fix: resolve the issue store path independently of the working directory

ISSUE_ROOT was the relative `tmp/issues`, so "the store" was whatever
directory the shell happened to be standing in. It is the --out default
in all eight scripts of both layers, which made one `cd` — and a `cd`
outlives the command that ran it — enough for readers to report an empty
store on a full one and for writers to quietly build a second store
beside the first. `issue_index.py` run from inside tmp/issues left
tmp/issues/tmp/issues/ behind and exited 0.

The anchor is issue.py's own __file__, not cwd. A script's location is a
fact about the installation; cwd is a fact about the last `cd`, and the
scripts are invoked by path from wherever the agent happens to be. From
there `store_root()` walks up to the nearest repo marker — `.git`
(exists(), not isdir(): a worktree's .git is a file) or AGENTS.md for a
copy taken out of git — and joins tmp/issues. Markers rather than a
fixed number of `..` hops, because the layout is not a promise. cwd is
tried only if the scripts are not inside a repository at all.

The function lives in the domain layer and skills/sync imports it, so
both layers agree by construction — the direction the layering rule
allows. skills/issue stays stdlib-only.

An explicit --out still wins and is used exactly as typed: a relative
--out stays relative to cwd, because that is what the operator asked
for. No new environment surface.

Two consequences the issue also asked for:

- Missing is no longer reported as empty. `store_error()` returns one
  message for a path that is not there and another for a store with no
  issues in it.
- Nothing conjures a store as a side effect of a write. save() and
  issue_index.build() require it instead of os.makedirs'ing it; only
  issue_new.py and pull.py create one, and both say so on stderr.

Establishes tests/ — plain stdlib unittest, no pytest, no dependencies.
The store tests build a throwaway repo in a TemporaryDirectory (a .git
marker, a copy of both script layers, fixture issues) and run the real
scripts inside it as subprocesses from five different working
directories; tmp/issues/ is never touched. Against the pre-fix scripts
15 of the 21 fail, reproducing the report exactly — five stray stores,
including tmp/issues/tmp/issues.

    python3 -m unittest discover -s tests -v

Closes claude-skills/tea#15

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

AGENTS.md

@@ -68,6 +68,25 @@ the domain layer, it is in the wrong place.
 - `hooks/` — PreToolUse hooks: `tea-guard` blocks or rewrites `tea` invocations
   that don't use the pinned login; `agents-sync` keeps every directory canonical
   (`AGENTS.md` real file, `CLAUDE.md` symlink to it)
+- `tests/` — stdlib `unittest`, no third-party anything
+
+## Tests
+
+```bash
+python3 -m unittest discover -s tests -v
+```
+
+Plain `unittest`; no pytest, no dependencies — the scripts under test are
+stdlib-only and the tests hold the same line. `skills/*/scripts/` are not
+packages, so a test that needs the domain module imports it with
+`sys.path.insert`.
+
+**A test never touches `tmp/issues/`.** Anything that needs a store builds a
+throwaway repository in a `tempfile.TemporaryDirectory()` — a `.git` marker, a
+copy of the script layers, fixture issues — and runs the real scripts inside it
+as subprocesses. That is the only way to test behavior that depends on where a
+script is run from, and it keeps the developer's own store out of the blast
+radius.
 
 ## Local issue store
 
@@ -75,6 +94,14 @@ the domain layer, it is in the wrong place.
 markdown file per issue, named by its slug, with one metadata field per line so
 plain grep works without a parser.
 
+- **The path is `<repo root>/tmp/issues`, resolved from `issue.py`'s own
+  location, not from cwd.** `issue.store_root()` walks up from `__file__` to the
+  nearest `.git` or `AGENTS.md` — so every script in both layers sees one store
+  whatever directory it is run from. An explicit `--out` overrides it and is
+  used exactly as typed; a relative `--out` stays relative to cwd.
+- Nothing creates the store as a side effect of a write. Readers distinguish
+  "does not exist" from "is empty"; only `issue_new.py` and `pull.py` create it,
+  and they say so on stderr.
 - Identity is the slug (`wire-sqlc-appclick.md`), never a tracker number.
   Numbers live in the `gitea:` field.
 - `origin: local` is a durable state. An issue that never leaves this machine is

skills/issue/SKILL.md

@@ -47,6 +47,24 @@ tmp/issues/wire-sqlc.comments.md    comment thread (written by /tea:sync only)
 tmp/issues/tree-<id>.md             saved graph (issue_tree.py --write)
 ```
 
+## Where the store is
+
+`<repo root>/tmp/issues` — **not** `tmp/issues` relative to wherever you are
+standing. The scripts resolve it by walking up from their own file to the
+nearest `.git` or `AGENTS.md`, so they all see one store no matter which
+directory you run them from, and a `cd` earlier in the session changes nothing.
+
+`--out` overrides that and is taken **literally**: an absolute path is used as
+given, a relative one stays relative to the current directory. Nothing rewrites
+what you typed.
+
+Two things follow, and both are deliberate:
+
+- A store that is not there reports `does not exist`; a store with no issues in
+  it reports `is empty`. They are different problems.
+- No script conjures a store as a side effect of writing. Only `issue_new.py`
+  creates one — the first issue in a fresh checkout — and it says so on stderr.
+
 ## Reading: grep, don't parse
 
 Metadata is one field per line with inline lists precisely so plain `grep`

skills/issue/scripts/issue.py

@@ -48,7 +48,67 @@ without a parser:
 import os
 import re
 
-ISSUE_ROOT = os.path.join("tmp", "issues")
+# --------------------------------------------------------------------------
+# where the store lives
+# --------------------------------------------------------------------------
+# `<repo root>/tmp/issues`, absolute, resolved once at import.
+#
+# It used to be the relative `tmp/issues`, which made "the store" whatever
+# directory the shell happened to be standing in. One `cd` — and a `cd` outlives
+# the command that ran it — was enough for readers to report an empty store on a
+# full one and for writers to quietly build a second store beside the first.
+#
+# The anchor is THIS FILE, not the working directory. A script's own location is
+# a fact about the installation; cwd is a fact about the last `cd`. Walking up
+# from __file__ therefore hands every script in both layers the same answer no
+# matter where it is invoked from — including from inside tmp/issues itself.
+#
+# An explicit --out still wins over all of this, and is used exactly as typed: a
+# relative --out stays relative to cwd, because that is what the operator asked
+# for. There is no environment override; the store is where the repo is.
+
+STORE_PARTS = ("tmp", "issues")
+
+# `.git` is a directory in a normal clone and a FILE in a worktree — hence
+# exists(), not isdir(). AGENTS.md is the fallback for a plugin copied out of
+# git; the agents-sync hook only ever puts one at a repository root.
+REPO_MARKERS = (".git", "AGENTS.md")
+
+_HERE = os.path.dirname(os.path.abspath(__file__))
+
+
+def repo_root(start):
+    """Nearest ancestor of `start` (inclusive) carrying a repo marker, or None.
+
+    Markers, not a fixed number of `..` hops: how deep this file sits below the
+    root is an implementation detail of the repo layout, and the layout is not
+    a promise."""
+    d = os.path.abspath(start)
+    while True:
+        if any(os.path.exists(os.path.join(d, m)) for m in REPO_MARKERS):
+            return d
+        parent = os.path.dirname(d)
+        if parent == d:
+            return None
+        d = parent
+
+
+def store_root(start=None):
+    """Absolute path of the issue store.
+
+    `start` overrides the anchor and exists so the resolution can be exercised
+    against a scratch tree. When these scripts are not inside a repository at
+    all, cwd gets a turn; failing that the historical cwd-relative location
+    stands, made absolute so an error message can name the directory it really
+    looked in."""
+    for anchor in ([start] if start is not None else [_HERE, os.getcwd()]):
+        root = repo_root(anchor)
+        if root:
+            return os.path.join(root, *STORE_PARTS)
+    return os.path.abspath(os.path.join(*STORE_PARTS))
+
+
+ISSUE_ROOT = store_root()
 
 # Domain-owned metadata, in render order. Foreign keys render after these,
 # sorted, so the sync layer can add fields without touching this list.
@@ -356,6 +416,55 @@ def validate(issue, known_ids=None):
 # store
 # --------------------------------------------------------------------------
 
+class StoreMissing(Exception):
+    """The store directory is not there.
+
+    Deliberately a different answer from "the store is empty". One is a path
+    that does not exist, the other is a repository with no issues filed yet, and
+    conflating the two is exactly what made a missed directory look like an
+    empty backlog."""
+
+    def __init__(self, root):
+        self.root = root
+        Exception.__init__(self, "store %s does not exist" % root)
+
+
+def store_exists(root):
+    return os.path.isdir(root)
+
+
+def require_store(root):
+    """Assert the store is there before reading or writing it."""
+    if not os.path.isdir(root):
+        raise StoreMissing(root)
+    return root
+
+
+def create_store(root):
+    """Create the store; True when it actually made the directory.
+
+    Only the commands that legitimately bootstrap a store call this — issue_new
+    and pull — and both announce it. Nothing creates a store as a side effect of
+    a write any more: a missing directory is something to report, not something
+    to conjure."""
+    if os.path.isdir(root):
+        return False
+    os.makedirs(root)
+    return True
+
+
+def store_error(root):
+    """Why `root` cannot be read as a store, or None when it holds issues.
+
+    The two messages are distinct on purpose — see StoreMissing."""
+    if not os.path.isdir(root):
+        return ("store %s does not exist — nothing was created; pass --out to "
+                "point elsewhere" % root)
+    if not all_ids(root):
+        return "store %s exists but is empty" % root
+    return None
+
+
 def path_of(root, id):
     return os.path.join(root, "%s.md" % id)
 
@@ -377,7 +486,7 @@ def load_all(root):
 
 
 def save(root, issue):
-    os.makedirs(root, exist_ok=True)
+    require_store(root)
     p = path_of(root, issue.id)
     with open(p, "w") as f:
         f.write(issue.to_text())

skills/issue/scripts/issue_check.py

@@ -26,16 +26,19 @@ def main():
     ap.add_argument("ids", nargs="*", help="ids to check (default: all)")
     ap.add_argument("--quiet", action="store_true", help="exit code only")
     ap.add_argument("--strict", action="store_true", help="treat warnings as errors")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
+    problem = issue.store_error(args.out)
+    if problem:
+        sys.exit("issue_check.py: %s" % problem)
+
     issues = issue.load_all(args.out)
     ids = args.ids or sorted(issues)
     for i in ids:
         if i not in issues:
             sys.exit("issue_check.py: no issue %r in %s" % (i, args.out))
-    if not ids:
-        sys.exit("issue_check.py: store %s is empty" % args.out)
 
     known = set(issues)
     bad = 0

skills/issue/scripts/issue_index.py

@@ -7,8 +7,12 @@ the index acknowledges that a tracker exists: `local` means the issue has never
 left this machine, `gitea` means the sync layer has pushed or pulled it. Both
 are ordinary issues here.
 
+The store is <repo root>/tmp/issues unless --out says otherwise; an existing
+store with nothing in it gets an "_empty_" table, a store that is not there is
+an error rather than a directory to create.
+
 Usage:
-    issue_index.py [--out tmp/issues]
+    issue_index.py [--out DIR]
 """
 import argparse
 import os
@@ -27,6 +31,9 @@ def cell(v):
 
 
 def build(root):
+    # An index of a store that is not there is not an empty index, it is a bad
+    # path. Raising beats writing INDEX.md into a directory nobody asked for.
+    issue.require_store(root)
     issues = issue.load_all(root)
     rows = []
     for i in sorted(issues):
@@ -71,7 +78,6 @@ def build(root):
 
     out.append("")
     path = os.path.join(root, "INDEX.md")
-    os.makedirs(root, exist_ok=True)
     with open(path, "w") as f:
         f.write("\n".join(out))
     return path, len(rows)
@@ -79,9 +85,16 @@ def build(root):
 
 def main():
     ap = argparse.ArgumentParser(description="Rebuild the local issue index (offline)")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
-    path, n = build(args.out)
+    # An existing store with nothing in it is a legitimate thing to index — it
+    # gets an "_empty_" table. A store that is not there is not.
+    try:
+        path, n = build(args.out)
+    except issue.StoreMissing as e:
+        sys.exit("issue_index.py: %s — nothing was created; create an issue with "
+                 "issue_new.py, or pass --out" % e)
     print("%s — %d issue(s)" % (path, n))
 
 

skills/issue/scripts/issue_new.py

@@ -151,7 +151,8 @@ def main():
     ap.add_argument("--assignee", action="append", default=[], help="assignee; repeat")
     ap.add_argument("--depends", action="append", default=[],
                     help="id this issue depends on; repeat")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
     labels = ["type/%s" % args.type]
@@ -177,6 +178,11 @@ def main():
         labels=labels, assignees=args.assignee, milestone=args.milestone,
         depends=args.depends)
 
+    # The first issue in a fresh checkout has to create the store, but it says
+    # so — and it says where, because the path is absolute.
+    if issue.create_store(args.out):
+        sys.stderr.write("created store %s\n" % os.path.abspath(args.out))
+
     path = issue.save(args.out, iss)
     issue_index.build(args.out)
     print("%s  [type/%s] %s" % (path, args.type, args.title))

skills/issue/scripts/issue_tree.py

@@ -66,12 +66,15 @@ def main():
     ap.add_argument("--depth", type=int, default=6, help="max depth (default: 6)")
     ap.add_argument("--write", action="store_true",
                     help="also write tmp/issues/tree-<slug>.md")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
+    problem = issue.store_error(args.out)
+    if problem:
+        sys.exit("issue_tree.py: %s" % problem)
+
     issues = issue.load_all(args.out)
-    if not issues:
-        sys.exit("issue_tree.py: store %s is empty" % args.out)
     edges = issue.graph(issues)
 
     roots = args.ids

skills/sync/SKILL.md

@@ -48,6 +48,12 @@ Key forms for `<key>`: `42`, `#42`, `owner/repo#42`, or a full issue URL. Repo
 defaults to the current directory's git remote; add `--repo owner/repo` outside
 one.
 
+`--out` defaults to `issue.ISSUE_ROOT` on every one of them — the domain layer's
+`<repo root>/tmp/issues`, resolved from the scripts' own location rather than
+cwd. Both layers therefore address the same store by construction, from any
+directory. Pass `--out` to override; a relative one stays relative to cwd. Only
+`pull.py` will create a missing store, and it says so on stderr.
+
 ## Identity mapping
 
 The local id is a slug; Gitea's is a number. The pair is recorded in the issue

skills/sync/scripts/comment.py

@@ -43,10 +43,13 @@ def main():
     ap.add_argument("--edit", type=int, metavar="COMMENT_ID",
                     help="PATCH an existing comment instead of posting a new one")
     ap.add_argument("--repo", help="owner/repo (default: auto-detect from CWD git remote)")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
     root = args.out
+    if not issue.store_exists(root):
+        _gitea.die("store %s does not exist — nothing was created" % root)
     if not os.path.isfile(issue.path_of(root, args.id)):
         _gitea.die("no issue %r in %s" % (args.id, root))
     iss = issue.load(root, args.id)

skills/sync/scripts/pull.py

@@ -108,7 +108,8 @@ def main():
     ap.add_argument("--cached", action="store_true",
                     help="skip issues already on disk instead of refetching")
     ap.add_argument("--repo", help="owner/repo (default: auto-detect from CWD git remote)")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
     filtered = bool(args.milestone or args.label or args.query)
@@ -118,6 +119,11 @@ def main():
         _gitea.die("nothing to pull: pass issue keys, or --milestone / --label / -q")
 
     root = args.out
+    # A first pull into a fresh checkout has to create the store; it says so,
+    # and the path is absolute, so it cannot be a stray cwd.
+    if issue.create_store(root):
+        sys.stderr.write("created store %s\n" % os.path.abspath(root))
+
     login = _gitea.require_login()
 
     # ---- which repo ------------------------------------------------------

skills/sync/scripts/push.py

@@ -90,13 +90,15 @@ def main():
     ap.add_argument("--dry-run", action="store_true", help="validate only, no network")
     ap.add_argument("--force", action="store_true", help="push despite format violations")
     ap.add_argument("--repo", help="owner/repo (default: auto-detect from CWD git remote)")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
     root = args.out
+    problem = issue.store_error(root)
+    if problem:
+        _gitea.die("%s — create an issue with issue_new.py first" % problem)
     issues = issue.load_all(root)
-    if not issues:
-        _gitea.die("store %s is empty — create an issue with issue_new.py first" % root)
 
     chosen = select(issues, args.ids, args.update)
 

skills/sync/scripts/remote.py

@@ -39,7 +39,8 @@ def main():
     ap.add_argument("--milestone", help="milestone id or title")
     ap.add_argument("--limit", type=int, default=30)
     ap.add_argument("--repo", help="owner/repo (default: auto-detect from CWD git remote)")
-    ap.add_argument("--out", default=issue.ISSUE_ROOT, help="store root (default: tmp/issues)")
+    ap.add_argument("--out", default=issue.ISSUE_ROOT,
+                    help="store root (default: <repo>/tmp/issues)")
     args = ap.parse_args()
 
     login = _gitea.require_login()

tests/test_store_path.py

@@ -0,0 +1,435 @@
+#!/usr/bin/env python3
+"""
+Where the issue store is, and that the answer does not depend on cwd.
+
+    python3 -m unittest discover -s tests -v
+
+Stdlib unittest, no third-party anything — the same rule the scripts under test
+live by. `skills/*/scripts/` are not packages, so the domain module is imported
+by path.
+
+Most of these tests do not touch this repository at all. They build a throwaway
+repo in a temp directory — a `.git` marker, a copy of both script layers, a
+store with two issues — and run the real scripts inside it as subprocesses with
+different working directories. That is the only honest way to test a cwd bug:
+importing the module would resolve the store once, against the wrong tree.
+"""
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+import unittest
+
+REPO = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+ISSUE_SCRIPTS = os.path.join(REPO, "skills", "issue", "scripts")
+SYNC_SCRIPTS = os.path.join(REPO, "skills", "sync", "scripts")
+
+sys.path.insert(0, ISSUE_SCRIPTS)
+import issue  # noqa: E402
+
+
+ALPHA = """\
+---
+id: alpha-issue
+state: open
+labels: [type/task]
+assignees: []
+milestone: none
+depends: []
+origin: local
+---
+# Alpha issue
+
+## Summary
+Первый issue фикстуры.
+
+## Spec
+none
+
+## Motivation
+Нужен, чтобы в store что-то лежало.
+
+## Acceptance criteria
+- [ ] проверяемое условие
+"""
+
+BETA = """\
+---
+id: beta-issue
+state: open
+labels: [type/task]
+assignees: []
+milestone: none
+depends: [alpha-issue]
+origin: local
+---
+# Beta issue
+
+## Summary
+Второй issue фикстуры, зависит от первого.
+
+## Spec
+none
+
+## Depends on
+- alpha-issue
+
+## Motivation
+Нужен, чтобы у графа было ребро.
+
+## Acceptance criteria
+- [ ] проверяемое условие
+"""
+
+
+def run(script, *args, **kw):
+    """Run one of the plugin's scripts and return (rc, stdout, stderr)."""
+    cwd = kw.pop("cwd")
+    env = dict(os.environ)
+    env.pop("PYTHONPATH", None)  # no leakage from the harness into the child
+    p = subprocess.run([sys.executable, script] + list(args), cwd=cwd, env=env,
+                       capture_output=True, text=True)
+    return p.returncode, p.stdout, p.stderr
+
+
+class FakeRepo(object):
+    """A self-contained repository in a temp directory.
+
+    Both script layers are copied in, so `__file__`-anchored resolution lands
+    inside the fixture and never on the developer's real store.
+    """
+
+    def __init__(self, with_store=True, issues=(ALPHA, BETA)):
+        self._tmp = tempfile.TemporaryDirectory()
+        # realpath: on macOS $TMPDIR is a symlink, and a child process reporting
+        # its own cwd would otherwise disagree with the path we handed it.
+        self.root = os.path.realpath(self._tmp.name)
+
+        os.makedirs(os.path.join(self.root, ".git"))  # the repo marker
+        skip = shutil.ignore_patterns("__pycache__")
+        shutil.copytree(ISSUE_SCRIPTS, self.path("skills", "issue", "scripts"), ignore=skip)
+        shutil.copytree(SYNC_SCRIPTS, self.path("skills", "sync", "scripts"), ignore=skip)
+        os.makedirs(self.path("sub", "deeper"))
+
+        if with_store:
+            os.makedirs(self.store)
+            for text in issues:
+                id = text.split("id: ", 1)[1].split("\n", 1)[0]
+                with open(os.path.join(self.store, "%s.md" % id), "w") as f:
+                    f.write(text)
+
+    def cleanup(self):
+        self._tmp.cleanup()
+
+    def path(self, *parts):
+        return os.path.join(self.root, *parts)
+
+    @property
+    def store(self):
+        return self.path("tmp", "issues")
+
+    def script(self, layer, name):
+        return self.path("skills", layer, "scripts", name)
+
+    def everywhere(self):
+        """Working directories that must all produce the same answer: the repo
+        root, a plain subdirectory, a deeper one, the script directory itself,
+        and — the case from the bug report — inside the store."""
+        return [self.root, self.path("sub"), self.path("sub", "deeper"),
+                self.path("skills", "issue", "scripts"), self.store]
+
+
+# --------------------------------------------------------------------------
+# resolution, in isolation
+# --------------------------------------------------------------------------
+
+class TestResolution(unittest.TestCase):
+
+    def setUp(self):
+        self.repo = FakeRepo()
+        self.addCleanup(self.repo.cleanup)
+
+    def test_repo_root_found_from_any_depth(self):
+        for start in self.repo.everywhere():
+            self.assertEqual(issue.repo_root(start), self.repo.root, start)
+
+    def test_agents_md_works_as_a_marker(self):
+        """A checkout without .git — the plugin copied out of git — still
+        resolves, because AGENTS.md marks the root too."""
+        shutil.rmtree(self.repo.path(".git"))
+        open(self.repo.path("AGENTS.md"), "w").close()
+        self.assertEqual(issue.repo_root(self.repo.path("sub", "deeper")),
+                         self.repo.root)
+
+    def test_nearest_marker_wins(self):
+        """A repo inside a repo (a worktree, a vendored copy) resolves to the
+        inner one, not the outer."""
+        inner = self.repo.path("sub", "inner")
+        os.makedirs(os.path.join(inner, ".git"))
+        self.assertEqual(issue.repo_root(inner), inner)
+        self.assertEqual(issue.repo_root(self.repo.root), self.repo.root)
+
+    def test_store_root_is_repo_root_plus_tmp_issues(self):
+        self.assertEqual(issue.store_root(self.repo.path("sub", "deeper")),
+                         self.repo.store)
+
+    def test_default_root_is_absolute(self):
+        """The whole point: a default that cannot mean two directories."""
+        self.assertTrue(os.path.isabs(issue.ISSUE_ROOT), issue.ISSUE_ROOT)
+        self.assertEqual(issue.ISSUE_ROOT,
+                         os.path.join(REPO, "tmp", "issues"))
+
+
+# --------------------------------------------------------------------------
+# the acceptance criterion: same answer from any subdirectory
+# --------------------------------------------------------------------------
+
+class TestSameFromAnywhere(unittest.TestCase):
+
+    def setUp(self):
+        self.repo = FakeRepo()
+        self.addCleanup(self.repo.cleanup)
+
+    def assertSameEverywhere(self, layer, name, *args):
+        """Run the script from the repo root and from every other directory;
+        every result must be byte-identical to the one from the root."""
+        dirs = self.repo.everywhere()
+        base = run(self.repo.script(layer, name), *args, cwd=dirs[0])
+        self.assertEqual(base[0], 0, "%s failed at the repo root:\n%s" % (name, base[2]))
+        for d in dirs[1:]:
+            self.assertEqual(run(self.repo.script(layer, name), *args, cwd=d), base,
+                             "%s disagrees when run from %s" % (name, d))
+        return base
+
+    def test_issue_check(self):
+        rc, out, _ = self.assertSameEverywhere("issue", "issue_check.py")
+        self.assertIn("ok    alpha-issue", out)
+        self.assertIn("2 issue(s) checked, 0 with errors", out)
+
+    def test_issue_tree(self):
+        _, out, _ = self.assertSameEverywhere("issue", "issue_tree.py")
+        self.assertIn("beta-issue", out)
+        self.assertIn("alpha-issue", out)
+
+    def test_issue_index(self):
+        _, out, _ = self.assertSameEverywhere("issue", "issue_index.py")
+        self.assertIn("2 issue(s)", out)
+        self.assertIn(os.path.join(self.repo.store, "INDEX.md"), out)
+
+    def test_no_second_store_is_ever_created(self):
+        """The bug's worst symptom: `issue_index.py` run from inside the store
+        used to leave tmp/issues/tmp/issues/ behind, silently."""
+        for d in self.repo.everywhere():
+            for name in ("issue_index.py", "issue_check.py", "issue_tree.py"):
+                run(self.repo.script("issue", name), cwd=d)
+
+        found = []
+        for dirpath, dirnames, filenames in os.walk(self.repo.root):
+            if "__pycache__" in dirnames:
+                dirnames.remove("__pycache__")
+            if "INDEX.md" in filenames:
+                found.append(dirpath)
+        self.assertEqual(found, [self.repo.store],
+                         "a second store appeared: %s" % found)
+
+
+# --------------------------------------------------------------------------
+# missing is not empty
+# --------------------------------------------------------------------------
+
+class TestMissingVersusEmpty(unittest.TestCase):
+
+    def test_missing_store_says_missing(self):
+        repo = FakeRepo(with_store=False)
+        self.addCleanup(repo.cleanup)
+        for name in ("issue_check.py", "issue_tree.py", "issue_index.py"):
+            rc, out, err = run(repo.script("issue", name), cwd=repo.root)
+            msg = out + err
+            self.assertNotEqual(rc, 0, "%s should fail on a missing store" % name)
+            self.assertIn("does not exist", msg, name)
+            self.assertNotIn("is empty", msg, name)
+
+    def test_empty_store_says_empty(self):
+        repo = FakeRepo(issues=())
+        self.addCleanup(repo.cleanup)
+        for name in ("issue_check.py", "issue_tree.py"):
+            rc, out, err = run(repo.script("issue", name), cwd=repo.root)
+            msg = out + err
+            self.assertNotEqual(rc, 0, name)
+            self.assertIn("is empty", msg, name)
+            self.assertNotIn("does not exist", msg, name)
+
+    def test_index_of_an_empty_store_is_legitimate(self):
+        """An existing store with nothing in it gets an index saying so. Only a
+        missing directory is an error."""
+        repo = FakeRepo(issues=())
+        self.addCleanup(repo.cleanup)
+        rc, out, err = run(repo.script("issue", "issue_index.py"), cwd=repo.root)
+        self.assertEqual(rc, 0, err)
+        self.assertIn("0 issue(s)", out)
+        with open(os.path.join(repo.store, "INDEX.md")) as f:
+            self.assertIn("_empty_", f.read())
+
+
+# --------------------------------------------------------------------------
+# nothing conjures a store
+# --------------------------------------------------------------------------
+
+class TestNoSilentCreation(unittest.TestCase):
+
+    def setUp(self):
+        self.repo = FakeRepo(with_store=False)
+        self.addCleanup(self.repo.cleanup)
+
+    def test_readers_and_the_indexer_create_nothing(self):
+        for d in (self.repo.root, self.repo.path("sub")):
+            for name in ("issue_check.py", "issue_tree.py", "issue_index.py"):
+                run(self.repo.script("issue", name), cwd=d)
+        self.assertFalse(os.path.exists(self.repo.path("tmp")),
+                         "the store was created by a read")
+        self.assertFalse(os.path.exists(self.repo.path("sub", "tmp")),
+                         "a store was created relative to cwd")
+
+    def test_explicit_out_pointing_nowhere_is_an_error_not_a_mkdir(self):
+        target = self.repo.path("sub", "nowhere")
+        rc, out, err = run(self.repo.script("issue", "issue_index.py"),
+                           "--out", target, cwd=self.repo.root)
+        self.assertNotEqual(rc, 0)
+        self.assertIn("does not exist", out + err)
+        self.assertFalse(os.path.exists(target))
+
+    def test_issue_new_creates_the_store_and_says_so(self):
+        """Creating the first issue in a fresh checkout must still work — but
+        out loud, and at the repo root, not below whatever cwd happens to be."""
+        rc, out, err = run(self.repo.script("issue", "issue_new.py"),
+                           "--type", "task", "--title", "Bootstrap the store",
+                           cwd=self.repo.path("sub", "deeper"))
+        self.assertEqual(rc, 0, err)
+        self.assertIn("created store", err)
+        self.assertIn(self.repo.store, err)
+        self.assertTrue(os.path.isfile(
+            os.path.join(self.repo.store, "bootstrap-the-store.md")))
+        self.assertFalse(os.path.exists(self.repo.path("sub", "deeper", "tmp")),
+                         "a store was created relative to cwd")
+
+
+# --------------------------------------------------------------------------
+# an explicit --out is the operator's, not ours to rewrite
+# --------------------------------------------------------------------------
+
+class TestExplicitOutWins(unittest.TestCase):
+
+    def setUp(self):
+        self.repo = FakeRepo()
+        self.addCleanup(self.repo.cleanup)
+
+    def test_absolute_out_is_honored(self):
+        other = self.repo.path("sub", "other-store")
+        os.makedirs(other)
+        shutil.copy(os.path.join(self.repo.store, "alpha-issue.md"), other)
+        rc, out, err = run(self.repo.script("issue", "issue_check.py"),
+                           "--out", other, cwd=self.repo.root)
+        self.assertEqual(rc, 0, err)
+        self.assertIn("1 issue(s) checked", out)
+
+    def test_relative_out_stays_relative_to_cwd(self):
+        """`--out tmp/issues` typed from a subdirectory means that
+        subdirectory's tmp/issues — which is not there. Auto-resolution must
+        not step in and "fix" what the operator typed."""
+        rc, out, err = run(self.repo.script("issue", "issue_check.py"),
+                           "--out", os.path.join("tmp", "issues"),
+                           cwd=self.repo.path("sub"))
+        self.assertNotEqual(rc, 0)
+        self.assertIn("does not exist", out + err)
+
+        # the same relative path from the root does resolve, by cwd alone
+        rc, out, err = run(self.repo.script("issue", "issue_check.py"),
+                           "--out", os.path.join("tmp", "issues"),
+                           cwd=self.repo.root)
+        self.assertEqual(rc, 0, err)
+        self.assertIn("2 issue(s) checked", out)
+
+    def test_relative_out_can_climb(self):
+        rc, out, err = run(self.repo.script("issue", "issue_check.py"),
+                           "--out", os.path.join("..", "tmp", "issues"),
+                           cwd=self.repo.path("sub"))
+        self.assertEqual(rc, 0, err)
+        self.assertIn("2 issue(s) checked", out)
+
+
+# --------------------------------------------------------------------------
+# both layers, one root
+# --------------------------------------------------------------------------
+
+class TestSyncLayerAgrees(unittest.TestCase):
+
+    def setUp(self):
+        self.repo = FakeRepo()
+        self.addCleanup(self.repo.cleanup)
+
+    def _probe(self, layer, cwd):
+        """Ask one layer, from `cwd`, which module defines the store and where
+        it lands. The sync scripts put the issue scripts on sys.path themselves
+        — `import map` is how they do it — so each layer is asked its own way.
+        """
+        scripts = self.repo.path("skills", layer, "scripts")
+        entry = "import map, issue" if layer == "sync" else "import issue"
+        code = ("import sys; sys.path.insert(0, %r)\n%s\n"
+                "print(issue.__file__)\nprint(issue.ISSUE_ROOT)\n") % (scripts, entry)
+        env = dict(os.environ)
+        env.pop("PYTHONPATH", None)
+        p = subprocess.run([sys.executable, "-c", code], cwd=cwd, env=env,
+                           capture_output=True, text=True)
+        self.assertEqual(p.returncode, 0, p.stderr)
+        return p.stdout.strip().splitlines()
+
+    def test_both_layers_resolve_the_same_store_from_anywhere(self):
+        for d in self.repo.everywhere():
+            mod_i, root_i = self._probe("issue", d)
+            mod_s, root_s = self._probe("sync", d)
+            # sync does not redefine the store; it imports the domain module
+            self.assertEqual(os.path.realpath(mod_i), os.path.realpath(mod_s), d)
+            self.assertEqual(root_i, self.repo.store, d)
+            self.assertEqual(root_s, self.repo.store, d)
+
+    def test_every_out_flag_defers_to_the_domain_layer(self):
+        """Both layers agree by construction, not by coincidence: no script
+        spells the default out for itself."""
+        for layer, names in (("issue", ("issue_new.py", "issue_check.py",
+                                        "issue_tree.py", "issue_index.py")),
+                             ("sync", ("pull.py", "push.py", "remote.py",
+                                       "comment.py"))):
+            for name in names:
+                with open(os.path.join(REPO, "skills", layer, "scripts", name)) as f:
+                    src = f.read()
+                self.assertIn('"--out", default=issue.ISSUE_ROOT', src,
+                              "%s/%s does not take its --out default from the "
+                              "domain layer" % (layer, name))
+
+
+# --------------------------------------------------------------------------
+# the layering rule, mechanically
+# --------------------------------------------------------------------------
+
+class TestLayering(unittest.TestCase):
+
+    def test_domain_layer_is_stdlib_only(self):
+        """skills/issue must keep working with skills/sync deleted — so no
+        transport, and above all no subprocess, in the domain layer."""
+        imported = set()
+        for name in sorted(os.listdir(ISSUE_SCRIPTS)):
+            if not name.endswith(".py"):
+                continue
+            with open(os.path.join(ISSUE_SCRIPTS, name)) as f:
+                for line in f:
+                    if line.startswith(("import ", "from ")):
+                        imported.add(line.split()[1].split(".")[0])
+        local = {"issue", "issue_index"}
+        self.assertEqual(imported - local, {"argparse", "os", "re", "sys"},
+                         "non-stdlib or unexpected import in the domain layer")
+        self.assertNotIn("subprocess", imported)
+
+
+if __name__ == "__main__":
+    unittest.main()