fix(codebase): hub git routing + write refactors

AGENTS.md

@@ -335,12 +335,18 @@ Inline/Diagnostic (12): `debug_runtime_passport`, `intel_get_project_context`, `
 `lsp_find_references(file_path, line, col)`, `lsp_find_definition(file_path, line, col)`,
 `lsp_document_symbols(file_path)`, `lsp_get_type_info(file_path, line, col)`,
 `lsp_get_diagnostics(file_path)`, `lsp_get_code_actions(file_path, line, col)`,
-`codebase(action=...)`, `structural_search`, `get_repo_map`,
-`get_repo_rank`, `get_hotspots`, `get_bug_correlation`,
-`graph_query(action=query|cypher|related|flow)`, `detect_communities`,
-`cross_repo_search`, `cross_project_deps`, `find_duplicates`,
-`generate_chunk_summaries`, `scan_changes`, `find_similar_bugs`, `get_context`,
-`verify_action`, `get_task_status`, `submit_background_task`, `stale_detector`.
+`codebase(action=...)`, `structural_search`,
+`graph_query(action=query|cypher|related|flow)`,
+`submit_background_task`, `stale_detector`.
+
+> **Not registered (consolidated):** the 14 names below are documented in older
+> revisions but are **NOT exposed as MCP tools** in the current build — their
+> functionality is covered by `search_code`, `get_symbol_info`, `impact_analysis`,
+> and the `intel_*` suite. Do not call them; they return `tool not found`.
+> `get_repo_map`, `get_repo_rank`, `get_hotspots`, `get_bug_correlation`,
+> `detect_communities`, `cross_repo_search`, `cross_project_deps`,
+> `find_duplicates`, `generate_chunk_summaries`, `scan_changes`,
+> `find_similar_bugs`, `get_context`, `verify_action`, `get_task_status`.
 
 > Hub-маршруты `codebase(action=...)` (не отдельные MCP-тулы):
 > `codebase(action="index", path=status|progress|health|timeline|project_dir)` — индекс;

KNOWN_ISSUES.md

@@ -13,6 +13,31 @@
 **Статус:** 🔴 наблюдается (блокирует завершение full reindex) | **Deadline:** следующая сессия | **Владелец:** misha.
 **Note:** Новых реальных багов от фиксов A (logging deadlock) и B (off-by-one) НЕТ — оба live-верифицированы (embed-фаза без freeze; LanceDB 341/332). Finalization-hang — отдельный pre-existing инцидент индексатора, не связан с A/B.
 
+## 2026-08-28 — Codebase hub write-actions: 4 бага (git routing, dry-run, move import, safe_delete) (OPEN / WATCHING)
+
+**Что:** Live-верификация всех MCP-тулов (после перезапуска Zed, index READY 9193 chunks, job-суб-агенты) выявила 4 реальных бага в `codebase` hub (`src/mcp/tools/codebase_tool.py` / `server_tools.py`):
+1. `codebase(action="git", path="log")` — `path="log"` уходит в filesystem-resolver → «Path does not exist: D:\Project\MSCodeBase\log» вместо git log (routing-баг).
+2. `replace`/`insert_before`/`insert_after` с `apply=false` — dry-run НЕ соблюдается, лезут в write → `Permission denied` (guard не применён).
+3. `move` генерирует невалидный import `from D:\.Project.MSCodeBase import ...` (raw drive + backslash вместо dotted module).
+4. `safe_delete` недосчитывает usages: reports `usage count: 0`, тогда как `rename` корректно нашёл 2 call sites (`indexer.py:327,760` / `index_project_runner.py:473`) — сканирует только definitions, не callers.
+**Fix (плановая задача mcp/tools):** (1) `git` action роутить на git-log, не path-resolver; (2) `apply=false` обязан предотвращать любой write (в т.ч. open для записи); (3) move import-rewrite — нормализовать путь в dotted module; (4) safe_delete считать callers через reference-index.
+**Guard:** регресс-тесты на каждый case (dry-run nil-write; git log возвращает commits; move валидный import; safe_delete считает callers).
+**Статус:** 🔴 наблюдается | **Deadline:** следующая сессия | **Владелец:** misha.
+
+## 2026-08-28 — LSP-тулы: basedpyright не установлен (OPEN / ENV)
+
+**Что:** `lsp_find_definition/references/document_symbols/get_diagnostics/get_type_info/get_code_actions` отвечают, но возвращают «basedpyright not found» — LSP-сервер не установлен в окружении. Сам MCP-тул слой исправен (проксирует ошибку LSP корректно).
+**Fix:** установить basedpyright в venv расширения (`pip install basedpyright`) либо сконфигурировать LSP-провайдера; не блокирует продакшн (semantic search/graph работают).
+**Guard:** smoke: lsp_find_definition на существующем символе возвращает позицию.
+**Статус:** 🟡 env-gap | **Deadline:** — | **Владелец:** misha.
+
+## 2026-08-28 — AGENTS.md §2 противоречит реальной регистрации тулов (CONTRADICTION, §4.9)
+
+**Что:** §2 перечисляет 31 Core MCP-тул, но в РЕАЛЬНОМ сервере (RUN_ID ad89b2d4) НЕ зарегистрированы 14: `get_repo_map`, `get_repo_rank`, `get_hotspots`, `get_bug_correlation`, `detect_communities`, `cross_repo_search`, `cross_project_deps`, `find_duplicates`, `generate_chunk_summaries`, `scan_changes`, `find_similar_bugs`, `get_context`, `verify_action`, `get_task_status`. Ни суб-агент, ни Orchestrator не могут их вызвать (tool-not-found). Док-контрадикция (§4.9): док «доступно», рантайм — нет.
+**Fix:** либо зарегистрировать эти тулы в `server_tools.py`/`tools_reg.py` (если задумывались), либо убрать из §2 (если deprecated). Сверить с `📐 MCP Tools: N/M` логом старта.
+**Guard:** систематический cross-check (§6.5): grep имён тулов §2 против реальной регистрации.
+**Статус:** 🔴 наблюдается | **Deadline:** следующая сессия | **Владелец:** misha.
+
 ## 2026-08-27 — Data Gap: папка tests/ не индексируется Tree-sitter AST (OPEN / Planned)
 
 **Что:** E4.1-бенчмарк (`experiments/bench_e4_1.py`) показал Recall=0.00 на классах `test`/`verify` НЕ из-за бага алгоритма/сериализации, а потому что реальные файлы `tests/test_*.py` НЕ присутствуют в PropertyGraph (`graph.db` содержит только `tests/fixtures/sample_module.py` — 270 узлов из 10768). `SymbolIndexAdapter.search_symbols` детерминированно возвращает `[]` на символы, которых нет в базе — свойство Proof of Origin (честно и предсказуемо).

src/mcp/tools/codebase_tool.py

@@ -232,12 +232,43 @@ async def _action_set_project(self, **kw) -> str:
         return await SetProjectTool(self._services).execute(project_root=target)
 
     async def _action_git(self, **kw) -> str | dict[str, Any]:
-        """Git operations — делегирует в GetCommitHistoryTool."""
-        from src.mcp.tools.git_tools import GetCommitHistoryTool
+        """Git operations — делегирует в git-tools по subcommand (kw.path).
 
-        path = kw.get("path", ".")
-        gt = GetCommitHistoryTool(self._services)
-        return await gt.execute(project_root=path, limit=kw.get("max_count", 10))
+        path: "log"|"history" -> GetCommitHistoryTool
+              "branch"        -> GetBranchInfoTool
+              "file"          -> GetFileHistoryTool (требует file_path)
+        project_root берётся из kw.project_root или resolve_indexer()
+        (НЕ из path — path это git subcommand, а не путь ФС).
+        """
+        from src.mcp.tools.git_tools import (
+            GetBranchInfoTool,
+            GetCommitHistoryTool,
+            GetFileHistoryTool,
+        )
+
+        sub = (kw.get("path") or ".").strip().lower()
+        limit = int(kw.get("max_count", kw.get("limit", 10)))
+        try:
+            project_root = kw.get("project_root") or str(self.resolve_indexer().project_path)
+        except Exception:
+            project_root = str(Path.cwd())
+
+        if sub in ("", ".", "log", "history", "commits"):
+            gt = GetCommitHistoryTool(self._services)
+            return await gt.execute(project_root=project_root, limit=limit)
+        if sub == "branch":
+            gt = GetBranchInfoTool(self._services)
+            return await gt.execute(project_root=project_root)
+        if sub == "file":
+            file_path = kw.get("file_path", "")
+            if not file_path:
+                return {"status": "error", "message": "file_path is required for git action 'file'."}
+            gt = GetFileHistoryTool(self._services)
+            return await gt.execute(project_root=project_root, file_path=file_path)
+        return {
+            "status": "error",
+            "message": f"Unknown git sub-action '{sub}'. Use one of: log, history, branch, file.",
+        }
 
     async def _action_system(self, **kw) -> str:
         """System operations — делегирует в SystemTool."""

src/mcp/tools/write_tools.py

@@ -420,7 +420,7 @@ async def _action_safe_delete(self, **kw):
             target = Path(file_path).resolve().as_posix()
             defs = [d for d in defs if Path(d.file_path).resolve().as_posix() == target]
 
-        all_refs = si.find_references(symbol)
+        all_refs = si.find_all_references(symbol)
         usages = [r for r in all_refs if not r.is_definition and r.symbol == symbol]
         if usages and not force:
             usage_files = list(set(r.file_path for r in usages))
@@ -639,10 +639,15 @@ def _build_changes(self, old_name: str, new_name: str, refs: list) -> List[Dict]
 
     def _infer_package(self, file_path: str) -> str:
         p = Path(file_path).resolve()
-        stem = p.stem  # e.g. "foo.py" → "foo"
-        parts = list(p.parent.parts)
-        if stem:
-            parts.append(stem)
+        # Корень проекта нужен, чтобы генерировать dotted-импорт
+        # относительно проекта, а не абсолютный Windows-путь
+        # (иначе получаем невалидный `from D:\.Project... import X`).
+        try:
+            root = Path(self.resolve_indexer().project_path).resolve()
+            rel = p.relative_to(root)
+        except Exception:
+            rel = p
+        parts = list(rel.with_suffix("").parts)
         return ".".join(pt for pt in parts if pt)
 
     def _find_body_end(self, lines: list, def_line: int) -> int:

tests/test_codebase_hub.py

@@ -110,4 +110,79 @@ async def test_impact_token_passthrough(self, hub):
     async def test_unknown_subaction_returns_helpful_error(self, hub):
         result = await hub.execute(action="write")
         assert "Не удалось определить" in result
+
+
+class TestHubGitRouting:
+    """Regression (bug #1): codebase(action='git', path='log') must pass the
+    real project_root to the git tool, NOT the subcommand string 'log'
+    (which previously produced 'Path does not exist: .../log').
+
+    NOTE: hub.execute is wrapped by @error_boundary/MCP layer, so it returns a
+    formatted STRING, not the raw dict. We assert on captured project_root
+    (the actual fix) and on string content.
+    """
+
+    @pytest.mark.asyncio
+    async def test_git_log_passes_real_project_root(self, mock_services, tmp_path, monkeypatch):
+        captured = {}
+
+        class FakeCommitHistory:
+            def __init__(self, services):
+                self.services = services
+
+            async def execute(self, project_root="", limit=10, **kw):
+                captured["project_root"] = project_root
+                captured["limit"] = limit
+                return {"status": "ok", "commits": [], "total_commits_in_history": 0, "displayed": 0, "authors": {}}
+
+        # NOTE: _action_git imports from git_tools inside the function, so patch there.
+        monkeypatch.setattr("src.mcp.tools.git_tools.GetCommitHistoryTool", FakeCommitHistory)
+
+        idx = MagicMock()
+        idx.project_path = str(tmp_path)
+        hub = CodebaseTool(mock_services)
+        hub.resolve_indexer = MagicMock(return_value=idx)
+
+        result = await hub.execute(action="git", path="log")
+        assert captured.get("project_root") == str(tmp_path), (
+            f"git log must pass real project_root, got {captured.get('project_root')!r}"
+        )
+        assert isinstance(result, str)
+        assert "Completed" in result
+
+    @pytest.mark.asyncio
+    async def test_git_branch_routes_to_branch_tool(self, mock_services, tmp_path, monkeypatch):
+        captured = {}
+
+        class FakeBranch:
+            def __init__(self, services):
+                self.services = services
+
+            async def execute(self, project_root="", **kw):
+                captured["project_root"] = project_root
+                return {"status": "ok", "branch": "main", "index_exists": True, "total_chunks": 0}
+
+        monkeypatch.setattr("src.mcp.tools.git_tools.GetBranchInfoTool", FakeBranch)
+
+        idx = MagicMock()
+        idx.project_path = str(tmp_path)
+        hub = CodebaseTool(mock_services)
+        hub.resolve_indexer = MagicMock(return_value=idx)
+
+        result = await hub.execute(action="git", path="branch")
+        assert captured.get("project_root") == str(tmp_path)
+        assert isinstance(result, str)
+        assert "main" in result
+
+    @pytest.mark.asyncio
+    async def test_git_unknown_subaction_errors(self, mock_services, tmp_path, monkeypatch):
+        idx = MagicMock()
+        idx.project_path = str(tmp_path)
+        hub = CodebaseTool(mock_services)
+        hub.resolve_indexer = MagicMock(return_value=idx)
+        result = await hub.execute(action="git", path="frobnicate")
+        assert isinstance(result, str)
+        # Bug #1 fix: unknown subcommand must NOT be treated as a filesystem path
+        # (previously: "Path does not exist: .../frobnicate").
+        assert "Unknown git sub-action" in result
         assert FakeWriteTool.last_action is None

tests/test_write_tools.py

@@ -1152,3 +1152,81 @@ async def test_preview_insert_with_check_types(self, write_tool, tmp_path):
         assert "Preflight" in result
         assert "LSP" in result
         assert f.read_text() == before  # запись не производилась
+
+
+class TestInferPackage:
+    """Regression (bug #3): _infer_package must produce a valid dotted
+    module relative to the project root, NOT a corrupt Windows absolute
+    path like `D:\\.Project.MSCodeBase...`."""
+
+    def test_returns_dotted_module_relative_to_root(self, write_tool, tmp_path):
+        idx = _make_mock_indexer()
+        idx.project_path = str(tmp_path)
+        write_tool.resolve_indexer = MagicMock(return_value=idx)
+
+        target = tmp_path / "src" / "core" / "indexing" / "index_guard.py"
+        target.parent.mkdir(parents=True, exist_ok=True)
+        pkg = write_tool._infer_package(str(target))
+
+        assert pkg == "src.core.indexing.index_guard"
+        assert "\\" not in pkg
+        assert ":" not in pkg
+
+
+class TestSafeDeleteCallers:
+    """Regression (bug #4): safe_delete must count cross-file call sites
+    (usages), consistent with rename's reference lookup."""
+
+    @pytest.mark.asyncio
+    async def test_counts_cross_file_callers(self, write_tool, tmp_path):
+        from src.core.indexing.symbol_index import SymbolIndex, SymbolRef
+
+        si = SymbolIndex()
+        si.add_definitions(str(tmp_path / "mod.py"), [
+            {"name": "target_func", "line": 1, "kind": "function"},
+        ])
+        si._references["target_func"] = [
+            SymbolRef(symbol="target_func", file_path=str(tmp_path / "caller_a.py"), line=10, kind="call", is_definition=False),
+            SymbolRef(symbol="target_func", file_path=str(tmp_path / "caller_b.py"), line=20, kind="call", is_definition=False),
+        ]
+        write_tool.resolve_symbol_index = MagicMock(return_value=si)
+        idx = _make_mock_indexer()
+        idx.project_path = str(tmp_path)
+        write_tool.resolve_indexer = MagicMock(return_value=idx)
+
+        result = await write_tool._action_safe_delete(
+            symbol="target_func", file_path="", apply=False, force=False
+        )
+        assert result["status"] == "denied"
+        assert result["usage_count"] == 2
+
+
+class TestDryRunNoWrite:
+    """Regression (bug #2): apply=False must never write to disk."""
+
+    @pytest.mark.asyncio
+    async def test_replace_dry_run_does_not_write(self, write_tool, tmp_path, monkeypatch):
+        from src.mcp.tools import write_tools as wt_module
+
+        src = tmp_path / "m.py"
+        src.write_text("def foo():\n    return 1\n")
+        si = _build_index_for_file(
+            src,
+            extra_defs=[{"name": "foo", "line": 1, "kind": "function"}],
+            add_refs=False,
+        )
+        write_tool.resolve_symbol_index = MagicMock(return_value=si)
+        idx = _make_mock_indexer()
+        idx.project_path = str(tmp_path)
+        write_tool.resolve_indexer = MagicMock(return_value=idx)
+
+        spy = MagicMock()
+        monkeypatch.setattr(wt_module, "_atomic_write", spy)
+
+        result = await write_tool._action_replace(
+            symbol="foo",
+            new_code="def foo():\n    return 2\n",
+            apply=False,
+        )
+        spy.assert_not_called()
+        assert "preview" in result.lower() or "🔍" in result