threadkeeper 0.17.4__tar.gz → 0.17.6__tar.gz

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: threadkeeper
-Version: 0.17.4
+Version: 0.17.6
 Summary: Multi-agent shared brain across Claude Code/Desktop, Codex, Antigravity CLI, Copilot, and VS Code. Cross-session memory, self-improving skill loops, inter-agent signaling — one local MCP server.
 Author: thread-keeper contributors
 License: MIT
@@ -137,6 +137,9 @@ config, copies hooks to
 each CLI's per-user instructions file (`CLAUDE.md` / `AGENTS.md` /
 `copilot-instructions.md` — Claude Desktop and VS Code
 have no global instructions file, so that step is skipped for them).
+The generated MCP entry pins imports to this configured installation, so an
+agent launched inside another thread-keeper checkout cannot load that checkout's
+unmerged code against the live memory database.
 
 Restart your CLI of choice. Hook-capable clients inject a brief on the first
 message; hookless clients such as Codex and Antigravity CLI either follow the
@@ -217,7 +220,7 @@ read/act split, plus MCP elicitation for host-native confirmations:
 
 | Primitive | Control | What thread-keeper exposes | When to use |
 |---|---|---|---|
-| **Tools** | model-controlled (may act) | the full surface — `brief`, `note`, `spawn`, `search`, `curator_review`, … | the agent decides to call them |
+| **Tools** | model-controlled (may act) | the full surface — `brief`, `note`, `spawn`, `search`, `curator_review`, `wikilink_health`, … | the agent decides to call them |
 | **Resources** | application-controlled, read-only | `memory://brief`, `memory://context`, `memory://dashboard`, `memory://agent-status` | the **host** attaches/pulls them automatically |
 | **Prompts** | user-controlled templates | `review_recent_threads`, `run_library_curation`, `audit_threadkeeper` | the user runs them (Claude Code: `/mcp__thread-keeper__<name>`) |
 
@@ -611,7 +614,14 @@ can correct one unique substring without reserializing a lesson. Shadow-origin
 though an existing same-slug long lesson may be corrected without increasing
 its body size; near-duplicate slugs are blocked, and semantic body matches are
 routed to the incumbent lesson or surfaced for curation instead of minting a
-sibling lesson.
+sibling lesson. A clear new directive or debunk also flags older permissive
+lessons on the same concrete practice for patch, cross-link, or supersession
+review.
+Before a genuinely new fallback lesson is written,
+`lesson_neighbors(title, body, summary, k=3)` shows the nearest existing lesson
+slugs (semantic, with a lexical fallback). Shadow and candidate reviewers use
+that preflight to patch/consolidate an incumbent or add a `[[slug]]` cross-link
+to a related, distinct lesson while its body is still editable.
 
 #### 3. Extract daemon
 
@@ -716,6 +726,14 @@ non-forced direct `curator_review()` calls return `not_due` inside the
 configured interval and record that status without spawning. A manual
 `curator_review(force=True)` bypasses the interval but still respects the lock.
 
+When a Curator reviews a lesson pair and deliberately keeps both, it records a
+structured `keep_both` merge verdict with the two slugs and a short reason.
+Later inventories show those prior verdicts and each lesson's current
+bidirectional `[[wikilink]]` adjacency (`links=[...]`), including for the
+relevant side of a multi-batch review. This preserves intentional
+general/specific and prevention/recovery layering without making a child
+re-read both lesson bodies to rediscover it.
+
 For automation-created skills, the audit keeps foreground consultation separate
 from maintenance: a background-review skill with `fg_uses=0` after 14 days is
 still a false-positive prune candidate even if automatic review or sync loops

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/README.md

@@ -93,6 +93,9 @@ config, copies hooks to
 each CLI's per-user instructions file (`CLAUDE.md` / `AGENTS.md` /
 `copilot-instructions.md` — Claude Desktop and VS Code
 have no global instructions file, so that step is skipped for them).
+The generated MCP entry pins imports to this configured installation, so an
+agent launched inside another thread-keeper checkout cannot load that checkout's
+unmerged code against the live memory database.
 
 Restart your CLI of choice. Hook-capable clients inject a brief on the first
 message; hookless clients such as Codex and Antigravity CLI either follow the
@@ -173,7 +176,7 @@ read/act split, plus MCP elicitation for host-native confirmations:
 
 | Primitive | Control | What thread-keeper exposes | When to use |
 |---|---|---|---|
-| **Tools** | model-controlled (may act) | the full surface — `brief`, `note`, `spawn`, `search`, `curator_review`, … | the agent decides to call them |
+| **Tools** | model-controlled (may act) | the full surface — `brief`, `note`, `spawn`, `search`, `curator_review`, `wikilink_health`, … | the agent decides to call them |
 | **Resources** | application-controlled, read-only | `memory://brief`, `memory://context`, `memory://dashboard`, `memory://agent-status` | the **host** attaches/pulls them automatically |
 | **Prompts** | user-controlled templates | `review_recent_threads`, `run_library_curation`, `audit_threadkeeper` | the user runs them (Claude Code: `/mcp__thread-keeper__<name>`) |
 
@@ -567,7 +570,14 @@ can correct one unique substring without reserializing a lesson. Shadow-origin
 though an existing same-slug long lesson may be corrected without increasing
 its body size; near-duplicate slugs are blocked, and semantic body matches are
 routed to the incumbent lesson or surfaced for curation instead of minting a
-sibling lesson.
+sibling lesson. A clear new directive or debunk also flags older permissive
+lessons on the same concrete practice for patch, cross-link, or supersession
+review.
+Before a genuinely new fallback lesson is written,
+`lesson_neighbors(title, body, summary, k=3)` shows the nearest existing lesson
+slugs (semantic, with a lexical fallback). Shadow and candidate reviewers use
+that preflight to patch/consolidate an incumbent or add a `[[slug]]` cross-link
+to a related, distinct lesson while its body is still editable.
 
 #### 3. Extract daemon
 
@@ -672,6 +682,14 @@ non-forced direct `curator_review()` calls return `not_due` inside the
 configured interval and record that status without spawning. A manual
 `curator_review(force=True)` bypasses the interval but still respects the lock.
 
+When a Curator reviews a lesson pair and deliberately keeps both, it records a
+structured `keep_both` merge verdict with the two slugs and a short reason.
+Later inventories show those prior verdicts and each lesson's current
+bidirectional `[[wikilink]]` adjacency (`links=[...]`), including for the
+relevant side of a multi-batch review. This preserves intentional
+general/specific and prevention/recovery layering without making a child
+re-read both lesson bodies to rediscover it.
+
 For automation-created skills, the audit keeps foreground consultation separate
 from maintenance: a background-review skill with `fg_uses=0` after 14 days is
 still a false-positive prune candidate even if automatic review or sync loops

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "threadkeeper"
-version = "0.17.4"
+version = "0.17.6"
 description = "Multi-agent shared brain across Claude Code/Desktop, Codex, Antigravity CLI, Copilot, and VS Code. Cross-session memory, self-improving skill loops, inter-agent signaling — one local MCP server."
 requires-python = ">=3.11"
 authors = [{ name = "thread-keeper contributors" }]

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_adapters.py

@@ -383,6 +383,7 @@ def test_codex_spawn_argv_skips_git_repo_check(tmp_path, monkeypatch):
     assert argv[:3] == ["/usr/local/bin/codex", "exec", "--skip-git-repo-check"]
     assert argv[-1] == "-"
     assert "-m" in argv and "gpt-5.5" in argv
+    assert 'mcp_servers.thread-keeper.env.PYTHONSAFEPATH="1"' in argv
     # Default (non-bypass) path still sandboxes.
     assert "--sandbox" in argv and "workspace-write" in argv
 

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_candidate_reviewer.py

@@ -203,6 +203,8 @@ def test_run_spawns_when_threshold_met(tmp_path, monkeypatch):
     assert "skill_manage" in allowed
     assert "accept_candidate" in allowed
     assert "reject_candidate" in allowed
+    assert "lesson_neighbors(title=<prospective>" in kw["prompt"]
+    assert "lesson_neighbors" in allowed
     assert "Bash" not in allowed
     # De-privileged (issue #76): no bare Read/Write/Edit — only the
     # path-scoped skill/lesson/candidate MCP tools.

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_curator.py

@@ -152,15 +152,15 @@ def test_collect_inventory_counts_lessons_and_skills(tmp_path, monkeypatch):
     conn.execute(
         "INSERT INTO skill_usage "
         "(name, created_at, created_by_origin, last_used_at, "
-        " use_count, pinned, state) "
-        "VALUES (?, ?, 'foreground', ?, 5, 1, 'active')",
+        " use_count, foreground_use_count, view_count, pinned, state) "
+        "VALUES (?, ?, 'foreground', ?, 5, 4, 3, 1, 'active')",
         ("pinned-skill", now - 86400, now - 3600),
     )
     conn.execute(
         "INSERT INTO skill_usage "
         "(name, created_at, created_by_origin, last_used_at, "
-        " use_count, state) "
-        "VALUES (?, ?, 'background_review', ?, 2, 'active')",
+        " use_count, foreground_use_count, view_count, state) "
+        "VALUES (?, ?, 'background_review', ?, 2, 1, 6, 'active')",
         ("auto-created-skill", now - 172800, now - 7200),
     )
     conn.commit()
@@ -177,6 +177,8 @@ def test_collect_inventory_counts_lessons_and_skills(tmp_path, monkeypatch):
     # background_review skill (not pinned) is NOT protected
     assert "SKILL auto-created-skill [PROTECTED]" not in dump
     assert "SKILL auto-created-skill" in dump
+    assert "fg_uses=4 uses=5 views=3 maintenance_patches=0" in dump
+    assert "fg_uses=1 uses=2 views=6 maintenance_patches=0" in dump
     assert "STALE LESSONS (dry-run decay ranking)" in dump
 
 
@@ -279,6 +281,64 @@ def test_collect_inventory_preview_truncates_large_store(tmp_path, monkeypatch):
     assert "live curator pass reviews complete bounded batches" in dump
 
 
+def test_curator_reuses_merge_verdicts_and_wikilink_adjacency(
+    tmp_path, monkeypatch,
+):
+    """A later pass receives durable keep-both context without body reads."""
+    pkg = _bootstrap(tmp_path, monkeypatch, min_lessons="2")
+    pkg["lessons"].append_lesson(
+        title="general-prevention",
+        body="The broad guard points to [[specific-recovery]].",
+        source="shadow",
+    )
+    pkg["lessons"].append_lesson(
+        title="specific-recovery",
+        body="The repair path points to [[general-prevention]].",
+        source="shadow",
+    )
+
+    import threadkeeper.tools.spawn as spawn_mod
+    captured: list[dict] = []
+
+    def fake_spawn(**kwargs):
+        captured.append(kwargs)
+        return f"spawn task_id=curator-{len(captured)} pid=0"
+
+    monkeypatch.setattr(spawn_mod, "spawn", fake_spawn)
+    assert "curator-1" in pkg["curator"].run_curator_pass(force=True)
+
+    from threadkeeper._mcp import mcp
+    verdict = mcp._tool_manager._tools["curator_merge_verdict"].fn
+    out = verdict(
+        "specific-recovery",
+        "general-prevention",
+        "prevention/recovery",
+    )
+    assert out == (
+        "ok merge_verdict=general-prevention,specific-recovery "
+        "decision=keep_both"
+    )
+
+    assert "curator-2" in pkg["curator"].run_curator_pass(force=True)
+    prompt = captured[-1]["prompt"]
+    assert "general-prevention" in prompt
+    assert "specific-recovery" in prompt
+    assert "links=[specific-recovery]" in prompt
+    assert "links=[general-prevention]" in prompt
+    assert "## PRIOR MERGE VERDICTS (n=1)" in prompt
+    assert "decision=keep_both reason=prevention/recovery" in prompt
+
+    conn = pkg["db"].get_db()
+    row = conn.execute(
+        "SELECT left_slug, right_slug, decision, reason "
+        "FROM curator_merge_verdicts"
+    ).fetchone()
+    assert tuple(row) == (
+        "general-prevention", "specific-recovery", "keep_both",
+        "prevention/recovery",
+    )
+
+
 # ──────────────────────────────────────────────────────────────────────
 # run_curator_pass — dispatch logic
 # ──────────────────────────────────────────────────────────────────────
@@ -362,6 +422,7 @@ def test_run_curator_pass_spawns_when_threshold_met(tmp_path, monkeypatch):
     assert "evolve_format" in allowed
     assert "Read" in allowed
     assert "curator_report_write" in allowed
+    assert "curator_merge_verdict" in allowed
     assert "Write" not in allowed
     assert "WebSearch" in allowed
     assert "WebFetch" in allowed
@@ -914,6 +975,68 @@ def test_skill_validate_tool_returns_post_change_contract(tmp_path, monkeypatch)
     }
 
 
+def test_wikilink_health_reports_dangling_lesson_and_skill_links(
+    tmp_path, monkeypatch,
+):
+    pkg = _bootstrap(tmp_path, monkeypatch)
+    pkg["lessons"].append_lesson(
+        title="valid lesson",
+        body="Available target.",
+        source="shadow",
+    )
+    pkg["lessons"].append_lesson(
+        title="lesson source",
+        body="See [[valid-lesson]] and [[missing-lesson]].",
+        source="shadow",
+    )
+    _write_audit_skill(
+        pkg["skills_dir"], "skill-source",
+        "See [[valid-lesson]] and [[missing-skill]].",
+    )
+    conn = pkg["db"].get_db()
+
+    from threadkeeper.link_health import scan_wikilink_health
+
+    result = scan_wikilink_health(conn)
+
+    assert result["summary"] == {
+        "lessons_scanned": 2,
+        "skills_scanned": 1,
+        "references_scanned": 4,
+        "dangling_references": 2,
+    }
+    assert result["dangling_references"] == [
+        {
+            "source_kind": "lesson",
+            "source": "lesson-source",
+            "target": "missing-lesson",
+        },
+        {
+            "source_kind": "skill",
+            "source": "skill-source",
+            "target": "missing-skill",
+        },
+    ]
+
+
+def test_wikilink_health_tool_exposes_checker_result(tmp_path, monkeypatch):
+    pkg = _bootstrap(tmp_path, monkeypatch)
+    pkg["lessons"].append_lesson(
+        title="lesson source", body="See [[missing-target]].", source="shadow",
+    )
+    from threadkeeper._mcp import mcp
+
+    result = mcp._tool_manager._tools["wikilink_health"].fn()
+    payload = json.loads(result)
+
+    assert payload["summary"]["dangling_references"] == 1
+    assert payload["dangling_references"] == [{
+        "source_kind": "lesson",
+        "source": "lesson-source",
+        "target": "missing-target",
+    }]
+
+
 def test_curator_report_write_is_path_scoped_and_replaceable(
     tmp_path, monkeypatch,
 ):

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_lessons.py

@@ -205,6 +205,73 @@ def test_mcp_lesson_append_validates_inputs(tmp_path, monkeypatch):
     assert out.startswith("ok slug=ok-one")
 
 
+def test_lesson_neighbors_previews_ranked_slugs_without_writing(
+    tmp_path, monkeypatch,
+):
+    pkg = _bootstrap(tmp_path, monkeypatch)
+    la = _tool(pkg, "lesson_append")
+    ln = _tool(pkg, "lesson_neighbors")
+    la(title="reset ios network", body="Reset iOS simulator network settings.")
+    la(title="serialize device boot", body="Serialize device boot locks.")
+    la(title="unrelated release notes", body="Document release notes.")
+
+    import threadkeeper.embeddings as embeddings
+
+    monkeypatch.setattr(
+        embeddings,
+        "encode_many",
+        lambda texts: [[1.0, 0.0], [0.96, 0.0], [0.83, 0.0], [0.40, 0.0]],
+    )
+
+    out = ln(
+        title="recover simulator connectivity",
+        summary="Restore device networking before a test run.",
+        body="Reset simulator network settings before retrying device tests.",
+        k=2,
+    )
+
+    assert out.splitlines() == [
+        "lesson_neighbors total=2 mode=semantic prospective_slug=recover-simulator-connectivity",
+        "  1. reset-ios-network score=0.96",
+        "  2. serialize-device-boot score=0.83",
+    ]
+    assert pkg["lessons"].count_lessons() == 3
+
+
+def test_lesson_neighbors_leaves_existing_lesson_write_semantics_unchanged(
+    tmp_path, monkeypatch,
+):
+    pkg = _bootstrap(tmp_path, monkeypatch)
+    ln = _tool(pkg, "lesson_neighbors")
+    la = _tool(pkg, "lesson_append")
+
+    assert ln(title="new lesson", body="new body") == (
+        "lesson_neighbors total=0 mode=semantic"
+    )
+    assert la(title="new lesson", body="new body") == (
+        f"ok slug=new-lesson path={pkg['path']}"
+    )
+
+
+def test_lesson_neighbors_falls_back_to_lexical_ranking(tmp_path, monkeypatch):
+    pkg = _bootstrap(tmp_path, monkeypatch)
+    la = _tool(pkg, "lesson_append")
+    ln = _tool(pkg, "lesson_neighbors")
+    la(
+        title="reset simulator network",
+        body="Reset simulator network settings before device tests.",
+    )
+    import threadkeeper.embeddings as embeddings
+
+    monkeypatch.setattr(embeddings, "encode_many", lambda texts: None)
+    out = ln(
+        title="repair simulator connectivity",
+        body="Reset simulator network before retrying device tests.",
+    )
+    assert "mode=lexical" in out
+    assert "reset-simulator-network" in out
+
+
 def test_mcp_lesson_patch_replaces_one_unique_substring(tmp_path, monkeypatch):
     pkg = _bootstrap(tmp_path, monkeypatch)
     la = _tool(pkg, "lesson_append")
@@ -356,6 +423,74 @@ def test_shadow_lesson_append_semantic_duplicate_patches_incumbent(
     assert "serialize AVD boot lock acquisition" in body
 
 
+def test_new_directive_flags_older_permissive_lesson_for_reconciliation(
+    tmp_path, monkeypatch,
+):
+    pkg = _bootstrap(tmp_path, monkeypatch, write_origin="shadow_review")
+    la = _tool(pkg, "lesson_append")
+
+    first = la(
+        title="module globals for test configuration",
+        body=(
+            "You can use module globals to pass test configuration between "
+            "runner steps when setup is simple."
+        ),
+        source="shadow",
+    )
+    assert first.startswith("ok")
+
+    out = la(
+        title="inject test configuration explicitly",
+        body=(
+            "Never use module globals to pass test configuration between "
+            "runner steps; inject dependencies explicitly instead."
+        ),
+        source="shadow",
+    )
+
+    assert out.startswith("ok slug=inject-test-configuration-explicitly")
+    assert "reconciliation=module-globals-for-test-configuration" in out
+    assert "review=patch_or_cross_link" in out
+    assert pkg["lessons"].count_lessons() == 2
+    row = pkg["db"].get_db().execute(
+        "SELECT target, summary FROM events WHERE kind='lesson_reconciliation'"
+    ).fetchone()
+    assert row["target"] == "module-globals-for-test-configuration"
+    assert "new=inject-test-configuration-explicitly" in row["summary"]
+    assert "reason=absolute_directive" in row["summary"]
+
+
+def test_new_debunk_flags_older_permissive_lesson_for_reconciliation(
+    tmp_path, monkeypatch,
+):
+    pkg = _bootstrap(tmp_path, monkeypatch, write_origin="shadow_review")
+    la = _tool(pkg, "lesson_append")
+
+    la(
+        title="shared runner environment state",
+        body=(
+            "It is safe to keep shared runner environment state throughout "
+            "a test workflow."
+        ),
+        source="shadow",
+    )
+
+    out = la(
+        title="shared runner environment state is unreliable",
+        body=(
+            "Keeping shared runner environment state is unreliable; pass the "
+            "environment to each command instead."
+        ),
+        source="shadow",
+    )
+
+    assert "reconciliation=shared-runner-environment-state" in out
+    row = pkg["db"].get_db().execute(
+        "SELECT summary FROM events WHERE kind='lesson_reconciliation'"
+    ).fetchone()
+    assert "reason=debunk" in row["summary"]
+
+
 def test_shadow_lesson_append_semantic_borderline_surfaces_duplicate(
     tmp_path, monkeypatch,
 ):

threadkeeper-0.17.6/tests/test_setup.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+
+def test_install_mcp_servers_pins_imports_to_configured_package(
+    tmp_path, monkeypatch,
+):
+    import threadkeeper._setup as setup_mod
+    import threadkeeper.adapters as adapters_mod
+
+    captured = {}
+
+    class FakeAdapter:
+        name = "fake"
+
+        def register_mcp_server(self, **kwargs):
+            captured.update(kwargs)
+            return "ok"
+
+    monkeypatch.setattr(setup_mod, "REPO_ROOT", tmp_path)
+    monkeypatch.setattr(
+        adapters_mod, "installed_adapters", lambda: [FakeAdapter()],
+    )
+
+    assert setup_mod.install_mcp_servers(dry_run=False) == [
+        "mcp_server[fake]: ok"
+    ]
+    assert captured["env"] == {
+        "PYTHONPATH": str(tmp_path),
+        "PYTHONSAFEPATH": "1",
+    }
+

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_shadow_review.py

@@ -373,8 +373,10 @@ def test_run_shadow_pass_spawns_when_threshold_met(tmp_path, monkeypatch):
     assert kw["write_origin"] == "shadow_review"
     assert "SHADOW LEARNING OBSERVER" in kw["prompt"]
     assert "lesson_list(k=80)" in kw["prompt"]
+    assert "lesson_neighbors(title=<prospective>" in kw["prompt"]
     assert "hard cap 450" in kw["prompt"]
     assert "mcp__thread-keeper__lesson_get" in kw["extra_allowed_tools"]
+    assert "mcp__thread-keeper__lesson_neighbors" in kw["extra_allowed_tools"]
     assert "mcp__thread-keeper__lesson_patch" in kw["extra_allowed_tools"]
     assert long_msg.strip()[:40] in kw["prompt"]
     # De-privileged (issue #76): no bare Read/Write — path-scoped skill/

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_skill_use_parser.py

@@ -182,11 +182,12 @@ def test_ingest_file_bumps_skill_usage(tmp_path, monkeypatch):
     conn.commit()
     assert added == 1
     row = conn.execute(
-        "SELECT use_count, last_used_at, created_by_origin "
+        "SELECT use_count, foreground_use_count, last_used_at, created_by_origin "
         "FROM skill_usage WHERE name='swift-ios'"
     ).fetchone()
     assert row is not None
     assert row["use_count"] == 1
+    assert row["foreground_use_count"] == 1
     assert row["last_used_at"] is not None
     assert row["created_by_origin"] == "foreground"
 

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_skills.py

@@ -466,6 +466,42 @@ def test_skill_record_bumps_counters(skills_pkg):
     assert r["last_viewed_at"] is not None
 
 
+def test_skill_list_records_views_for_returned_skills(skills_pkg):
+    _seed_skill(skills_pkg, name="listed-active")
+    _seed_skill(skills_pkg, name="listed-archived")
+    conn = skills_pkg["db"].get_db()
+    conn.execute(
+        "UPDATE skill_usage SET state='archived' WHERE name='listed-archived'"
+    )
+    conn.commit()
+
+    listed = _tool(skills_pkg, "skill_list")
+    rendered = listed()
+    assert "listed-active" in rendered
+    assert "views=1" in rendered
+    rows = {
+        row["name"]: row
+        for row in conn.execute(
+            "SELECT name, view_count, last_viewed_at FROM skill_usage "
+            "WHERE name IN ('listed-active', 'listed-archived')"
+        ).fetchall()
+    }
+    assert rows["listed-active"]["view_count"] == 1
+    assert rows["listed-active"]["last_viewed_at"] is not None
+    assert rows["listed-archived"]["view_count"] == 0
+
+    assert "listed-archived" in listed(include_archived=True)
+    rows = {
+        row["name"]: row
+        for row in conn.execute(
+            "SELECT name, view_count FROM skill_usage "
+            "WHERE name IN ('listed-active', 'listed-archived')"
+        ).fetchall()
+    }
+    assert rows["listed-active"]["view_count"] == 2
+    assert rows["listed-archived"]["view_count"] == 1
+
+
 def test_skill_list_omits_archived_by_default(skills_pkg):
     _seed_skill(skills_pkg, name="alive")
     _seed_skill(skills_pkg, name="ghost")

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_spawn_slim.py

@@ -59,6 +59,7 @@ def test_build_slim_mcp_config_from_claude_json(tmp_path, monkeypatch):
     assert mp["command"] == "/path/to/python"
     assert mp["args"] == ["-m", "threadkeeper.server"]
     assert mp["env"]["PYTHONPATH"] == "/path/to/repo"
+    assert mp["env"]["PYTHONSAFEPATH"] == "1"
     assert mp["env"]["THREADKEEPER_FORCE_CID"] == _FAKE_CID
     assert mp["env"]["THREADKEEPER_SPAWNED_CHILD"] == "1"
     assert mp["env"]["THREADKEEPER_NO_EMBEDDINGS"] == "1"
@@ -92,6 +93,7 @@ def test_build_slim_mcp_config_synthesizes_when_no_claude_json(tmp_path, monkeyp
     assert mp["command"] == sys.executable
     assert "threadkeeper.server" in mp["args"]
     assert "PYTHONPATH" in mp["env"]
+    assert mp["env"]["PYTHONSAFEPATH"] == "1"
     assert mp["env"]["THREADKEEPER_SPAWNED_CHILD"] == "1"
     assert mp["env"]["THREADKEEPER_NO_EMBEDDINGS"] == "1"
 
@@ -142,6 +144,7 @@ def test_slim_config_is_owner_only_and_minimizes_env(tmp_path, monkeypatch):
     env = json.loads(slim_path.read_text())["mcpServers"]["thread-keeper"]["env"]
     # Needed keys survive: package discovery + thread-keeper knobs + overrides.
     assert env["PYTHONPATH"] == "/path/to/repo"
+    assert env["PYTHONSAFEPATH"] == "1"
     assert env["THREADKEEPER_TZ"] == "Europe/Kyiv"
     assert env["THREADKEEPER_FORCE_CID"] == _FAKE_CID
     assert env["THREADKEEPER_NO_EMBEDDINGS"] == "1"

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/tests/test_tool_annotations.py

@@ -33,9 +33,10 @@ READ_TOOLS = {
     "memory_guard_status", "mp_dashboard", "mp_health", "neighbors", "peers",
     "pending_distillates", "pickup_candidates", "reliability_for",
     "review_candidates", "run_probe", "search", "shadow_review_status",
-    "skill_list", "skill_validate", "spawn_budget_status", "spawn_status",
+    "skill_validate", "spawn_budget_status", "spawn_status",
     "sync_peers", "sync_status", "task_logs",
-    "task_thread", "tasks", "weak_spots", "whoami",
+    "task_thread", "tasks", "weak_spots", "whoami", "wikilink_health",
+    "lesson_neighbors",
 }
 
 # --- delete/overwrite/kill tools: destructiveHint=True -----------------------
@@ -50,7 +51,8 @@ DELETE_CLASS_TOOLS = {
 WRITE_TOOLS = {
     "accept_candidate", "ask", "auto_review_trigger", "broadcast",
     "candidate_review_run", "claim_pickup", "close_thread", "config_reload",
-    "convene_panel", "core_set", "curator_report_write", "curator_review",
+    "convene_panel", "core_set", "curator_merge_verdict",
+    "curator_report_write", "curator_review",
     "db_compact", "db_deduplicate_embeddings", "dialectic_claim",
     "dialectic_evidence", "dialectic_mine_run", "dialectic_observation_resolve",
     "dialectic_supersede", "dialectic_validate_run", "distill", "evolve_apply",
@@ -65,7 +67,7 @@ WRITE_TOOLS = {
     "open_dialog_window", "open_thread", "presence", "record_attempt",
     "register_concept", "register_probe", "reject_candidate", "release_pickup",
     "respond", "review_thread", "search_via_parent", "session_end",
-    "shadow_review_run", "skill_record", "spawn", "spawn_budget_set",
+    "shadow_review_run", "skill_list", "skill_record", "spawn", "spawn_budget_set",
     "style_set", "sync_now", "tag_signal", "tournament", "validate_threads",
     "verbatim_user", "vote_distill", "wait", "whisper",
 }

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/threadkeeper/_setup.py

@@ -128,7 +128,14 @@ def install_mcp_servers(dry_run: bool) -> list[str]:
     if venv_python.exists():
         python_bin = str(venv_python)
     args = ["-m", "threadkeeper.server"]
-    env = {"PYTHONPATH": str(REPO_ROOT)}
+    env = {
+        "PYTHONPATH": str(REPO_ROOT),
+        # MCP clients often launch the server from the agent's current
+        # checkout.  Without safe-path mode, ``python -m`` puts that checkout
+        # ahead of the configured install and can import unmerged Evolve code
+        # against the live DB.
+        "PYTHONSAFEPATH": "1",
+    }
 
     lines: list[str] = []
     adapters = installed_adapters()

{threadkeeper-0.17.4 → threadkeeper-0.17.6}/threadkeeper/adapters/codex.py

@@ -337,6 +337,14 @@ class CodexAdapter(CLIAdapter):
         if {"websearch", "webfetch"} & requested_tools:
             argv.append("--search")
         argv += ["exec", "--skip-git-repo-check"]
+        # Codex launches configured stdio MCP servers from the agent cwd.  A
+        # repository checkout can therefore shadow the installed package used
+        # by thread-keeper's MCP entry.  Scope safe-path mode to the MCP server
+        # only; shell/test Python processes in the child keep normal semantics.
+        argv += [
+            "-c",
+            'mcp_servers.thread-keeper.env.PYTHONSAFEPATH="1"',
+        ]
         if model:
             argv += ["-m", model]
         if effort: