feat(autotune): persist skills to repo and mirrors

A skill written only under .claude/skills is lost on the next install, and
one written only into the skills repository is not live until the next
restart, so both writers now do both: locate the operator's skills
repository through an ordered first-hit lookup, write the source of truth
there, then mirror the whole skill directory into the live locations so
hooks and references come along.

The lookup ends in a question to the operator rather than a silent skip
when no repository matches. autoskill routes to the same section instead
of carrying its own copy of the paths.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

skills/autoskill/SKILL.md

@@ -18,10 +18,12 @@ vary), do the following:
 3. On approval, write the skill:
    - a conversation shortcut or expansion: add it to the `shortcuts` skill
      table instead of creating a new skill.
-   - project-specific behavior: create it in the project's own skills
+   - anything else: persist it exactly as the `autotune` skill's
-     directory (e.g. `skills/<name>/SKILL.md` in the repository).
+     **Persistence** section specifies — locate the operator's skills
-   - portable behavior: create `skills/<name>/SKILL.md` in the operator's
+     repository, write `skills/<name>/SKILL.md` there (or in the current
-     skills repository.
+     project for project-specific behavior), then mirror the skill directory
+     into `~/.claude/skills/` and `~/.agents/skills/`, plus the project's
+     `.claude/skills/` and `.agents/skills/` when it is project-specific.
    Follow the local naming conventions and keep the skill a thin,
    single-purpose instruction; route to an authoritative doc when one
    exists instead of duplicating it.

skills/autotune/SKILL.md

@@ -65,10 +65,35 @@ for a final `Write it` / `Revise it` / `Discard` confirmation before touching
 disk. Rewrites of an existing skill additionally show a before/after diff of
 the changed lines in that confirmation.
 
+## Persistence
+
+A skill that exists only under `.claude/skills` is lost on the next install, and
+one that exists only in the repository is not live until the next restart — so
+every skill is written to **both**, in this order:
+
+1. **Locate the operator's skills repository.** Take the first hit: the
+   `SKILLS_REPO` environment variable; the current repository, when it holds
+   `skills-lock.json` and a `skills/` directory; `pkgmgr path skills`; a git
+   checkout named `skills` under the usual roots
+   (`~/Repositories/*/*/skills`, `~/git`, `~/src`, `~/Projects`) carrying
+   `skills-lock.json`. If none matches, ask the operator for the path with a
+   single-select question — never skip the repository and write only the live
+   copies.
+2. **Write the source of truth**: `skills/<name>/SKILL.md` in that repository
+   (portable skills), or `skills/<name>/SKILL.md` in the current project
+   (project-specific ones). This is the copy that gets committed.
+3. **Mirror it live**, so it works without a reinstall: copy the skill's whole
+   directory to `~/.claude/skills/<name>/` and `~/.agents/skills/<name>/`, and
+   for a project-specific skill additionally to that project's
+   `.claude/skills/<name>/` and `.agents/skills/<name>/`. Copy the directory,
+   not just `SKILL.md`, so hooks and references come along.
+
+Report all written paths. Deleting or renaming a skill follows the same list in
+reverse — remove the mirrors too, or the old name keeps firing.
+
 ## Step 3: write
 
-- Portable skills go to `skills/<name>/SKILL.md` in the operator's skills
+- Write the skill to every location the **Persistence** section lists.
-  repository; project-specific ones to that project's skills directory.
 - Frontmatter carries `name` and a `description` that states what the skill
   does **and** when to trigger it - the description is the only part loaded into
   every session, so it decides whether the skill ever fires.

tests/test_autotune.py

@@ -37,6 +37,20 @@ class TestAutotuneSkill(unittest.TestCase):
         self.assertIn("multiSelect: false", text)
 
 
+class TestSkillPersistence(unittest.TestCase):
+    """Both skill writers must persist to the skills repository AND the live dirs."""
+
+    def test_autotune_names_every_target(self):
+        text = SKILL.read_text(encoding="utf-8")
+        for target in ("SKILLS_REPO", "skills/<name>/SKILL.md", "~/.claude/skills/", "~/.agents/skills/"):
+            self.assertIn(target, text)
+
+    def test_autoskill_routes_to_the_same_persistence(self):
+        text = (REPO_ROOT / "skills" / "autoskill" / "SKILL.md").read_text(encoding="utf-8")
+        for target in ("Persistence", "~/.claude/skills/", "~/.agents/skills/"):
+            self.assertIn(target, text)
+
+
 class TestAutotuneHook(unittest.TestCase):
     def setUp(self):
         self.tmp = tempfile.TemporaryDirectory()