid creating it in folders that are not git repositories.

packages/kilo-vscode/src/agent-manager/WorktreeManager.ts

@@ -277,8 +277,10 @@ export class WorktreeManager {
   /** Adopt leftover pooled slots at startup and discard broken ones. */
   async reconcilePool(): Promise<void> {
     await this.ensureMigrated()
-    await this.ensureDir()
+    // Exclude before creating anything: a repository that cannot be excluded
+    // must not leave an untracked `.kilo/worktrees` directory behind.
     await this.ensureGitExclude()
+    await this.ensureDir()
     return this.pool.reconcile()
   }
 
@@ -427,7 +429,8 @@ export class WorktreeManager {
 
     const requested = params.existingBranch ?? params.branchName
     const { resolvedRemote } = await this.preflight(params, requested)
-    await Promise.all([this.ensureDir(), this.ensureGitExclude()])
+    await this.ensureGitExclude()
+    await this.ensureDir()
 
     // Resolve start point (parent branch + remote)
     let parent: string
@@ -1057,8 +1060,7 @@ export class WorktreeManager {
   // ---------------------------------------------------------------------------
 
   async ensureGitExclude(): Promise<void> {
-    const gitDir = await resolveGitDir(this.root)
-    const excludePath = path.join(gitDir, "info", "exclude")
+    const target = await this.excludeTarget()
     const items = [
       [".kilo/worktrees/", "Kilo Code agent worktrees"],
       [".kilo/agent-manager.json", "Kilo Agent Manager state"],
@@ -1077,10 +1079,36 @@ export class WorktreeManager {
     ] as const
 
     for (const [entry, comment] of items) {
-      await this.addExcludeEntry(excludePath, entry, comment)
+      await this.addExcludeEntry(target.file, `${target.prefix}${entry}`, comment)
     }
   }
 
+  /**
+   * Resolve the repository exclude file and the repository-relative path to
+   * this manager's root.
+   *
+   * Git answers both questions for a linked worktree and for a workspace that
+   * is a subdirectory of a repository. `--show-prefix` is already relative and
+   * uses forward slashes, so it avoids symlink mismatches such as macOS
+   * `/var` versus `/private/var`. The anchored ignore patterns then point at
+   * the real `.kilo` directory instead of the repository root.
+   *
+   * `--git-path` is used without `--path-format=absolute`, because older Git
+   * echoes unsupported rev-parse flags to stdout with exit code 0, which would
+   * silently corrupt the path. Its result is relative to this command's cwd,
+   * so it is resolved against this root.
+   *
+   * Failures propagate: callers decide whether to continue without excludes.
+   * There is deliberately no silent fallback, because a guessed prefix would
+   * write ignore patterns anchored to the wrong directory.
+   */
+  private async excludeTarget(): Promise<{ file: string; prefix: string }> {
+    const exclude = (await this.git.raw(["rev-parse", "--git-path", "info/exclude"])).trim()
+    if (!exclude || exclude.startsWith("--")) throw new Error("git rev-parse did not return an exclude path")
+    const prefix = (await this.git.raw(["rev-parse", "--show-prefix"])).trim()
+    return { file: path.resolve(this.root, exclude), prefix }
+  }
+
   /**
    * Returns true when target is strictly inside the managed worktrees directory.
    * Prevents sibling-prefix confusion such as "/worktrees-evil".
@@ -1102,7 +1130,7 @@ export class WorktreeManager {
     let content = ""
     if (fs.existsSync(excludePath)) {
       content = await fs.promises.readFile(excludePath, "utf-8")
-      if (content.includes(entry)) return
+      if (content.split(/\r?\n/).includes(entry)) return
     }
 
     const pad = content.endsWith("\n") || content === "" ? "" : "\n"

packages/kilo-vscode/tests/unit/worktree-manager.test.ts

@@ -1231,6 +1231,32 @@ describe("WorktreeManager.ensureGitExclude", () => {
     const count = content.split(".kilo/worktrees/").length - 1
     expect(count).toBe(1)
   })
+
+  it("prefixes ignore entries when the root is a subdirectory of the repository", async () => {
+    const root = await createTempRepo()
+    const sub = path.join(root, "packages", "app")
+    await fs.mkdir(sub, { recursive: true })
+    const mgr = createManager(sub)
+
+    await mgr.ensureGitExclude()
+
+    const content = await fs.readFile(path.join(root, ".git", "info", "exclude"), "utf-8")
+    expect(content).toContain("packages/app/.kilo/worktrees/")
+    expect(content).toContain("packages/app/.kilo/agent-manager.json")
+  })
+
+  it("keeps a subdirectory workspace clean after pool reconcile", async () => {
+    const root = await createTempRepo()
+    const sub = path.join(root, "packages", "app")
+    await fs.mkdir(sub, { recursive: true })
+    const mgr = createManager(sub)
+
+    await mgr.reconcilePool()
+
+    const status = await simpleGit(root).raw(["status", "--porcelain", "--untracked-files=all"])
+    expect(status.trim()).toBe("")
+    expect(existsSync(path.join(sub, ".kilo", "worktrees"))).toBe(true)
+  })
 })
 
 // ---------------------------------------------------------------------------