fix(worktrees): the injected agent skill no longer blocks removal

With Codeman Agent Skill on (agentSkillEnabled), every session create
writes the skill into the folder the session runs in, so a session in a
worktree leaves an untracked .claude/skills/codeman/ (claude) or
.agents/skills/codeman/ (codex, gemini and the rest) behind. git then
refuses `git worktree remove` for that worktree forever, and an agent
running `git add -A` there would commit Codeman's skill into its branch
(reproduced: the worktree's status showed "?? .agents/" and
"?? .claude/").

A create now excludes <skills dir>/codeman/ next to the hooks file, for
every skills folder the registry names (capabilities.agentSkillDir,
read at call time by the route and passed in as data, so no CLI id is
branched on). Like the other lines it is only added when git does not
already ignore the path, and only to the repository's local
info/exclude.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

src/git-worktrees.ts

@@ -18,7 +18,9 @@
  * already ignore it. `/.claude/settings.local.json` gets the same treatment: Codeman installs its
  * hooks there for every claude session, and an untracked copy in a worktree makes
  * `git worktree remove` refuse forever (Claude Code itself ignores that file through the global
- * excludes file, which is not guaranteed to be set up on a given machine).
+ * excludes file, which is not guaranteed to be set up on a given machine). The copy of Codeman's
+ * agent skill (`<skills dir>/codeman/`, injected while `agentSkillEnabled` is on) is excluded for
+ * the same reason, for every skills folder the registry names (`WorktreeOptions.agentSkillDirs`).
  *
  * Split like the other git modules: a PURE half (name and branch validation, `worktree list`
  * parsing, exclude text, the managed-path rule) unit-tested without git, and an IO half that
@@ -88,6 +90,19 @@ export const WORKTREES_EXCLUDE_LINE = '/.claude/worktrees/';
 /** The `info/exclude` line for the hooks file Codeman writes into every claude workspace. */
 export const SETTINGS_LOCAL_EXCLUDE_LINE = '/.claude/settings.local.json';
 
+/** A workspace-relative skills folder (`.claude/skills`, `.agents/skills`): plain segments only. */
+const SKILLS_DIR_RE = /^[A-Za-z0-9._-]+(?:\/[A-Za-z0-9._-]+)*$/;
+
+/**
+ * The `info/exclude` line for the copy of Codeman's agent skill in `skillsDir` of a workspace
+ * (`<skillsDir>/codeman/`, written into the folder a session runs in while `agentSkillEnabled`
+ * is on), or null for a folder that is not a plain relative path.
+ */
+export function agentSkillExcludeLine(skillsDir: string): string | null {
+  if (!SKILLS_DIR_RE.test(skillsDir) || skillsDir.split('/').some((s) => s === '.' || s === '..')) return null;
+  return `/${skillsDir}/codeman/`;
+}
+
 // ─── Pure: names ─────────────────────────────────────────────────────────────
 
 const WORKTREE_NAME_RE = /^[A-Za-z0-9][A-Za-z0-9._-]*$/;
@@ -301,7 +316,7 @@ export function excludeAppendText(existing: string, lines: readonly string[]): {
   if (added.length === 0) return { text: '', added };
   const lead = existing.length > 0 && !existing.endsWith('\n') ? '\n' : '';
   return {
-    text: `${lead}# Added by Codeman: git worktrees and the per-workspace hooks file stay local\n${added.join('\n')}\n`,
+    text: `${lead}# Added by Codeman: git worktrees and the files Codeman writes into each workspace stay local\n${added.join('\n')}\n`,
     added,
   };
 }
@@ -450,6 +465,13 @@ export interface WorktreeOptions {
   dockerWorkspaces?: string[];
   /** Overrides `os.homedir()` for the unrelated-ancestor rule (tests). */
   home?: string;
+  /**
+   * Every workspace skills folder a session can get Codeman's agent skill in (the registry's
+   * `capabilities.agentSkillDir` values, passed in as data by the caller). A create excludes
+   * `<dir>/codeman/` for each, like the hooks file: a session in a worktree gets an untracked
+   * copy there, and `git worktree remove` would refuse that worktree forever.
+   */
+  agentSkillDirs?: readonly string[];
 }
 
 const realOr = async (p: string): Promise<string> => {
@@ -797,11 +819,17 @@ export async function createCaseWorktree(
       return fail('OPERATION_FAILED', `Could not inspect ${target}: ${(err as Error).message}`);
     }
 
+    const skillProbes: Array<{ line: string; probe: string }> = [];
+    for (const dir of new Set(opts.agentSkillDirs ?? [])) {
+      const line = agentSkillExcludeLine(dir);
+      if (line) skillProbes.push({ line, probe: `${dir}/codeman` });
+    }
     const excluded = await ensureExcluded(
       repo,
       [
         { line: WORKTREES_EXCLUDE_LINE, probe: `${WORKTREES_DIR_SEGMENTS.join('/')}/${req.name}` },
         { line: SETTINGS_LOCAL_EXCLUDE_LINE, probe: '.claude/settings.local.json' },
+        ...skillProbes,
       ],
       git
     );

src/web/routes/worktree-routes.ts

@@ -29,6 +29,8 @@ import { readDockerCases } from '../../docker-hosts.js';
 import { readRemoteCases } from '../../remote-hosts.js';
 import { dataPath, getDataDir } from '../../config/instance.js';
 import { isMultiUserMode } from '../../config/multiuser.js';
+import { listClis } from '../../config/cli-registry/registry.js';
+import { agentSkillDir } from '../../hooks-config.js';
 import { describeUnknownPath, probePathKind } from '../../utils/index.js';
 import {
   createCaseWorktree,
@@ -65,6 +67,19 @@ const SAFE_CASE_NAME = /^[a-zA-Z0-9_-]+$/;
 const defaultDockerWorkspaces = async (): Promise<string[]> =>
   (await readDockerCases(getDataDir()).catch(() => [])).map((c) => c.hostWorkspacePath).filter(Boolean);
 
+/**
+ * Every workspace skills folder a session of some registry CLI gets Codeman's agent skill in
+ * (`capabilities.agentSkillDir`), read from the registry at call time as data, never by CLI id.
+ */
+const registryAgentSkillDirs = (): string[] => {
+  const dirs = new Set<string>();
+  for (const cli of listClis()) {
+    const dir = agentSkillDir(cli.capabilities);
+    if (dir) dirs.add(dir);
+  }
+  return [...dirs];
+};
+
 /** A live session in a worktree, as the list reports it to a caller who may see it. */
 export interface WorktreeSessionRef {
   id: string;
@@ -239,7 +254,10 @@ export function registerWorktreeRoutes(
     if (nameError) return failWith(reply, ApiErrorCode.INVALID_INPUT, nameError);
     const resolved = await caseRepository(req, reply, name);
     if (!resolved.ok) return resolved.fail;
-    const created = await createCaseWorktree(resolved.repo, body, { git: deps.git });
+    const created = await createCaseWorktree(resolved.repo, body, {
+      git: deps.git,
+      agentSkillDirs: registryAgentSkillDirs(),
+    });
     if (!created.ok) return failFrom(reply, created);
     reply.code(201);
     return { success: true, data: { worktree: created.worktree } };