java-codebase-rag 0.11.2__py3-none-any.whl → 0.12.1__py3-none-any.whl

java_codebase_rag/mcp/server.py

@@ -1,884 +0,0 @@
-#!/usr/bin/env python3
-"""LanceDB code-search MCP (stdio)."""
-from __future__ import annotations
-
-import asyncio
-import os
-import sys
-import time
-from pathlib import Path
-from typing import Literal
-
-from java_codebase_rag.mcp import mcp_v2
-from java_codebase_rag.analysis import resolve_service
-from java_codebase_rag.search.index_common import SBERT_MODEL
-from java_codebase_rag.cli_progress import (
-    accumulate_and_relay_subprocess_streams,
-)
-from java_codebase_rag.pipeline import (
-    VECTORS_SKIPPED_GRAPH_ONLY,
-    cocoindex_bin as resolve_cocoindex_bin,
-    vector_stack_installed,
-)
-from java_codebase_rag.progress import ProgressEvent
-from java_codebase_rag._fdlimit import raise_fd_limit
-from java_codebase_rag.config import (
-    cocoindex_subprocess_env_defaults,
-    discover_project_root,
-    emit_legacy_env_hints_if_present,
-    resolved_sbert_model_for_process_env,
-    resolve_operator_config,
-)
-from java_codebase_rag.graph.ladybug_queries import LadybugGraph, resolve_ladybug_path
-from mcp.server.fastmcp import FastMCP
-from pydantic import BaseModel, Field
-# NOTE: search_lancedb.TABLES is imported lazily in list_code_index_tables_payload() — it
-# pulls lancedb/torch and is unavailable on graph-only installs (macOS Intel).
-
-_COCOINDEX_TARGET = "java_index_flow_lancedb.py:JavaCodeIndexLance"
-
-# Package-internal locations of the cocoindex flow and the graph builder, both
-# executed by file path (see java_codebase_rag.pipeline). Derived from this
-# file's location so they resolve under editable and wheel installs alike.
-_PKG_DIR = Path(__file__).resolve().parent.parent
-_FLOW_FILE = _PKG_DIR / "index" / "java_index_flow_lancedb.py"
-_BUILDER_FILE = _PKG_DIR / "graph" / "build_ast_graph.py"
-_INSTRUCTIONS = (
-    "Java codebase graph navigator over an indexed Java codebase. "
-    "Tools: search (NL/code locate), find (structured NodeFilter), describe (one node + edge_summary: stored edge-label counts and optional composed keys for type Symbols and override-axis virtual keys for method Symbols), "
-    "neighbors (one hop; you MUST pass direction in|out AND edge_types list — no defaults), "
-    "resolve (identifier-shaped lookup for symbol/route/client/producer — three statuses: one | many | none). "
-    "Unknown filter keys and populated fields not applicable to the effective node kind fail with success=false and message. "
-    "Successful responses from any tool may include `hints_structured` (tool call suggestions with a `reason` field) and `advisories` (pure informational text) when hints are enabled. "
-    "Edge labels: EXTENDS, IMPLEMENTS, INJECTS, OVERRIDES, DECLARES, DECLARES_CLIENT, DECLARES_PRODUCER, CALLS, EXPOSES, HTTP_CALLS, ASYNC_CALLS; "
-    "type Symbols may also use composed neighbors edge_types DECLARES.DECLARES_CLIENT, DECLARES.DECLARES_PRODUCER, DECLARES.EXPOSES (out only, type Symbol origin). "
-    "Reprocess/init, meta, tables, diagnose-ignore, analyze-pr: use java-codebase-rag CLI — not MCP."
-)
-
-
-class GraphMetaOutput(BaseModel):
-    success: bool
-    enabled: bool
-    db_path: str
-    ontology_version: int = 0
-    built_at: int = 0
-    source_root: str = ""
-    parse_errors: int = 0
-    counts: dict[str, int] = Field(default_factory=dict)
-    module_counts: dict[str, int] = Field(default_factory=dict)
-    microservice_counts: dict[str, int] = Field(default_factory=dict)
-    routes_total: int = 0
-    exposes_total: int = 0
-    routes_by_framework: dict[str, int] = Field(default_factory=dict)
-    routes_resolved_pct: float = 0.0
-    routes_from_brownfield_pct: float = 0.0
-    routes_by_layer: dict[str, int] = Field(default_factory=dict)
-    edge_counts: dict[str, int] = Field(default_factory=dict)
-    http_calls_match_breakdown: dict[str, int] = Field(default_factory=dict)
-    async_calls_match_breakdown: dict[str, int] = Field(default_factory=dict)
-    cross_service_calls_total: int = 0
-    cross_service_resolution: str | None = None
-    message: str | None = None
-
-
-class RefreshIndexOutput(BaseModel):
-    """Structured result for ``run_refresh_pipeline`` / CLI ``reprocess`` JSON.
-
-    ``phases_run`` records which phase subprocesses actually started; the CLI maps
-    failures to exit **2** when it is empty (setup / nothing spawned) and exit **1**
-    when it is non-empty (build failure). Callers constructing this model manually
-    must set ``phases_run`` accordingly — omitting it leaves the default ``[]``,
-    which the CLI treats like a preflight failure.
-    """
-
-    success: bool
-    exit_code: int | None = None
-    stdout: str = ""
-    stderr: str = ""
-    message: str | None = None
-    graph_exit_code: int | None = None
-    graph_stdout: str = ""
-    graph_stderr: str = ""
-    phases_run: list[Literal["vectors", "graph"]] = Field(default_factory=list)
-    optimize_error: str | None = None
-
-
-class IndexInfoOutput(BaseModel):
-    lancedb_uri: str
-    embedding_model: str
-    project_root: str
-    cocoindex_target: str
-    tables: dict[str, str]
-    graph: GraphMetaOutput
-
-
-# Module-level scope manager, initialized in main()
-_scope_manager: ScopeManager | None = None
-
-
-class ScopeManager:
-    """Manages automatic microservice scope detection and injection."""
-
-    def __init__(self, source_root: Path):
-        self.source_root = source_root
-        self.default_scope: str | None = self._detect_scope()
-        self._log_detection()
-
-    def _detect_scope(self) -> str | None:
-        from java_codebase_rag.graph.graph_enrich import detect_microservice_from_path
-
-        candidate = detect_microservice_from_path(Path.cwd(), self.source_root)
-        if candidate is None:
-            return None
-        # Only auto-scope to a microservice that actually has indexed code.
-        # detect_microservice_from_path can mislabel a non-microservice
-        # top-level child of source_root — most importantly the config/context
-        # directory the MCP server is launched from (no build marker, no
-        # source) — via its "first path segment under root" fallback. Scoping
-        # every query to such a name yields zero matches, so all tools return
-        # empty. A real microservice the operator is working in is, by
-        # definition, present in the index, so validating against the indexed
-        # set cannot suppress a legitimate scope. When the index is unreadable
-        # (empty known set) we keep the detected candidate rather than silently
-        # disabling auto-scope on a transient graph error.
-        known = self._indexed_microservices()
-        if known and candidate not in known:
-            return None
-        return candidate
-
-    def _indexed_microservices(self) -> set[str]:
-        """Microservice names that have indexed type symbols.
-
-        Graph-only source of truth: the graph is always built alongside Lance,
-        and a Lance-only index (no graph) is not a supported state. Any failure
-        (graph missing, open error, empty index) returns an empty set, which
-        ``_detect_scope`` treats as "cannot validate — keep detection".
-        """
-        try:
-            if not LadybugGraph.exists():
-                return set()
-            # LadybugGraph.get() opens the DB and runs meta(); it can raise
-            # (e.g. RuntimeError on ontology-version mismatch). Caught here ->
-            # empty set -> _detect_scope keeps the detected scope.
-            counts = LadybugGraph.get().microservice_counts()
-            return {name for name in counts if name}
-        except Exception:
-            return set()
-
-    def _log_detection(self) -> None:
-        if self.default_scope:
-            print(f"[scope] Detected microservice: {self.default_scope}", file=sys.stderr)
-            print(f"[scope] Queries scoped to {self.default_scope}", file=sys.stderr)
-        else:
-            print("[scope] No microservice detected (at project root)", file=sys.stderr)
-            print("[scope] Queries will span all microservices", file=sys.stderr)
-
-    def apply_auto_scope(self, node_filter: mcp_v2.NodeFilter | None) -> mcp_v2.NodeFilter | None:
-        """Apply auto-detected scope to filter if no explicit microservice is set."""
-        if self.default_scope is None:
-            return node_filter
-        if node_filter is None:
-            return mcp_v2.NodeFilter(microservice=self.default_scope)
-        if node_filter.microservice is None:
-            return node_filter.model_copy(update={"microservice": self.default_scope})
-        return node_filter
-
-
-def _resolve_lancedb_uri() -> str:
-    raw = os.environ.get("JAVA_CODEBASE_RAG_INDEX_DIR", "").strip()
-    if not raw:
-        raw = str((_project_root() / ".java-codebase-rag").resolve())
-    p = Path(raw).expanduser()
-    if not str(raw).startswith(("s3://", "gs://", "az://")):
-        try:
-            return str(p.resolve())
-        except OSError:
-            return str(p)
-    return raw
-
-
-def _project_root() -> Path:
-    env = os.environ.get("JAVA_CODEBASE_RAG_SOURCE_ROOT", "").strip()
-    if env:
-        return Path(env).expanduser().resolve()
-    discovered = discover_project_root(Path.cwd())
-    return discovered if discovered is not None else Path.cwd().resolve()
-
-
-def _source_root_for_operator_config() -> Path | None:
-    """``source_root`` arg to hand ``resolve_operator_config`` from the MCP server.
-
-    Returns ``JAVA_CODEBASE_RAG_SOURCE_ROOT`` when set (an explicit operator
-    override that wins and suppresses the YAML ``source_root`` field, exactly
-    like CLI ``--source-root``), otherwise ``None`` — so
-    ``resolve_operator_config`` runs its OWN walk-up discovery and HONORS the
-    YAML ``source_root`` field, matching the CLI (``init`` / ``increment`` /
-    ``reprocess``) path.
-
-    Do NOT pass ``_project_root()`` (the walk-up-discovered dir) here: a
-    non-``None`` value routes into the "explicit source root" branch that
-    skips the YAML ``source_root`` field, which made the MCP server and the
-    CLI resolve different ``source_root`` / ``index_dir`` from the same config
-    file (the init-vs-MCP index_dir divergence). ``_project_root()`` is kept
-    only for the ``_resolve_lancedb_uri()`` fallback below.
-    """
-    env = os.environ.get("JAVA_CODEBASE_RAG_SOURCE_ROOT", "").strip()
-    return Path(env).expanduser().resolve() if env else None
-
-
-def _cocoindex_subprocess_env(project_root: Path) -> dict[str, str]:
-    sub_env = os.environ.copy()
-    sub_env["JAVA_CODEBASE_RAG_SOURCE_ROOT"] = str(project_root)
-    idx = os.environ.get("JAVA_CODEBASE_RAG_INDEX_DIR", "").strip()
-    if idx:
-        sub_env["JAVA_CODEBASE_RAG_INDEX_DIR"] = str(Path(idx).expanduser().resolve())
-    # Cap CocoIndex concurrency to avoid EMFILE ("too many open files") under
-    # default OS fd limits. See: https://github.com/HumanBean17/java-codebase-rag/issues/306
-    for _k, _v in cocoindex_subprocess_env_defaults().items():
-        sub_env.setdefault(_k, _v)
-    return sub_env
-
-
-def _graph_enabled() -> bool:
-    return LadybugGraph.exists()
-
-
-def _graph_meta_output() -> GraphMetaOutput:
-    if not LadybugGraph.exists():
-        return GraphMetaOutput(
-            success=True,
-            enabled=False,
-            db_path=resolve_ladybug_path(),
-            message="Ladybug graph not present; run java-codebase-rag reprocess or build_ast_graph.py",
-        )
-    try:
-        graph = LadybugGraph.get()
-        meta = graph.meta()
-    except Exception as e:
-        return GraphMetaOutput(
-            success=False,
-            enabled=_graph_enabled(),
-            db_path=resolve_ladybug_path(),
-            message=f"Ladybug open failed: {e}",
-        )
-    if "error" in meta:
-        return GraphMetaOutput(
-            success=False,
-            enabled=_graph_enabled(),
-            db_path=meta.get("db_path", resolve_ladybug_path()),
-            message=str(meta["error"]),
-        )
-    try:
-        mod_counts = graph.module_counts()
-    except Exception:
-        mod_counts = {}
-    try:
-        ms_counts = graph.microservice_counts()
-    except Exception:
-        ms_counts = {}
-    rfw = meta.get("routes_by_framework") or {}
-    routes_by_framework = {str(k): int(v) for k, v in rfw.items()} if isinstance(rfw, dict) else {}
-    rbl = meta.get("routes_by_layer") or {}
-    routes_by_layer = {str(k): int(v) for k, v in rbl.items()} if isinstance(rbl, dict) else {}
-    return GraphMetaOutput(
-        success=True,
-        enabled=_graph_enabled(),
-        db_path=meta.get("db_path", resolve_ladybug_path()),
-        ontology_version=int(meta.get("ontology_version") or 0),
-        built_at=int(meta.get("built_at") or 0),
-        source_root=str(meta.get("source_root") or ""),
-        parse_errors=int(meta.get("parse_errors") or 0),
-        counts={k: int(v) for k, v in (meta.get("counts") or {}).items()},
-        module_counts=mod_counts,
-        microservice_counts=ms_counts,
-        routes_total=int(meta.get("routes_total") or 0),
-        exposes_total=int(meta.get("exposes_total") or 0),
-        routes_by_framework=routes_by_framework,
-        routes_resolved_pct=float(meta.get("routes_resolved_pct") or 0.0),
-        routes_from_brownfield_pct=float(meta.get("routes_from_brownfield_pct") or 0.0),
-        routes_by_layer=routes_by_layer,
-        edge_counts={str(k): int(v) for k, v in (meta.get("edge_counts") or {}).items()},
-        http_calls_match_breakdown={
-            str(k): int(v) for k, v in (meta.get("http_calls_match_breakdown") or {}).items()
-        },
-        async_calls_match_breakdown={
-            str(k): int(v) for k, v in (meta.get("async_calls_match_breakdown") or {}).items()
-        },
-        cross_service_calls_total=int(meta.get("cross_service_calls_total") or 0),
-        cross_service_resolution=meta.get("cross_service_resolution"),
-    )
-
-
-def list_code_index_tables_payload() -> IndexInfoOutput:
-    try:
-        from java_codebase_rag.search.search_lancedb import TABLES
-
-        tables = dict(TABLES)
-    except ImportError:
-        # Graph-only install (no lancedb): no Lance vector tables exist.
-        tables = {}
-    return IndexInfoOutput(
-        lancedb_uri=_resolve_lancedb_uri(),
-        embedding_model=resolved_sbert_model_for_process_env(SBERT_MODEL),
-        project_root=str(_project_root()),
-        cocoindex_target=_COCOINDEX_TARGET,
-        tables=tables,
-        graph=_graph_meta_output(),
-    )
-
-
-async def _run_graph_phase(
-    root: Path,
-    *,
-    quiet: bool,
-    verbose: bool,
-    on_progress: object | None,
-    on_progress_console: object | None,
-) -> tuple[int | None, str, str, bool]:
-    """Run ``build_ast_graph.py`` and return ``(code, stdout, stderr, started)``.
-
-    Shared by the vectors→graph refresh path and the graph-only path (macOS Intel,
-    where the vector stack is gated off). ``started`` is True only when the graph
-    subprocess was actually created, so callers set ``phases_run`` accurately — the
-    CLI maps an empty ``phases_run`` to a preflight exit code 2 (nothing spawned).
-    A missing builder or a spawn failure returns ``started=False`` with the graph
-    code carrying the reason (``None`` for missing builder, ``-1`` for spawn error).
-    """
-    builder = _BUILDER_FILE
-    if not builder.is_file():
-        return None, "", "", False
-    try:
-        graph_args = [
-            sys.executable,
-            str(builder),
-            "--source-root",
-            str(root),
-            "--ladybug-path",
-            resolve_ladybug_path(),
-        ]
-        if not quiet:
-            graph_args.append("--verbose")
-        gproc = await asyncio.create_subprocess_exec(
-            *graph_args,
-            cwd=str(root),
-            env=_cocoindex_subprocess_env(root),
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-        if quiet:
-            gout_b, gerr_b = await gproc.communicate()
-        else:
-            gout_b, gerr_b = await accumulate_and_relay_subprocess_streams(
-                gproc, relay=True, verbose=verbose,
-                on_progress=on_progress, on_progress_console=on_progress_console,
-            )
-        return (
-            gproc.returncode,
-            gout_b.decode(errors="replace"),
-            gerr_b.decode(errors="replace"),
-            True,
-        )
-    except Exception as exc:
-        return -1, "", f"graph builder spawn failed: {exc}", False
-
-
-async def run_refresh_pipeline(
-    *,
-    quiet: bool = False,
-    verbose: bool = True,
-    on_progress=None,
-    on_progress_console: object | None = None,
-) -> RefreshIndexOutput:
-    root = _project_root()
-    if not vector_stack_installed():
-        # Graph-only install (macOS Intel): the vector stack (cocoindex/lancedb/
-        # sentence-transformers) is gated off by PEP 508 markers and uninstallable,
-        # so the cocoindex binary is absent. Skip the vectors phase and build the
-        # graph only — mirroring init/increment, which treat cocoindex-absent as a
-        # skip, not a failure (the graph layer is the supported surface there). No
-        # vectors progress event is emitted, so the renderer's vectors task stays
-        # invisible (its "never spawned" invariant) instead of hanging at running.
-        print(VECTORS_SKIPPED_GRAPH_ONLY, file=sys.stderr, flush=True)
-        if not quiet:
-            print(file=sys.stderr, flush=True)
-        graph_code, graph_out, graph_err, started = await _run_graph_phase(
-            root, quiet=quiet, verbose=verbose,
-            on_progress=on_progress, on_progress_console=on_progress_console,
-        )
-        ok = graph_code == 0
-        if not ok:
-            message = (
-                f"graph builder exit {graph_code}"
-                if graph_code is not None
-                else (graph_err.strip() or "graph builder unavailable")
-            )
-        else:
-            message = "reprocess completed (graph-only; vectors skipped — vector stack not installed)"
-        return RefreshIndexOutput(
-            success=ok,
-            exit_code=None,
-            stdout="",
-            stderr="",
-            message=message,
-            graph_exit_code=graph_code,
-            graph_stdout=graph_out[-4000:] if len(graph_out) > 4000 else graph_out,
-            graph_stderr=graph_err[-4000:] if len(graph_err) > 4000 else graph_err,
-            phases_run=["graph"] if started else [],
-            optimize_error=None,
-        )
-    # Resolve cocoindex the same way the sync path does (pipeline.cocoindex_bin):
-    # next to the interpreter first, then via PATH (``shutil.which``). A console
-    # script legitimately lives away from the venv python — e.g. ``pip install
-    # --user`` places it in ``~/.local/bin``. Honoring PATH keeps ``reprocess``
-    # (no flags) consistent with init/increment/``reprocess --vectors-only``,
-    # which all resolve through cocoindex_bin(); previously this path checked
-    # only next-to-python and failed with "cocoindex not found next to Python"
-    # even though cocoindex was reachable on PATH.
-    cocoindex_bin = resolve_cocoindex_bin()
-    if not cocoindex_bin.is_file():
-        # 127 pre-spawn: emit a terminal failed vectors event so the renderer's
-        # task doesn't hang at running (matches the sync pipeline path).
-        if on_progress is not None:
-            on_progress(ProgressEvent(kind="vectors", phase=None, pass_=None, done=None, total=None, status="failed", elapsed_s=None))
-        return RefreshIndexOutput(
-            success=False,
-            message=(
-                f"cocoindex not found next to Python ({cocoindex_bin}) or on PATH; "
-                "install cocoindex[lancedb] into the same venv or add its bin/ to PATH."
-            ),
-            phases_run=[],
-        )
-    flow_path = _FLOW_FILE
-    if not flow_path.is_file():
-        if on_progress is not None:
-            on_progress(ProgressEvent(kind="vectors", phase=None, pass_=None, done=None, total=None, status="failed", elapsed_s=None))
-        return RefreshIndexOutput(
-            success=False,
-            message=f"java_index_flow_lancedb.py not found at {flow_path}",
-            phases_run=[],
-        )
-    proc: asyncio.subprocess.Process | None = None
-    out_b, err_b = b"", b""
-    # DROP the Lance target tables so the update takes the fast INSERT path
-    # instead of cocoindex's in-place bulk-update, which emits ~one deletion-
-    # vector + version commit PER matched row — O(rows) of tiny file IO that
-    # hangs for many minutes on large repos. Drop+recreate is identical output
-    # for a full rebuild (the very thing --full-reprocess means). Same fix on
-    # the sync path: pipeline.run_cocoindex_update. Drop failure is non-fatal:
-    # the update falls back to the slow in-place path.
-    try:
-        drop_proc = await asyncio.create_subprocess_exec(
-            str(cocoindex_bin),
-            "drop",
-            _COCOINDEX_TARGET,
-            "-f",
-            cwd=str(flow_path.parent),
-            env=_cocoindex_subprocess_env(root),
-            stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.PIPE,
-        )
-        await drop_proc.communicate()
-    except Exception as exc:
-        print(
-            f"java-codebase-rag: drop-before-reprocess failed ({exc!s}); "
-            "falling back to in-place update",
-            file=sys.stderr,
-        )
-    if quiet:
-        try:
-            proc = await asyncio.create_subprocess_exec(
-                str(cocoindex_bin),
-                "update",
-                _COCOINDEX_TARGET,
-                "--full-reprocess",
-                "-f",
-                cwd=str(flow_path.parent),
-                env=_cocoindex_subprocess_env(root),
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-            )
-            out_b, err_b = await proc.communicate()
-        except Exception as exc:
-            if on_progress is not None:
-                on_progress(ProgressEvent(kind="vectors", phase=None, pass_=None, done=None, total=None, status="failed", elapsed_s=None))
-            return RefreshIndexOutput(
-                success=False,
-                message=f"spawn failed: {exc!s}",
-                phases_run=[],
-            )
-    else:
-        t0 = time.perf_counter()
-        code_c = -1
-        try:
-            proc = await asyncio.create_subprocess_exec(
-                str(cocoindex_bin),
-                "update",
-                _COCOINDEX_TARGET,
-                "--full-reprocess",
-                "-f",
-                cwd=str(flow_path.parent),
-                env=_cocoindex_subprocess_env(root),
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-            )
-            # The vectors task is fed by the child's per-file ticks + the
-            # approximate total line, parsed by the ProgressRelay inside the
-            # async drain and routed to on_progress.
-            out_b, err_b = await accumulate_and_relay_subprocess_streams(
-                proc, relay=True, verbose=verbose,
-                on_progress=on_progress, on_progress_console=on_progress_console,
-            )
-            code_c = proc.returncode if proc.returncode is not None else -1
-        except Exception as exc:
-            if on_progress is not None:
-                on_progress(ProgressEvent(kind="vectors", phase=None, pass_=None, done=None, total=None, status="failed", elapsed_s=None))
-            return RefreshIndexOutput(
-                success=False,
-                message=f"spawn failed: {exc!s}",
-                phases_run=[],
-            )
-        finally:
-            # The parent emits the terminal vectors event (the flow can't — no
-            # "all files done" hook). Drives clamp-on-completion + phase
-            # transition to Optimize.
-            if on_progress is not None:
-                elapsed = time.perf_counter() - t0
-                status = "done" if code_c == 0 else "failed"
-                on_progress(ProgressEvent(kind="vectors", phase=None, pass_=None, done=None, total=None, status=status, elapsed_s=elapsed))
-    assert proc is not None
-    out = out_b.decode(errors="replace")
-    err = err_b.decode(errors="replace")
-    ok = proc.returncode == 0
-    phases_run: list[Literal["vectors", "graph"]] = ["vectors"]
-    graph_code: int | None = None
-    graph_out = ""
-    graph_err = ""
-    optimize_error: str | None = None
-    if ok:
-        if not quiet:
-            print(file=sys.stderr, flush=True)
-        # Serialized post-flow Lance optimize: the flow disabled its background
-        # optimize, so with cocoindex returned exit 0 there are no concurrent
-        # writers — this is the safe window to compact. An optimize failure is
-        # surfaced via optimize_error / stderr and must NOT flip the success of
-        # a vectors phase that succeeded; the index is still searchable.
-        try:
-            from java_codebase_rag.lance_optimize import optimize_lance_tables
-
-            idx_raw = os.environ.get("JAVA_CODEBASE_RAG_INDEX_DIR", "").strip()
-            if idx_raw and not idx_raw.startswith(("s3://", "gs://", "az://")):
-                idx_dir = Path(idx_raw).expanduser().resolve()
-            elif idx_raw:
-                idx_dir = Path(idx_raw)
-            else:
-                idx_dir = (root / ".java-codebase-rag").resolve()
-            await optimize_lance_tables(idx_dir, quiet=quiet, on_progress=on_progress)
-        except Exception as exc:
-            optimize_error = f"lance optimize failed: {exc}"
-            print(f"java-codebase-rag: {optimize_error}", file=sys.stderr)
-        graph_code, graph_out, graph_err, graph_started = await _run_graph_phase(
-            root, quiet=quiet, verbose=verbose,
-            on_progress=on_progress, on_progress_console=on_progress_console,
-        )
-        if graph_started:
-            phases_run = ["vectors", "graph"]
-    message: str | None = None
-    if not ok:
-        message = f"cocoindex exit {proc.returncode}"
-    elif graph_code is not None and graph_code != 0:
-        message = f"graph builder exit {graph_code}"
-    # Surface a post-flow optimize failure in the message too (success is not
-    # flipped — the vectors phase succeeded and the index is still usable).
-    if optimize_error is not None:
-        message = optimize_error if message is None else f"{message}; {optimize_error}"
-    return RefreshIndexOutput(
-        success=ok and (graph_code is None or graph_code == 0),
-        exit_code=proc.returncode,
-        stdout=out[-8000:] if len(out) > 8000 else out,
-        stderr=err[-8000:] if len(err) > 8000 else err,
-        message=message,
-        graph_exit_code=graph_code,
-        graph_stdout=graph_out[-4000:] if len(graph_out) > 4000 else graph_out,
-        graph_stderr=graph_err[-4000:] if len(graph_err) > 4000 else graph_err,
-        phases_run=phases_run,
-        optimize_error=optimize_error,
-    )
-
-
-def create_mcp_server() -> FastMCP:
-    mcp = FastMCP("java-codebase-rag", instructions=_INSTRUCTIONS)
-
-    @mcp.tool(
-        name="search",
-        description=(
-            "Ranked chunk retrieval over content tables (java/sql/yaml); `query` is opaque text (natural language or code "
-            "fragments) and results are score-ranked, not boolean-matched. For graph-structured listing "
-            "(symbols/routes/clients/producers) use `find`, not `search`. Optional `filter` uses the same NodeFilter "
-            "schema as `find` but only **symbol-applicable** fields apply — others return success=false. Substring "
-            "fields match literally (no `*`/`?` metacharacters)—use ranked `query` text for fuzzy discovery. There is **no** "
-            "structured DSL inside `query`; structured predicates belong in `find`. "
-            "For identifier-shaped lookups (FQN, id, route/client identifiers, …), use `resolve` first; "
-            "use `search` for natural-language or ranked fuzzy discovery. "
-            "Set `explain=true` to include score breakdown per hit. "
-            "Successful responses echo `limit`/`offset`."
-        ),
-    )
-    async def search(
-        query: str = Field(description="Search query"),
-        table: Literal["java", "sql", "yaml", "all"] = Field(
-            default="java",
-            description="Which content table to search. 'all' fuses java/sql/yaml results.",
-        ),
-        hybrid: bool = Field(
-            default=False,
-            description="If true, fuse FTS + vector. Requires a single table (java/sql/yaml); hybrid with table='all' returns success=false.",
-        ),
-        limit: int = Field(default=5, ge=1, le=50, description="Max hits to return"),
-        offset: int = Field(default=0, ge=0, le=500, description="Skip this many hits (pagination)"),
-        path_contains: str | None = Field(
-            default=None,
-            description="Substring match on file path (pre-filter from index)",
-        ),
-        filter: mcp_v2.NodeFilter | None = Field(
-            default=None,
-            description=(
-                "Optional NodeFilter post-filter on symbol-oriented hit rows. An empty object or omitted means no "
-                "predicate. Unknown keys or populated fields not applicable to symbols return success=false."
-            ),
-        ),
-        explain: bool = Field(
-            default=False,
-            description="If true, include score_components in each SearchHit (breakdown of distance/rrf, role, symbol, import_penalty).",
-        ),
-        chunks: bool = Field(
-            default=False,
-            description="If true, show every chunk (default collapses to one row per symbol/type).",
-        ),
-    ) -> mcp_v2.SearchOutput:
-        scoped_filter = _scope_manager.apply_auto_scope(filter) if _scope_manager else filter
-        return await asyncio.to_thread(
-            mcp_v2.search_v2,
-            query,
-            table,
-            hybrid,
-            limit,
-            offset,
-            path_contains,
-            scoped_filter,
-            explain,
-            None,
-            not chunks,  # dedup=True by default; chunks=True opts out
-        )
-
-    @mcp.tool(
-        name="find",
-        description=(
-            "Exact structured listing for one node kind. Per-kind applicable fields: **symbol** — "
-            "microservice, module, role, exclude_roles, annotation, capability, fqn_contains, symbol_kind, symbol_kinds; "
-            "**route** — microservice, module, http_method, path_contains, framework; **client** — microservice, module, "
-            "source_layer, client_kind, target_service, target_path_contains, http_method; **producer** — microservice, "
-            "module, source_layer, producer_kind, topic_contains. "
-            "`role` is singular and `exclude_roles` plural; `capability` is a functional tag assigned during indexing. "
-            "`fqn_contains` is a substring predicate — for exact FQN or id lookup use `resolve`/`describe`. "
-            "Substring fields match literally (Cypher `CONTAINS`); no wildcard metacharacters. An empty filter (`{}`) or `filter=None` means no predicate (all nodes of "
-            "that kind; use pagination). Unknown keys or inapplicable populated fields return success=false. "
-            "Successful responses echo `limit`/`offset`."
-        ),
-    )
-    async def find(
-        kind: Literal["symbol", "route", "client", "producer"] = Field(
-            description=(
-                "Which graph table to search. 'symbol' = declarations, "
-                "'route' = endpoints, 'client' = outbound HTTP clients, "
-                "'producer' = outbound async producers."
-            )
-        ),
-        filter: mcp_v2.NodeFilter = Field(
-            ...,
-            description=(
-                "Required NodeFilter object (extra keys forbidden). Fields must be applicable to `kind`."
-            ),
-        ),
-        limit: int = Field(default=25, ge=1, le=500, description="Max nodes to return"),
-        offset: int = Field(default=0, ge=0, le=499, description="Skip this many nodes (pagination)"),
-    ) -> mcp_v2.FindOutput:
-        scoped_filter = _scope_manager.apply_auto_scope(filter) if _scope_manager else filter
-        return await asyncio.to_thread(mcp_v2.find_v2, kind, scoped_filter, limit, offset, None)
-
-    @mcp.tool(
-        name="describe",
-        description=(
-            "Full node record plus `edge_summary` (in/out counts per stored edge label). For type Symbols, `edge_summary` "
-            "also exposes composed keys (DECLARES.DECLARES_CLIENT, DECLARES.DECLARES_PRODUCER, DECLARES.EXPOSES); for "
-            "non-static method Symbols it adds override-axis virtual keys (OVERRIDDEN_BY and its composed forms, plus an "
-            "`OVERRIDES` map merging stored `[:OVERRIDES]` counts with the dispatch-up rollup). These composed/override keys "
-            "are out-only and navigable via `neighbors`; the stored `OVERRIDES` is also a normal edge label (in toward declaration). "
-            "Pass `id` for any kind, or exact `fqn` for Symbol lookup (`id` wins when both are set). "
-            "`describe(fqn=…)` keeps the first graph row when multiple symbols share that FQN; when an FQN may collide, "
-            "prefer `resolve(identifier=…, hint_kind='symbol')` first, then `describe(id=…)` on the chosen node."
-        ),
-    )
-    async def describe(
-        id: str | None = Field(
-            default=None,
-            description=(
-                "Graph node id: sym:, route:, client:, or producer: prefix "
-                '(e.g. sym:com.bank.chat.core.api.ChatController#joinOperator(JoinOperatorRequest); '
-                "producer: p:a1b2c3d4e5f67890 — the stored id from the graph, not a human-readable "
-                "pipe key). For producers by topic, prefer resolve(identifier=<topic>, hint_kind='producer'). "
-                "When set, takes precedence over fqn."
-            ),
-        ),
-        fqn: str | None = Field(
-            default=None,
-            description="Exact FQN for Symbol lookup (alternative to id; Symbol kind only)",
-        ),
-    ) -> mcp_v2.DescribeOutput:
-        return await asyncio.to_thread(mcp_v2.describe_v2, id, fqn, None)
-
-    @mcp.tool(
-        name="neighbors",
-        description=(
-            "Graph walk: **direction** (`in` | `out`) and non-empty **edge_types** are required (one hop over stored edge "
-            "labels; type/method Symbol origins may also pass composed or override-axis keys — see `edge_types`). From a "
-            "type Symbol, `direction='out'` with EXPOSES yields route nodes and HTTP_CALLS/ASYNC_CALLS yield client/producer "
-            "nodes; `direction='in'` reverses each relationship. "
-            "`direction` and `edge_types` have no defaults; an empty `edge_types` fails. The CALLS-only features — "
-            "`edge_filter`, `include_unresolved`, `dedup_calls` — each require `edge_types=['CALLS']`; `edge_filter` and "
-            "`include_unresolved` are mutually exclusive. Violating a precondition (wrong CALLS context, composed/override "
-            "keys on an ineligible origin or with `direction='in'`, unknown filter keys) returns "
-            "success=false with a message; `dedup_calls` with other edge_types is a silent no-op. "
-            "Optional `filter` applies to each neighbor endpoint row; populated fields must be applicable to that "
-            "neighbor's kind—mixed-kind result sets fail on the first inapplicable neighbor (per-neighbor strict frame). "
-            "Each edge's `attrs.strategy` indicates resolution quality (brownfield/fallback vs primary paths). "
-            "Successful responses echo `requested_edge_types`."
-        ),
-    )
-    async def neighbors(
-        ids: str | list[str] = Field(
-            description="Origin symbol/route/client/producer id, or list for batch",
-        ),
-        direction: Literal["in", "out"] = Field(
-            description="Required. 'in' = predecessors (callers), 'out' = successors (callees). No default.",
-        ),
-        edge_types: list[mcp_v2.NeighborEdgeType] = Field(
-            description=(
-                "Required non-empty list of stored edge labels (e.g. CALLS, EXPOSES, HTTP_CALLS, OVERRIDES) "
-                "and/or composed DECLARES.DECLARES_* (type Symbol origin, out only) or OVERRIDDEN_BY* "
-                "(non-static method Symbol origin, out only)"
-            ),
-        ),
-        limit: int = Field(
-            default=25,
-            ge=1,
-            le=500,
-            description=(
-                "Max edges after concatenating all origins (ids order; offset/limit on merged list)"
-            ),
-        ),
-        offset: int = Field(
-            default=0,
-            ge=0,
-            le=1000,
-            description="Skip this many edges after merge (pagination)",
-        ),
-        filter: mcp_v2.NodeFilter | None = Field(
-            default=None,
-            description=(
-                "Optional NodeFilter on the neighbor node. An empty object or omitted means no predicate. "
-                "Same applicability rules as `find` for that node's kind."
-            ),
-        ),
-        edge_filter: mcp_v2.EdgeFilter | None = Field(
-            default=None,
-            description=(
-                "Optional EdgeFilter on CALLS edge attributes (edge_types=['CALLS'] only). Use "
-                "callee_declaring_role for callee stereotype projection — not NodeFilter.role on method neighbors. "
-                "Mutually exclusive with include_unresolved."
-            ),
-        ),
-        include_unresolved: bool = Field(
-            default=False,
-            description=(
-                "When true with edge_types=['CALLS'] and direction='out', interleave UnresolvedCallSite "
-                "rows (row_kind='unresolved_call_site') with resolved CALLS in source order. "
-                "Mutually exclusive with edge_filter."
-            ),
-        ),
-        dedup_calls: bool = Field(
-            default=False,
-            description=(
-                "When true with edge_types=['CALLS'], collapse identical (origin, callee) CALLS to one row "
-                "with call_site_count and call_site_lines; unresolved sites are not deduped."
-            ),
-        ),
-    ) -> mcp_v2.NeighborsOutput:
-        scoped_filter = _scope_manager.apply_auto_scope(filter) if _scope_manager else filter
-        return await asyncio.to_thread(
-            mcp_v2.neighbors_v2,
-            ids,
-            direction,
-            edge_types,
-            limit,
-            offset,
-            scoped_filter,
-            edge_filter,
-            include_unresolved,
-            dedup_calls,
-            None,
-        )
-
-    @mcp.tool(
-        name="resolve",
-        description=(
-            "Identifier-shaped node lookup (FQN, sym:/route:/client:/producer: id, HTTP method+path, "
-            "route path template, client target_service, target+path pair, or producer topic). Returns "
-            "status=one (single node), many (≥2 ranked candidates with reason), or none "
-            "(no match — fall back to search(query=...) for natural language or fuzzy text). "
-            "Optional hint_kind narrows to symbol, route, client, or producer. "
-            "Malformed empty/whitespace identifier returns success=false. "
-            "Examples: resolve('com.foo.Bar', hint_kind='symbol'); "
-            "resolve('GET /api/v1/customers', hint_kind='route'); "
-            "resolve('PaymentClient', hint_kind='client'); "
-            "resolve('order.created', hint_kind='producer'); "
-            "resolve('the client that handles assignments') → none (use search instead)."
-        ),
-    )
-    async def resolve(
-        identifier: str = Field(
-            description=(
-                "Identifier-shaped node lookup (FQN, id prefix, route path, client target, producer topic, …)"
-            ),
-        ),
-        hint_kind: Literal["symbol", "route", "client", "producer"] | None = Field(
-            default=None,
-            description="Optional kind constraint. Omit to search symbol, route, client, and producer.",
-        ),
-    ) -> mcp_v2.ResolveOutput:
-        return await asyncio.to_thread(mcp_v2.resolve_v2, identifier, hint_kind, None)
-
-    return mcp
-
-
-def main() -> None:
-    raise_fd_limit()
-    emit_legacy_env_hints_if_present()
-
-    # Load YAML config and apply embedding settings to environment
-    # This ensures SBERT_MODEL and SBERT_DEVICE from .java-codebase-rag.yml are available
-    # before any tool handler runs (same behavior as CLI path)
-    cfg = resolve_operator_config(source_root=_source_root_for_operator_config())
-    cfg.apply_to_os_environ()
-    mcp_v2.set_hints_enabled(cfg.hints_enabled)
-    mcp_v2.set_absence_config(cfg)
-    resolve_service.set_absence_config(cfg)
-
-    # Initialize scope manager for automatic microservice detection
-    global _scope_manager
-    _scope_manager = ScopeManager(cfg.source_root)
-
-    asyncio.run(create_mcp_server().run_stdio_async())
-
-
-if __name__ == "__main__":
-    main()