java-codebase-rag 0.8.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

java_codebase_rag/lance_optimize.py

@@ -184,6 +184,49 @@ async def optimize_lance_tables(
 
                 if last_exc is None:
                     results[name] = "ok"
+                    # Best-effort BTREE scalar index on the primary key ("id").
+                    # cocoindex's merge_insert defaults to use_index=True but
+                    # never creates a scalar PK index itself (declaring
+                    # primary_key in the schema does NOT auto-build a lance
+                    # index), so without this every merge_insert — increment
+                    # included — is a forced full scan of the PK column,
+                    # O(existing rows). On a large repo that scan dominates
+                    # increment wall-clock; with the index present the join does
+                    # lookups (~O(batch*log N)). Failure is non-fatal (the table
+                    # is still correct, just un-indexed) and never alters the
+                    # "ok" status, mirroring the FTS block below. ``replace=True``
+                    # keeps it idempotent across runs; table.optimize() above
+                    # maintains it on subsequent runs.
+                    try:
+                        from lancedb.index import BTree
+                        await table.create_index("id", config=BTree(), replace=True)
+                    except Exception as exc:
+                        low = str(exc).lower()
+                        if not any(
+                            w in low for w in ("exist", "duplicate", "already", "same name")
+                        ) and not quiet:
+                            print(
+                                f"java-codebase-rag: optimize: {name} id-index skipped: {exc}",
+                                file=sys.stderr,
+                            )
+                    # Best-effort FTS index at index time (PR-SEARCH-3) so hybrid
+                    # search works on all tables (java/sql/yaml) without a
+                    # first-query race. Failure is non-fatal — the lazy
+                    # ensure_text_fts_index in search_lancedb.py is the runtime
+                    # fallback — so it never alters the "ok" optimize status; we
+                    # only log the skip when verbose.
+                    try:
+                        from lancedb.index import FTS
+                        await table.create_index("text", config=FTS(), replace=True)
+                    except Exception as exc:
+                        low = str(exc).lower()
+                        if not any(
+                            w in low for w in ("exist", "duplicate", "already", "same name")
+                        ) and not quiet:
+                            print(
+                                f"java-codebase-rag: optimize: {name} fts skipped: {exc}",
+                                file=sys.stderr,
+                            )
                     if not quiet:
                         print(
                             f"java-codebase-rag: optimize: {name} ok",

java_codebase_rag/pipeline.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import asyncio
+import importlib.util
 import os
 import shutil
 import subprocess
@@ -131,6 +132,26 @@ def run_cocoindex_update(
     on_progress: Callable[[ProgressEvent], None] | None = None,
     on_progress_console: object | None = None,
 ) -> subprocess.CompletedProcess[str]:
+    if full_reprocess:
+        # A full reprocess rebuilds every row, so DROP the Lance target tables
+        # first and let cocoindex recreate them via the fast INSERT path. The
+        # in-place alternative (cocoindex's bulk-update merge_insert) emits
+        # ~one deletion-vector + version commit PER matched row — O(rows) of
+        # tiny file IO that scales to multi-minute hangs on large repos
+        # (measured ~83s sys time / 3474 deletion files for 3475 chunks on
+        # Shopizer; drop+recreate is ~3.6s sys / 0 deletions, ~3.7x faster and
+        # hang-free). Output is identical either way (full recompute); only the
+        # write path differs. Drop failure is non-fatal — if it somehow fails,
+        # the update falls back to the slow in-place path. The same fix is
+        # applied on the async server path (``server.run_refresh_pipeline``).
+        drop = run_cocoindex_drop(env, quiet=quiet)
+        if drop.returncode != 0 and not is_cocoindex_preflight_blocker(drop):
+            print(
+                "java-codebase-rag: drop-before-reprocess failed "
+                f"(exit {drop.returncode}); falling back to in-place update: "
+                f"{(drop.stderr or '').strip()[:200]}",
+                file=sys.stderr,
+            )
     result = _run_cocoindex_update_impl(
         env,
         full_reprocess=full_reprocess,
@@ -200,6 +221,19 @@ def is_graph_preflight_blocker(proc: subprocess.CompletedProcess[str]) -> bool:
     return bool(proc.returncode in (126, 127) and len(getattr(proc, "args", ()) or ()) <= 1)
 
 
+def vector_stack_installed() -> bool:
+    """True when the optional vector stack (cocoindex/lancedb/sentence-transformers) is importable.
+
+    False on graph-only installs (macOS Intel), where PEP 508 markers exclude the trio.
+    Used to skip vector-only wizard steps (e.g. embedding-model selection) and to preflight
+    branching without spawning cocoindex. Probes all three since they are gated together.
+    """
+    return all(
+        importlib.util.find_spec(m) is not None
+        for m in ("cocoindex", "lancedb", "sentence_transformers")
+    )
+
+
 def _run_cocoindex_update_impl(
     env: dict[str, str],
     *,

{java_codebase_rag-0.8.0.dist-info → java_codebase_rag-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: java-codebase-rag
-Version: 0.8.0
+Version: 0.9.1
 Summary: MCP server for semantic + structural search over Java codebases
 Author: HumanBean17
 License-Expression: MIT
@@ -122,7 +122,7 @@ If you prefer manual configuration, see [`docs/JAVA-CODEBASE-RAG-CLI.md`](./docs
 
 ## Tools & commands at a glance
 
-Pick a surface once at install time — `java-codebase-rag install --surface mcp|cli` (default `mcp`). Both surfaces walk the same LanceDB vectors + LadybugDB graph.
+Pick a surface at install time — `java-codebase-rag install --surface mcp|cli` (default `cli`, recommended). Both surfaces walk the same LanceDB vectors + LadybugDB graph. Switch an existing install later with `java-codebase-rag update --surface mcp|cli`.
 
 **MCP surface — five tools over stdio**
 

{java_codebase_rag-0.8.0.dist-info → java_codebase_rag-0.9.1.dist-info}/RECORD

@@ -5,39 +5,39 @@ chunk_heuristics.py,sha256=aQk2NOKxzUdqoUAJUO3G3LE0MN_bYZWNLQ0tkmj5uts,1813
 graph_enrich.py,sha256=Fxp7JurH9wWTOTX1nErjH4H6Jw5bB68YCqR17rsX6gw,62829
 graph_types.py,sha256=P6RVdEiqZlaSgTyXepnGbtMoZq0m_MaP2q6M6i7Uxlc,4539
 index_common.py,sha256=HT6FKHFJ084eFvd3fR1j8z8gf4eWoPHVW8GXLpw464I,285
-java_index_flow_lancedb.py,sha256=OFrvOV2xWPvBkQ1kS6nxcOjdJbYAGcEirzeevrOU1PM,25598
+java_index_flow_lancedb.py,sha256=kDkhnRxl-Kz0YNMY27DTk3gwa8H2nWyGDCQC8hxx-jI,28970
 java_index_v1_common.py,sha256=nF1KrSqboF_RRvWerG9knRRFmWwsrG_CvhgnsoZ8KqA,1154
 java_ontology.py,sha256=ooqr8GucOINpzhdEQ3QzVe5A9GfiR0nUTlySDehn9GA,17129
 ladybug_queries.py,sha256=rVnVEHwWwE4USeX7tICYEl1SSiSxJGnBNe1VX66R3Xk,100531
 mcp_hints.py,sha256=zp-4cnOmbYD0YovmZiLS2oGcvWcWE7n8jKVz4_xifno,42512
-mcp_v2.py,sha256=_pSZrbbImgLOrq8RxBhggoaKHP8oOroUiqh3jz86gG0,66084
+mcp_v2.py,sha256=ABNHiZEEwQ76uPF9E5fQWncJ4JmmgtG3vmt5TDxBGVo,68901
 path_filtering.py,sha256=R--XzI51LXBu5IBKMCnJWbkNr6I5d-SDmltyQQnWco0,17674
 pr_analysis.py,sha256=zrmZZD5yotJtM02Kif6_jgI_oeformOao793akp0N6Y,18394
 resolve_service.py,sha256=tC5FQsGmqhqn0EOexVDlRq5egnzKDTrI7CMzk0nPpG8,25135
-search_lancedb.py,sha256=MKnrRpRQnZNbp5oAFHMBFILoKcQEMaJBouTXakXPSXM,37390
-server.py,sha256=o5TQTO76CEK0SngU5JwGfd8MPn1wyPQODf2zNfbfBTw,35406
+search_lancedb.py,sha256=1sGSZ6H8J9hGcKAwHpzB7F0_in3A_sEtOI5LvlZYIRI,43864
+server.py,sha256=nOK3DOr-i3PJnVmE7neye_tptJumgXfIXPlTIn01MPQ,37065
 java_codebase_rag/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 java_codebase_rag/_fdlimit.py,sha256=vkwjsPbZfxzZ2DZTPWO5DxtuNlLzOADzIq07iYX7GCU,2465
 java_codebase_rag/_stdio.py,sha256=TDNbpt2EP0_Zd622ihdlKwlMfxkKHWOfgLVcU6TcNbo,1458
-java_codebase_rag/cli.py,sha256=0W14fsod0ZJSfSD15BRE4A16V5f5hy_bZ_A1-jZPO4w,44738
+java_codebase_rag/cli.py,sha256=8WKk-_Zl1Sp7wHX4Y5f3bkIy8hHRH_QWrNuX_3WYTm4,45269
 java_codebase_rag/cli_format.py,sha256=CT7-xdwZ0bMCdP68_UOwkvm-mnLluU3LutlM-mDNk60,1839
 java_codebase_rag/cli_progress.py,sha256=q6Wh97yzLGs1B8UFk_WAKivfQu7Y5RnUUE-T2YHWkIs,3237
-java_codebase_rag/config.py,sha256=Yl7Nf0O_ZOZTPtyPMap83jRM7qNhWwfbVJTKSEdERi4,24916
-java_codebase_rag/installer.py,sha256=NgOdsML1BOmqIoIXyoDDLg4r3JxQ9hqqYGCwVW6FHQs,67582
-java_codebase_rag/jrag.py,sha256=K1_QNMO2mRWSeatJIEJ0esVZztraiA8VB6Pkphg6ITU,187655
-java_codebase_rag/jrag_envelope.py,sha256=mvAgoZm5XIpmV-J1ntlBzwJW62Fs71RGcpxFQa-l0lc,47484
+java_codebase_rag/config.py,sha256=1EAlKtQx7LUo-gPoE6BOVLz0YEl1OpWFRABkF06zjgk,26464
+java_codebase_rag/installer.py,sha256=c-_tR1Ct_O3yhmruFRnDoM1Wilz-igD9qdkDPsNqLMI,79934
+java_codebase_rag/jrag.py,sha256=cVUWrKOtkwe2r4u1nknzmrMQMy16bdt1n-dZQpiSFWs,191811
+java_codebase_rag/jrag_envelope.py,sha256=5jD3p2O-p9acAKHqoif5FFoqgP7Q2ziCuKSiPCHoywc,47505
 java_codebase_rag/jrag_hints.py,sha256=k2PFE4s3lZgBYHMdZcTjx1-w28nfQcBtQEVsSxI_DvE,9262
-java_codebase_rag/jrag_render.py,sha256=tIKdOQOO1-uimS2MBxrLma5tjiid0nG0OcaPRgR7uEk,31611
-java_codebase_rag/lance_optimize.py,sha256=25Rwj7HNO8F-35MxhFK6naqgbjd3H-T0zKb3pXB4H0s,9268
-java_codebase_rag/pipeline.py,sha256=4o5SdvHC4z4PTtzkjnhmkolODXnlibndCorI6gDUyPI,15903
+java_codebase_rag/jrag_render.py,sha256=1nUyamL-MOOXDlKvssp-LsBgEtznUnGj_cPteSwuS90,31953
+java_codebase_rag/lance_optimize.py,sha256=HI3aFebP1fenLL6Cav1jMG5kLXSrHLndO_MIJY6qQVo,11977
+java_codebase_rag/pipeline.py,sha256=L65mjK-IxkVWazUNVyIvzfQNi24behQu-Kdc7o_HwEk,17754
 java_codebase_rag/progress.py,sha256=2IxdMALDM0wAQCyJrrfZ975zM_85C-4BfHxf4AtYifE,23212
-java_codebase_rag/install_data/agents/explorer-rag-cli.md,sha256=Ahjq39Kgyydgr_Vno-gFj02DZQQX-a65AvzEl1K1nss,12923
-java_codebase_rag/install_data/agents/explorer-rag-enhanced.md,sha256=O8twSh5aOVe2s_8HdwFKBTl_VxgwiVPm2YlyQAPXhh0,14614
-java_codebase_rag/install_data/skills/explore-codebase/SKILL.md,sha256=7SQSC0sHD_2F64QdEiwgSyVWHQXLxsOBxWWqJpIGPbk,12485
-java_codebase_rag/install_data/skills/explore-codebase-cli/SKILL.md,sha256=qSGsC90LpjTZSUV6v3YtgFSHVb_hd4S1QlOedKm2NnU,14319
-java_codebase_rag-0.8.0.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
-java_codebase_rag-0.8.0.dist-info/METADATA,sha256=VnPaESLzcc1V_ltQw6U1Ehyk6HV1TbTZjgGphLO6tWQ,19996
-java_codebase_rag-0.8.0.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
-java_codebase_rag-0.8.0.dist-info/entry_points.txt,sha256=cj3QTc11UYVQnj9T3orc4daiIGaCYrXP149vKbH2R4U,168
-java_codebase_rag-0.8.0.dist-info/top_level.txt,sha256=8vC-VN3cMwz5vhkSTaeJ1a1bDeqLWEfrTks1CvEvIg0,273
-java_codebase_rag-0.8.0.dist-info/RECORD,,
+java_codebase_rag/install_data/agents/explorer-rag-cli.md,sha256=mMij_BIQM4agaYhGVYjC-fQSe3We1HFeBvc5JBjJj6A,10071
+java_codebase_rag/install_data/agents/explorer-rag-enhanced.md,sha256=gZsNFbuK0lSnOIlplbbS_muz2ozokJqvFUv65QM0NDM,10406
+java_codebase_rag/install_data/skills/explore-codebase/SKILL.md,sha256=A-v2dueVnxwBzBlxoRjZ2zOJk8DranLQ1TElwn94h0s,11529
+java_codebase_rag/install_data/skills/explore-codebase-cli/SKILL.md,sha256=V5gIKKGkgk2KlAFf9JqPareQDMt1iQOI7cwhfOqJL1c,11348
+java_codebase_rag-0.9.1.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
+java_codebase_rag-0.9.1.dist-info/METADATA,sha256=v3Zl2nJ80PhrygxQD-aojw6z1CSZ_uRrOdkIWuA65No,20088
+java_codebase_rag-0.9.1.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
+java_codebase_rag-0.9.1.dist-info/entry_points.txt,sha256=cj3QTc11UYVQnj9T3orc4daiIGaCYrXP149vKbH2R4U,168
+java_codebase_rag-0.9.1.dist-info/top_level.txt,sha256=8vC-VN3cMwz5vhkSTaeJ1a1bDeqLWEfrTks1CvEvIg0,273
+java_codebase_rag-0.9.1.dist-info/RECORD,,

java_index_flow_lancedb.py

@@ -112,6 +112,38 @@ _NUM_TXN_BEFORE_OPTIMIZE = 10**12
 # parent clamps to total on the terminal event anyway).
 _VECTORS_TICK_EVERY = 25
 
+# Bounded concurrency for the per-file drain in app_main. cocoindex's embedder
+# is ``@coco.fn.as_async(batching=True, runner=GPU, max_batch_size=64)`` — but
+# its batching layer only coalesces calls that are in flight SIMULTANEOUSLY. A
+# serial ``async for … await`` loop keeps just one file's chunks (avg 1–3) in
+# flight, so real batches stay tiny and MPS idles between them (measured ~138
+# chunks/s vs the ~235 chunks/s ceiling at batch=64 for all-MiniLM-L6-v2).
+# Draining many files at once with a semaphore puts their chunks in flight
+# together → the embedder coalesces them into full batches → MPS climbs toward
+# the ceiling. Measured on Shopizer (1167 files / 3475 chunks): full init drops
+# from ~46.7s (serial) to ~36.0s (32) / ~34.3s (64), with identical row output.
+#
+# This stays inside ONE component, so the earlier mount_each→app_main win is
+# preserved: still exactly ONE merge_insert per table at commit. Memoization
+# (``@coco.fn(memo=True)``) and the lock-guarded tick counter are safe under
+# concurrency; ``parse_java`` uses a per-thread tree-sitter Parser (already
+# routed via ``asyncio.to_thread``) and ``splitter.split`` is synchronous so the
+# event loop cannot reenter it.
+#
+# Default 64 is sized to MATCH the embedder's hardcoded max_batch_size=64 (the
+# decorator above; not a constructor arg, so not raisable from the flow): ~64
+# files in flight reliably fills a 64-chunk batch and saturates MPS. Going higher
+# buys nothing — the batch is already capped — and lower underfills it. Memory
+# is NOT the limiting factor here: cocoindex buffers ALL staged rows until the
+# single final merge_insert regardless of concurrency, so peak RSS is set by
+# total chunk count (the commit buffer), not by how many files process at once.
+# Set to ``1`` for the old serial behavior; raise/lower only if you have also
+# changed the effective batch size or are constraining the commit buffer itself.
+_FILE_CONCURRENCY = max(
+    1,
+    int(os.environ.get("JAVA_CODEBASE_RAG_FILE_CONCURRENCY", "64") or "64"),
+)
+
 # Thread-safe counter: cocoindex may call process_*_file concurrently
 # (mount_each parallelism is implementation-defined). A module-level lock guards
 # both the counter and the emission so two threads never interleave a tick.
@@ -533,6 +565,29 @@ async def process_yaml_file(
         )
 
 
+async def _drain_files_concurrently(
+    files: Any, process_fn: Any, table: Any, sem: asyncio.Semaphore
+) -> None:
+    """Run ``process_fn(file, table)`` over every file with bounded concurrency.
+
+    Replaces the serial ``async for … await process_*_file`` loop so the
+    embedder's batching layer sees many files' chunks in flight at once (see
+    ``_FILE_CONCURRENCY``). Materializes the async iterable up front — file
+    handles are lightweight and cocoindex already realized the collection when
+    the walker mounted, so this is not a second walk. An empty collection is a
+    no-op (e.g. SQL/YAML tables on a repo with none).
+    """
+    items = [f async for _, f in files.items()]
+    if not items:
+        return
+
+    async def _one(_file: Any) -> None:
+        async with sem:
+            await process_fn(_file, table)
+
+    await asyncio.gather(*(_one(f) for f in items))
+
+
 @coco.fn
 async def app_main() -> None:
     java_schema = await lancedb.TableSchema.from_class(
@@ -646,12 +701,17 @@ async def app_main() -> None:
     # unchanged files still skip re-embedding on incremental; _RowHandler.
     # reconcile skips rows whose fingerprint is unchanged → increment carries
     # only changed rows in its single merge_insert.
-    async for _key, _file in java_files.items():
-        await process_java_file(_file, java_table)
-    async for _key, _file in sql_files.items():
-        await process_sql_file(_file, sql_table)
-    async for _key, _file in yaml_files.items():
-        await process_yaml_file(_file, yaml_table)
+    #
+    # PERF (concurrency): drain files with a bounded semaphore instead of a
+    # serial ``async for … await``. See ``_FILE_CONCURRENCY`` — this is what
+    # lets the embedder's batching layer fill real batches (embedding dominates
+    # init cost, and serial files starve it). One shared semaphore bounds total
+    # in-flight work; tables are drained in order (java dominates, sql/yaml are
+    # usually near-empty).
+    _sem = asyncio.Semaphore(_FILE_CONCURRENCY)
+    await _drain_files_concurrently(java_files, process_java_file, java_table, _sem)
+    await _drain_files_concurrently(sql_files, process_sql_file, sql_table, _sem)
+    await _drain_files_concurrently(yaml_files, process_yaml_file, yaml_table, _sem)
 
 
 app = coco.App(

mcp_v2.py

@@ -466,6 +466,8 @@ class SearchHit(BaseModel):
     role: str | None = None
     filename: str | None = None
     start_line: int | None = None
+    score_components: dict[str, float] | None = None
+    chunks: int | None = None
 
 
 # NodeRef is now defined in graph_types.py and imported above
@@ -583,7 +585,7 @@ def _chunk_id_from_row(row: dict[str, Any]) -> str:
     return f"{filename}:{sb}:{eb}"
 
 
-def _row_to_search_hit(row: dict[str, Any]) -> SearchHit:
+def _row_to_search_hit(row: dict[str, Any], explain: bool = False) -> SearchHit:
     score = float(row.get("_rrf_score") or row.get("_score") or 0.0)
     filename = str(row.get("filename") or "") or None
     start_line: int | None = None
@@ -595,6 +597,8 @@ def _row_to_search_hit(row: dict[str, Any]) -> SearchHit:
                 start_line = int(ln)
             except (TypeError, ValueError):
                 start_line = None
+    chunks = row.get("_chunks_collapsed")
+    chunks_int = int(chunks) if chunks is not None and int(chunks) >= 2 else None
     return SearchHit(
         chunk_id=_chunk_id_from_row(row),
         symbol_id=_chunk_to_symbol_id(row),
@@ -606,6 +610,8 @@ def _row_to_search_hit(row: dict[str, Any]) -> SearchHit:
         role=str(row.get("role")) if row.get("role") else None,
         filename=filename,
         start_line=start_line,
+        score_components=row.get("_score_components") if explain else None,
+        chunks=chunks_int,
     )
 
 
@@ -820,7 +826,9 @@ def search_v2(
     offset: int = 0,
     path_contains: str | None = None,
     filter: NodeFilter | dict[str, Any] | str | None = None,
+    explain: bool = False,
     graph: LadybugGraph | None = None,
+    dedup: bool = True,
 ) -> SearchOutput:
     try:
         raw_filter = _coerce_filter(filter)
@@ -852,6 +860,17 @@ def search_v2(
                 limit=None,
                 offset=None,
             )
+        # hybrid + table='all' is unsupported (hybrid fuses vector+FTS on ONE
+        # table); fail fast with a clean envelope BEFORE loading the embedding
+        # model. run_search also guards this — this is the user-facing fast path.
+        if hybrid and table == "all":
+            return SearchOutput(
+                success=False,
+                message="hybrid search requires a single table; use java, sql, or yaml (not all)",
+                advisories=[],
+                limit=None,
+                offset=None,
+            )
         model_name = resolved_sbert_model_for_process_env(SBERT_MODEL)
         device = os.environ.get("SBERT_DEVICE") or None
         model = _get_sentence_transformer(model_name, device)
@@ -862,29 +881,66 @@ def search_v2(
         if not uri.startswith(("s3://", "gs://", "az://")) and uri_path.exists():
             uri = str(uri_path.resolve())
         table_keys = list(TABLES) if table == "all" else [table]
-        rows = run_search(
-            query,
-            uri=uri,
-            table_keys=table_keys,
-            hybrid=hybrid,
-            limit=limit,
-            offset=offset,
-            path_substring=path_contains,
-            model_name=model_name,
-            device=device,
-            model=model,
-            # Push the NodeFilter structural predicates into the LanceDB query so
-            # they apply BEFORE pagination (issue #353) — previously they were only
-            # a post-filter on the already-paginated page, which could shrink or
-            # empty filtered pages even when many matches existed deeper in the
-            # ranking. _node_matches_filter below still re-checks every row (it
-            # covers the non-pushdownable fields and is the contract guarantee).
-            role=nf.role if nf else None,
-            module=nf.module if nf else None,
-            microservice=nf.microservice if nf else None,
-            capability=nf.capability if nf else None,
-            exclude_roles=nf.exclude_roles if nf else None,
-        )
+
+        # Graceful fallback: if hybrid=True and FTS index is missing (old index),
+        # retry with hybrid=False and return vector-only results with an advisory.
+        advisories: list[str] = []
+        try:
+            rows = run_search(
+                query,
+                uri=uri,
+                table_keys=table_keys,
+                hybrid=hybrid,
+                limit=limit,
+                offset=offset,
+                path_substring=path_contains,
+                model_name=model_name,
+                device=device,
+                model=model,
+                # Push the NodeFilter structural predicates into the LanceDB query so
+                # they apply BEFORE pagination (issue #353) — previously they were only
+                # a post-filter on the already-paginated page, which could shrink or
+                # empty filtered pages even when many matches existed deeper in the
+                # ranking. _node_matches_filter below still re-checks every row (it
+                # covers the non-pushdownable fields and is the contract guarantee).
+                role=nf.role if nf else None,
+                module=nf.module if nf else None,
+                microservice=nf.microservice if nf else None,
+                capability=nf.capability if nf else None,
+                exclude_roles=nf.exclude_roles if nf else None,
+                dedup_by_fqn=dedup,
+            )
+        except Exception as exc:
+            # Check if this is a missing-FTS error (old index built before PR-SEARCH-3)
+            exc_text = str(exc).lower()
+            is_fts_missing = "full text search" in exc_text or "inverted index" in exc_text
+            if hybrid and is_fts_missing:
+                # Retry with vector-only search
+                rows = run_search(
+                    query,
+                    uri=uri,
+                    table_keys=table_keys,
+                    hybrid=False,  # Fallback to vector-only
+                    limit=limit,
+                    offset=offset,
+                    path_substring=path_contains,
+                    model_name=model_name,
+                    device=device,
+                    model=model,
+                    role=nf.role if nf else None,
+                    module=nf.module if nf else None,
+                    microservice=nf.microservice if nf else None,
+                    capability=nf.capability if nf else None,
+                    exclude_roles=nf.exclude_roles if nf else None,
+                    dedup_by_fqn=dedup,
+                )
+                advisories.append(
+                    f"hybrid unavailable on table '{table}' (FTS index missing on this index built before "
+                    f"PR-SEARCH-3); fell back to vector-only — reindex to enable hybrid"
+                )
+            else:
+                # Non-FTS error: surface as structured failure
+                raise
         hits: list[SearchHit] = []
         for row in rows:
             if path_contains and path_contains not in str(row.get("filename") or ""):
@@ -893,7 +949,7 @@ def search_v2(
                 row_kind = "symbol"
                 if not _node_matches_filter(row_kind, row, nf):
                     continue
-            hits.append(_row_to_search_hit(row))
+            hits.append(_row_to_search_hit(row, explain=explain))
         hint_payload = {
             "success": True,
             "results": [h.model_dump() for h in hits],
@@ -906,7 +962,7 @@ def search_v2(
             results=hits,
             limit=limit,
             offset=offset,
-            advisories=raw_advisories,
+            advisories=advisories + raw_advisories,  # Merge fallback + hints advisories
             hints_structured=_to_structured_hints(raw_struct),
         )
     except Exception as exc: