java-codebase-rag 0.9.5__py3-none-any.whl → 0.9.7__py3-none-any.whl

absence_diagnosis.py → java_codebase_rag/absence/absence_diagnosis.py

@@ -30,7 +30,7 @@ from collections import Counter
 from difflib import SequenceMatcher
 from typing import Any, Literal
 
-from absence_types import (
+from java_codebase_rag.absence.absence_types import (
     AbsenceDiagnosis,
     AbsenceProof,
     ExternalIdentity,
@@ -38,9 +38,9 @@ from absence_types import (
     FilterRelaxationDim,
     VocabularyContext,
 )
-from absence_vocab import SymbolRecord, VocabularyIndex, _normalize_name
-from graph_types import NodeRef
-from mcp_hints import _IDENTIFIER_FILTER_FIELDS
+from java_codebase_rag.absence.absence_vocab import SymbolRecord, VocabularyIndex, _normalize_name
+from java_codebase_rag.graph.graph_types import NodeRef
+from java_codebase_rag.mcp.mcp_hints import _IDENTIFIER_FILTER_FIELDS
 
 log = logging.getLogger(__name__)
 

absence_types.py → java_codebase_rag/absence/absence_types.py

@@ -8,7 +8,7 @@ from typing import Literal
 
 from pydantic import BaseModel, Field
 
-from graph_types import NodeRef
+from java_codebase_rag.graph.graph_types import NodeRef
 
 __all__ = [
     "AbsenceVerdict",

absence_vocab.py → java_codebase_rag/absence/absence_vocab.py

@@ -204,7 +204,7 @@ class VocabularyIndex:
             VocabIndexStale: If sidecar format_version or ontology_version
                 doesn't match expected
         """
-        from ast_java import ONTOLOGY_VERSION
+        from java_codebase_rag.ast.ast_java import ONTOLOGY_VERSION
 
         with open(path, encoding="utf-8") as f:
             data = json.load(f)
@@ -304,7 +304,7 @@ class VocabularyIndex:
         Returns:
             (is_external, reason) tuple
         """
-        from ladybug_queries import _is_external_fqn, _EXTERNAL_PREFIXES
+        from java_codebase_rag.graph.ladybug_queries import _is_external_fqn, _EXTERNAL_PREFIXES
 
         # First, check if it's an external prefix (highest priority)
         if _is_external_fqn(name):
@@ -354,7 +354,7 @@ def get_vocabulary_index(graph: Any, cfg: Any) -> VocabularyIndex:
     Returns:
         VocabularyIndex (cached or newly built)
     """
-    from ast_java import ONTOLOGY_VERSION
+    from java_codebase_rag.ast.ast_java import ONTOLOGY_VERSION
 
     # Determine graph db path for cache key
     db_path = graph.db_path if hasattr(graph, 'db_path') else str(cfg.ladybug_path)
@@ -375,8 +375,13 @@ def get_vocabulary_index(graph: Any, cfg: Any) -> VocabularyIndex:
         # (JSONDecodeError/KeyError) — all subsumed by Exception; rebuild.
         log.debug(f"Vocab index missing/stale/corrupt ({e}), rebuilding from graph")
 
-        # Build from graph
-        index = VocabularyIndex.build(graph, q=cfg.absence_ngram_q)
+        # Build from graph. Coerce q to int (mirror absence_diagnosis.py's
+        # int(getattr(cfg, ...)) pattern): a non-int cfg.absence_ngram_q (e.g. a
+        # MagicMock cfg from a leaked test mock, or a YAML string) would otherwise
+        # crash _qgrams at `len(text) < q` ('int < MagicMock'). Default 3 = the
+        # config default for absence_ngram_q.
+        q = int(getattr(cfg, "absence_ngram_q", 3) or 3)
+        index = VocabularyIndex.build(graph, q=q)
 
         # Save to sidecar (best-effort)
         try:
@@ -403,7 +408,7 @@ def reset_cache() -> None:
 
 def _row_to_symbol_record(row: dict[str, Any]) -> SymbolRecord:
     """Convert a Ladybug row to a SymbolRecord."""
-    from ladybug_queries import _type_part_fqn
+    from java_codebase_rag.graph.ladybug_queries import _type_part_fqn
 
     fqn = row.get("fqn") or ""
     name = row.get("name") or ""

pr_analysis.py → java_codebase_rag/analysis/pr_analysis.py

@@ -12,7 +12,7 @@ from typing import Any
 from unidiff import PatchSet
 from unidiff.errors import UnidiffParseError
 
-from ladybug_queries import SymbolHit, find_symbols_in_file_range, _row_to_symbol
+from java_codebase_rag.graph.ladybug_queries import SymbolHit, find_symbols_in_file_range, _row_to_symbol
 
 
 @dataclass

resolve_service.py → java_codebase_rag/analysis/resolve_service.py

@@ -10,10 +10,10 @@ from typing import Any, Literal
 
 from pydantic import BaseModel, ConfigDict, Field
 
-from absence_types import AbsenceDiagnosis
-from absence_diagnosis import diagnose
-from absence_vocab import get_vocabulary_index
-from graph_types import (
+from java_codebase_rag.absence.absence_types import AbsenceDiagnosis
+from java_codebase_rag.absence.absence_diagnosis import diagnose
+from java_codebase_rag.absence.absence_vocab import get_vocabulary_index
+from java_codebase_rag.graph.graph_types import (
     NodeRef,
     StructuredHint,
     _hints_or_skip,
@@ -21,9 +21,9 @@ from graph_types import (
     _to_structured_hints,
     set_hints_enabled,
 )
-from java_ontology import ResolveReason
-from ladybug_queries import LadybugGraph
-from mcp_hints import MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION
+from java_codebase_rag.graph.java_ontology import ResolveReason
+from java_codebase_rag.graph.ladybug_queries import LadybugGraph
+from java_codebase_rag.mcp.mcp_hints import MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION
 
 __all__ = [
     "resolve_v2",

ast_java.py → java_codebase_rag/ast/ast_java.py

@@ -20,7 +20,7 @@ from typing import Iterable
 
 import tree_sitter_java as _ts_java
 
-from brownfield_events import (
+from java_codebase_rag.ast.brownfield_events import (
     emit_brownfield_exclusivity_shadowing,
     emit_brownfield_method_string_literal,
 )
@@ -1617,7 +1617,7 @@ def _parse_codebase_http_client_annotation(
         val, vkind = _annotation_value(pairs["clientKind"], src)
         if val and vkind == "enum":
             kind_val = str(val)
-            from java_ontology import VALID_CLIENT_KINDS  # deferred: java_ontology imports ast_java
+            from java_codebase_rag.graph.java_ontology import VALID_CLIENT_KINDS  # deferred: java_ontology imports ast_java
             if kind_val in VALID_CLIENT_KINDS:
                 client_kind = kind_val
             else:
@@ -1697,7 +1697,7 @@ def _parse_codebase_producer_annotation(
         val, vkind = _annotation_value(kind_node, src)
         if val and vkind == "enum":
             kind_val = str(val)
-            from java_ontology import VALID_PRODUCER_KINDS  # deferred: java_ontology imports ast_java
+            from java_codebase_rag.graph.java_ontology import VALID_PRODUCER_KINDS  # deferred: java_ontology imports ast_java
             if kind_val in VALID_PRODUCER_KINDS:
                 client_kind = kind_val
             else:
@@ -1868,7 +1868,7 @@ def _collect_outgoing_calls(
     file_rel: str,
 ) -> list[OutgoingCallDecl]:
     del project_root
-    from java_ontology import (  # deferred: java_ontology imports ast_java
+    from java_codebase_rag.graph.java_ontology import (  # deferred: java_ontology imports ast_java
         CLIENT_KIND_FEIGN_METHOD,
         CLIENT_KIND_REST_TEMPLATE,
         CLIENT_KIND_WEB_CLIENT,

java_codebase_rag/cli.py

@@ -36,7 +36,7 @@ from java_codebase_rag.pipeline import (
     run_cocoindex_update,
     run_incremental_graph,
 )
-from java_ontology import VALID_UNRESOLVED_CALL_REASONS
+from java_codebase_rag.graph.java_ontology import VALID_UNRESOLVED_CALL_REASONS
 
 LADYBUG_INCREMENTAL_TRACKING_ISSUE_URL = "https://github.com/HumanBean17/java-codebase-rag/issues/73"
 
@@ -602,7 +602,7 @@ def _cmd_reprocess(args: argparse.Namespace) -> int:
             _emit_reprocess_outcome(payload, selective_tty_mode="graph" if ok else None)
             return _reprocess_exit_code(payload)
 
-        import server  # lazy: pulls sentence_transformers/torch/lancedb/ladybug
+        from java_codebase_rag.mcp import server  # lazy: pulls sentence_transformers/torch/lancedb/ladybug
 
         result = asyncio.run(
             server.run_refresh_pipeline(
@@ -677,7 +677,7 @@ def _cmd_erase(args: argparse.Namespace) -> int:
     # tree_sitter (~54ms), and these filenames are only needed on the erase path.
     # Keeping it out of the top-level import lets `java-codebase-rag --help` (and
     # every other command) stay fast -- see the lazy-import invariant atop this file.
-    from build_ast_graph import BUILDER_OWNED_INDEX_FILES
+    from java_codebase_rag.graph.build_ast_graph import BUILDER_OWNED_INDEX_FILES
     builder_paths = [cfg.ladybug_path.parent / name for name in BUILDER_OWNED_INDEX_FILES]
     operator_paths = [cfg.index_dir / name for name in OPERATOR_OWNED_INDEX_FILES]
     to_describe: list[Path] = [
@@ -768,12 +768,12 @@ def _cmd_erase(args: argparse.Namespace) -> int:
 
 
 def _cmd_meta(args: argparse.Namespace) -> int:
-    import server  # lazy
+    from java_codebase_rag.mcp import server  # lazy
 
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
     cfg.apply_to_os_environ()
-    from ladybug_queries import LadybugGraph  # lazy
+    from java_codebase_rag.graph.ladybug_queries import LadybugGraph  # lazy
 
     LadybugGraph._instance = None
     LadybugGraph._instance_path = None
@@ -792,7 +792,7 @@ def _cmd_meta(args: argparse.Namespace) -> int:
 
 
 def _cmd_tables(args: argparse.Namespace) -> int:
-    import server  # lazy
+    from java_codebase_rag.mcp import server  # lazy
 
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
@@ -803,8 +803,8 @@ def _cmd_tables(args: argparse.Namespace) -> int:
 
 
 def _cmd_diagnose_ignore(args: argparse.Namespace) -> int:
-    import server  # lazy
-    from path_filtering import LayeredIgnore  # lazy
+    from java_codebase_rag.mcp import server  # lazy
+    from java_codebase_rag.graph.path_filtering import LayeredIgnore  # lazy
 
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
@@ -833,7 +833,7 @@ def _cmd_unresolved_calls_list(args: argparse.Namespace) -> int:
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
     cfg.apply_to_os_environ()
-    from ladybug_queries import LadybugGraph  # lazy
+    from java_codebase_rag.graph.ladybug_queries import LadybugGraph  # lazy
 
     if not LadybugGraph.exists():
         _emit({"success": False, "message": "LadybugDB graph not found"})
@@ -854,7 +854,7 @@ def _cmd_unresolved_calls_stats(args: argparse.Namespace) -> int:
     cfg = _resolved_from_ns(args)
     _startup_hints(cfg)
     cfg.apply_to_os_environ()
-    from ladybug_queries import LadybugGraph  # lazy
+    from java_codebase_rag.graph.ladybug_queries import LadybugGraph  # lazy
 
     if not LadybugGraph.exists():
         _emit({"success": False, "message": "LadybugDB graph not found"})
@@ -878,8 +878,8 @@ def _cmd_analyze_pr(args: argparse.Namespace) -> int:
     if not diff_text.strip():
         _emit({"success": False, "message": "Diff is empty"})
         return 1
-    import pr_analysis  # lazy
-    from ladybug_queries import LadybugGraph  # lazy
+    from java_codebase_rag.analysis import pr_analysis  # lazy
+    from java_codebase_rag.graph.ladybug_queries import LadybugGraph  # lazy
 
     if not LadybugGraph.exists():
         _emit({"success": False, "message": "LadybugDB graph not found"})

build_ast_graph.py → java_codebase_rag/graph/build_ast_graph.py

@@ -41,7 +41,7 @@ from pathlib import Path
 import ladybug
 import pyarrow as pa
 
-from ast_java import (
+from java_codebase_rag.ast.ast_java import (
     ONTOLOGY_VERSION,
     CallSite,
     JavaFileAst,
@@ -52,7 +52,7 @@ from ast_java import (
     lombok_required_args_annotations,
     parse_java,
 )
-from graph_enrich import (
+from java_codebase_rag.graph.graph_enrich import (
     _load_config_cross_service_resolution,
     classify_java_file,
     collect_annotation_meta_chain,
@@ -67,8 +67,8 @@ from graph_enrich import (
     resolve_routes_for_method,
     symbol_id,
 )
-from path_filtering import LayeredIgnore, iter_java_source_files
-from java_ontology import (
+from java_codebase_rag.graph.path_filtering import LayeredIgnore, iter_java_source_files
+from java_codebase_rag.graph.java_ontology import (
     CLIENT_KIND_FEIGN_METHOD,
     CLIENT_KIND_REST_TEMPLATE,
     VALID_CLIENT_KINDS,
@@ -4256,8 +4256,8 @@ def _try_build_vocabulary_index(db_path: Path, source_root: Path, verbose: bool)
         verbose: Whether to emit verbose progress
     """
     try:
-        from absence_vocab import VocabularyIndex, VOCAB_INDEX_FILENAME
-        from ladybug_queries import LadybugGraph
+        from java_codebase_rag.absence.absence_vocab import VocabularyIndex, VOCAB_INDEX_FILENAME
+        from java_codebase_rag.graph.ladybug_queries import LadybugGraph
 
         t0 = time.time()
         if verbose:

graph_enrich.py → java_codebase_rag/graph/graph_enrich.py

@@ -25,7 +25,7 @@ from dataclasses import dataclass, field, replace
 from functools import lru_cache
 from pathlib import Path
 from typing import Any, TypeVar
-from ast_java import (
+from java_codebase_rag.ast.ast_java import (
     AnnotationRef,
     JavaFileAst,
     MethodDecl,
@@ -43,7 +43,7 @@ from ast_java import (
     _METHOD_ANN_TO_CAPABILITY,
     _TYPE_ANN_TO_CAPABILITY,
 )
-from java_ontology import (
+from java_codebase_rag.graph.java_ontology import (
     CLIENT_KIND_REST_TEMPLATE,
     VALID_CAPABILITIES,
     VALID_CLIENT_KINDS,
@@ -52,7 +52,7 @@ from java_ontology import (
     VALID_ROUTE_FRAMEWORKS,
     VALID_ROUTE_KINDS,
 )
-from path_filtering import LayeredIgnore, iter_java_source_files
+from java_codebase_rag.graph.path_filtering import LayeredIgnore, iter_java_source_files
 
 __all__ = [
     "AnnotationDecl",

graph_types.py → java_codebase_rag/graph/graph_types.py

@@ -10,8 +10,8 @@ from typing import Any, Literal
 
 from pydantic import BaseModel
 
-from ladybug_queries import LadybugGraph
-from mcp_hints import generate_hints
+from java_codebase_rag.graph.ladybug_queries import LadybugGraph
+from java_codebase_rag.mcp.mcp_hints import generate_hints
 
 __all__ = [
     "NodeRef",

java_ontology.py → java_codebase_rag/graph/java_ontology.py

@@ -7,7 +7,7 @@ from __future__ import annotations
 from dataclasses import dataclass
 from typing import Literal
 
-from ast_java import (
+from java_codebase_rag.ast.ast_java import (
     ROLE_ANNOTATIONS,
     _INJECTED_TYPES_TO_CAPABILITY,
     _METHOD_ANN_TO_CAPABILITY,

ladybug_queries.py → java_codebase_rag/graph/ladybug_queries.py

@@ -6,7 +6,7 @@ so the MCP server can serialize them without further mapping.
 The Ladybug database is opened read-only and cached per-process. This module is
 intentionally dependency-light: nothing here imports LanceDB or sentence-transformers.
 
-Cypher pitfalls (see also ``AGENTS.md``): avoid ``label(e) IN $list`` in ``WHERE`` for
+Cypher pitfalls (see also ``CLAUDE.md``): avoid ``label(e) IN $list`` in ``WHERE`` for
 relationship-type filters; use OR of ``label(e) = $param`` with bound parameters.
 Typed unions ``-[e:A|B]-`` require every ``RETURN`` column on ``e`` to exist on all
 listed rel types, or the binder may fail.
@@ -24,7 +24,7 @@ from typing import Any, Literal
 
 import ladybug
 
-from ast_java import ONTOLOGY_VERSION as _ONTOLOGY_VERSION
+from java_codebase_rag.ast.ast_java import ONTOLOGY_VERSION as _ONTOLOGY_VERSION
 
 log = logging.getLogger(__name__)
 

java_index_flow_lancedb.py → java_codebase_rag/index/java_index_flow_lancedb.py

@@ -41,7 +41,7 @@ from cocoindex.resources.file import PatternFilePathMatcher
 
 from java_codebase_rag.config import resolved_sbert_model_for_process_env
 from java_codebase_rag.lance_optimize import LANCE_TABLE_NAMES
-from java_index_v1_common import (
+from java_codebase_rag.index.java_index_v1_common import (
     JAVA_CHUNK,
     SBERT_MODEL,
     SQL_CHUNK,
@@ -49,9 +49,9 @@ from java_index_v1_common import (
     chunk_key_range,
     position_to_json,
 )
-from path_filtering import LayeredIgnore
-from ast_java import ONTOLOGY_VERSION, parse_java
-from graph_enrich import (
+from java_codebase_rag.graph.path_filtering import LayeredIgnore
+from java_codebase_rag.ast.ast_java import ONTOLOGY_VERSION, parse_java
+from java_codebase_rag.graph.graph_enrich import (
     classify_java_file,
     collect_annotation_meta_chain,
     enrich_chunk,

java_codebase_rag/jrag.py

@@ -134,7 +134,7 @@ def _apply_auto_scope(args: argparse.Namespace, cfg, graph) -> None:
     source_root = cfg.source_root if cfg.source_root else None
     if not source_root:
         return
-    from graph_enrich import detect_microservice_from_path
+    from java_codebase_rag.graph.graph_enrich import detect_microservice_from_path
 
     candidate = detect_microservice_from_path(Path.cwd(), Path(source_root))
     if not candidate:
@@ -1217,7 +1217,7 @@ def _load_graph(cfg):  # type: ignore[no-untyped-def]
     * ontology-mismatch (``RuntimeError`` from ``LadybugGraph.get``) ->
       ``_IndexStale`` (caught in ``main`` -> envelope with a rebuild hint).
     """
-    from ladybug_queries import LadybugGraph
+    from java_codebase_rag.graph.ladybug_queries import LadybugGraph
 
     ladybug_path = str(cfg.ladybug_path)
     if not LadybugGraph.exists(ladybug_path):
@@ -1233,8 +1233,8 @@ def _load_graph(cfg):  # type: ignore[no-untyped-def]
 
 def _cmd_vocab_index(args: argparse.Namespace) -> int:
     """Rebuild the vocabulary index sidecar from the Ladybug graph."""
-    from ast_java import ONTOLOGY_VERSION
-    from absence_vocab import VocabularyIndex, VOCAB_INDEX_FILENAME
+    from java_codebase_rag.ast.ast_java import ONTOLOGY_VERSION
+    from java_codebase_rag.absence.absence_vocab import VocabularyIndex, VOCAB_INDEX_FILENAME
 
     cfg = _resolve_cfg(args)
     try:
@@ -1565,7 +1565,7 @@ def _build_node_filter_or_error(filter_dict: dict):
     A bad enum (e.g. ``--role FOO``) should be a user-facing validation error,
     not an internal crash. Returns ``(node_filter, None)`` on success.
     """
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     from java_codebase_rag.jrag_envelope import Envelope
     from pydantic import ValidationError
@@ -1591,7 +1591,7 @@ def _cmd_find_filter_mode(
     limit: int,
 ) -> int:
     """Find filter mode: build NodeFilter and call find_v2."""
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     from java_codebase_rag.jrag_envelope import Envelope, next_actions_hook, normalize_enum, to_envelope_rows
     from java_codebase_rag.jrag_render import render
@@ -1674,7 +1674,7 @@ def _cmd_find_filter_mode(
 
 
 def _cmd_inspect(args: argparse.Namespace) -> int:
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     from java_codebase_rag.jrag_envelope import Envelope, next_actions_hook, resolve_query
     from java_codebase_rag.jrag_render import render
@@ -2574,7 +2574,7 @@ def _cmd_callees(args: argparse.Namespace) -> int:
     # Producer root -> ASYNC_CALLS out (Producer -> :Route, the kafka_topic
     # Route this producer publishes to — NOT a :Producer node).
     if node.kind in ("client", "producer"):
-        import mcp_v2
+        from java_codebase_rag.mcp import mcp_v2
 
         edge_types = ["HTTP_CALLS"] if node.kind == "client" else ["ASYNC_CALLS"]
         out = mcp_v2.neighbors_v2(
@@ -2710,7 +2710,7 @@ def _cmd_callees(args: argparse.Namespace) -> int:
 
 
 def _cmd_hierarchy(args: argparse.Namespace) -> int:
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     cfg, graph, rc = _load_graph_or_error(args)
     if rc:
@@ -2863,7 +2863,7 @@ def _cmd_subclasses(args: argparse.Namespace) -> int:
 
 
 def _cmd_overrides(args: argparse.Namespace) -> int:
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     cfg, graph, rc = _load_graph_or_error(args)
     if rc:
@@ -2916,7 +2916,7 @@ def _cmd_overrides(args: argparse.Namespace) -> int:
 
 
 def _cmd_overridden_by(args: argparse.Namespace) -> int:
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     cfg, graph, rc = _load_graph_or_error(args)
     if rc:
@@ -3224,7 +3224,7 @@ def _cmd_flow(args: argparse.Namespace) -> int:
 
 
 def _cmd_dependencies(args: argparse.Namespace) -> int:
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     cfg, graph, rc = _load_graph_or_error(args)
     if rc:
@@ -3559,7 +3559,7 @@ def _cmd_outline(args: argparse.Namespace) -> int:
     start_line<1). ``--limit`` caps the entry count (the file's symbol table
     is otherwise unbounded); ``truncated`` is set when more entries exist.
     """
-    from ladybug_queries import find_symbols_in_file_range
+    from java_codebase_rag.graph.ladybug_queries import find_symbols_in_file_range
 
     from java_codebase_rag.jrag_envelope import Envelope, mark_truncated, next_actions_hook
     from java_codebase_rag.jrag_render import render
@@ -3629,8 +3629,8 @@ def _cmd_imports(args: argparse.Namespace) -> int:
     a node per import: resolved graph Symbol when resolve_v2 hits (status=one),
     or an unresolved placeholder carrying the raw FQN otherwise.
     """
-    from ast_java import parse_java
-    from resolve_service import resolve_v2
+    from java_codebase_rag.ast.ast_java import parse_java
+    from java_codebase_rag.analysis.resolve_service import resolve_v2
 
     from java_codebase_rag.jrag_envelope import Envelope, next_actions_hook
     from java_codebase_rag.jrag_render import render
@@ -4195,7 +4195,7 @@ def _zero_result_guidance(args: argparse.Namespace, graph) -> str | None:
     empty (truly no matches for this query), or the probe itself errored
     (non-fatal — the empty result still renders).
     """
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
     from collections import Counter
 
     from java_codebase_rag.jrag_envelope import normalize_enum
@@ -4250,7 +4250,7 @@ def _cmd_search(args: argparse.Namespace) -> int:
     truncation, and renders. --fuzzy is rejected IN-HANDLER (not argparse-exit)
     so the error carries the canonical envelope shape.
     """
-    import mcp_v2
+    from java_codebase_rag.mcp import mcp_v2
 
     from java_codebase_rag.jrag_envelope import Envelope, mark_truncated, next_actions_hook, normalize_enum
     from java_codebase_rag.jrag_render import render
@@ -4375,7 +4375,7 @@ def _cmd_search(args: argparse.Namespace) -> int:
             # explain renderer from there would crash `jrag search ... --explain` on the
             # exact Intel install that runs the lexical path. search_scoring is
             # dependency-free and always installed, so the explain import works everywhere.
-            from search_scoring import explain_score_components
+            from java_codebase_rag.search.search_scoring import explain_score_components
             comps = d.get("score_components")
             d["explain"] = explain_score_components(
                 comps,

java_codebase_rag/jrag_envelope.py

@@ -16,10 +16,11 @@ from __future__ import annotations
 import json
 import re
 from dataclasses import dataclass, field
+from pathlib import Path
 from typing import Any, Literal
 
-from absence_types import AbsenceDiagnosis
-from graph_types import NodeRef
+from java_codebase_rag.absence.absence_types import AbsenceDiagnosis
+from java_codebase_rag.graph.graph_types import NodeRef
 
 __all__ = [
     "Envelope",
@@ -274,10 +275,22 @@ def simple_name(node_dict: dict[str, Any]) -> str:
 
     ``NodeRef`` carries no ``name`` field; the rendering layer derives a short
     label from the FQN on demand. Empty/missing FQN returns "".
+
+    File/package Symbol nodes are the exception: their ``fqn`` is a filesystem
+    path (e.g. ``chat-assign/.../AssignConfiguration.java``), so the dot-split
+    would yield the file *extension* (``java``) instead of a name. When the fqn
+    is a path (contains ``/`` — the indexer POSIX-normalizes via ``.as_posix()``
+    so backslashes don't occur) we return the basename. Route fqns
+    (``"GET /api/x"``) also contain ``/`` but carry a space, so they're excluded
+    here and stay on the dot-split path.
     """
     fqn = str(node_dict.get("fqn") or "")
     if not fqn:
         return ""
+    if "/" in fqn and " " not in fqn:
+        base = Path(fqn).name
+        if base:
+            return base
     return fqn.rsplit(".", 1)[-1]
 
 
@@ -532,10 +545,10 @@ def resolve_query(
     means ``--service`` disambiguates which microservice's route is selected.
     """
     # Lazy imports — keeps build_parser() / `jrag --help` free of resolve/ladybug.
-    from resolve_service import resolve_v2
+    from java_codebase_rag.analysis.resolve_service import resolve_v2
 
     if graph is None:
-        from ladybug_queries import LadybugGraph
+        from java_codebase_rag.graph.ladybug_queries import LadybugGraph
 
         graph = LadybugGraph.get(str(cfg.ladybug_path))
 

java_codebase_rag/jrag_hints.py

@@ -143,7 +143,7 @@ def next_actions(
     # EDGE_SCHEMA is the canonical label set; we use it to skip labels we don't
     # recognize (avoids emitting hints for spurious / future edge types the
     # command map doesn't cover).
-    from java_ontology import EDGE_SCHEMA
+    from java_codebase_rag.graph.java_ontology import EDGE_SCHEMA
 
     # Known virtual labels not in EDGE_SCHEMA (describe-time rollup constructs).
     _VIRTUAL_LABELS = frozenset({"OVERRIDDEN_BY"})

java_codebase_rag/jrag_render.py

@@ -12,7 +12,7 @@ from __future__ import annotations
 
 from typing import Any
 
-from absence_types import AbsenceDiagnosis
+from java_codebase_rag.absence.absence_types import AbsenceDiagnosis
 from java_codebase_rag.jrag_envelope import Envelope, project_envelope, simple_name
 
 __all__ = ["render", "tiered_name", "display_name"]

mcp_hints.py → java_codebase_rag/mcp/mcp_hints.py

@@ -13,7 +13,7 @@ from __future__ import annotations
 import json
 from typing import Any, Literal, NamedTuple
 
-from java_ontology import EDGE_SCHEMA, FUZZY_STRATEGY_SET
+from java_codebase_rag.graph.java_ontology import EDGE_SCHEMA, FUZZY_STRATEGY_SET
 
 # Normative schema description (propose §3.1) — imported by ``mcp_v2`` for Field(description=...).
 MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION = (

mcp_v2.py → java_codebase_rag/mcp/mcp_v2.py

@@ -31,10 +31,10 @@ if TYPE_CHECKING:
     # installs ship without torch/lancedb); it is imported lazily in _get_sentence_transformer.
     from sentence_transformers import SentenceTransformer
 
-from absence_types import AbsenceDiagnosis
-from absence_diagnosis import diagnose
-from absence_vocab import get_vocabulary_index
-from graph_types import (
+from java_codebase_rag.absence.absence_types import AbsenceDiagnosis
+from java_codebase_rag.absence.absence_diagnosis import diagnose
+from java_codebase_rag.absence.absence_vocab import get_vocabulary_index
+from java_codebase_rag.graph.graph_types import (
     NodeRef,
     StructuredHint,
     _hints_or_skip,
@@ -43,11 +43,11 @@ from graph_types import (
     _to_structured_hints,
     set_hints_enabled,
 )
-from index_common import SBERT_MODEL
+from java_codebase_rag.search.index_common import SBERT_MODEL
 from java_codebase_rag.config import resolved_sbert_model_for_process_env
-from java_ontology import EDGE_SCHEMA
-from ladybug_queries import LadybugGraph, OVERRIDE_AXIS_COMPOSED_EDGE_TYPES
-from mcp_hints import MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION
+from java_codebase_rag.graph.java_ontology import EDGE_SCHEMA
+from java_codebase_rag.graph.ladybug_queries import LadybugGraph, OVERRIDE_AXIS_COMPOSED_EDGE_TYPES
+from java_codebase_rag.mcp.mcp_hints import MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION
 
 # The vector stack (lancedb/torch, reached via search_lancedb) is optional — it is absent on
 # graph-only installs (macOS Intel). Import eagerly when available so ``run_search``/``TABLES``
@@ -55,7 +55,7 @@ from mcp_hints import MCP_HINTS_STRUCTURED_FIELD_DESCRIPTION
 # fall back to sentinels on ImportError so importing this module never fails and ``search_v2``
 # can return a clean "vector search unavailable" envelope instead of crashing.
 try:
-    from search_lancedb import TABLES, run_search
+    from java_codebase_rag.search.search_lancedb import TABLES, run_search
 except ImportError:  # graph-only install: no torch/lancedb
     TABLES = {}
     run_search = None
@@ -924,7 +924,7 @@ def search_v2(
             # try -> success=False. It returns [] for sql/yaml (advisory below) and for
             # empty-but-valid results.
             try:
-                from search_lexical import run_lexical_search
+                from java_codebase_rag.search.search_lexical import run_lexical_search
             except ImportError:  # pragma: no cover - search_lexical has no heavy deps
                 run_lexical_search = None  # type: ignore[assignment]
             if run_lexical_search is None:
@@ -1120,6 +1120,20 @@ def find_v2(
         fetch_cap = int(limit) + int(offset) + 1
         if kind == "symbol":
             where, params = _symbol_where_from_filter(nf)
+            # Exclude structural Symbol nodes. Files and packages are :Symbol-
+            # labeled (kind='file'/'package') but aren't code declarations —
+            # without this, `fqn_contains` matches their filesystem-path fqn
+            # (e.g. 'Assign' in '.../DevAssignmentController.java') and surfaces
+            # them as hits. Mirrors search_lexical.py. Safe to apply
+            # unconditionally: DeclarationSymbolKind (the only values
+            # symbol_kind/symbol_kinds can take) excludes 'file'/'package', so no
+            # filter ever requests them.
+            struct_pred = "(s.kind <> 'file' AND s.kind <> 'package')"
+            where = (
+                f"WHERE {struct_pred}"
+                if not where
+                else where.replace("WHERE ", f"WHERE {struct_pred} AND ", 1)
+            )
             params["lim"] = fetch_cap
             rows = g._rows(  # noqa: SLF001
                 f"MATCH (s:Symbol) {where} RETURN s.id AS id, s.fqn AS fqn, s.microservice AS microservice, "
@@ -1711,7 +1725,7 @@ def neighbors_v2(
                 # RETURN anti-pattern, which errors on stricter binders (e.g. Kùzu).
                 # Run one single-label query per type, RETURNing only that type's
                 # columns, and merge the rows. `label(e) = $label` scalar equality
-                # (not `label(e) IN [...]`) per the AGENTS.md Cypher note.
+                # (not `label(e) IN [...]`) per the CLAUDE.md Cypher note.
                 rows: list[dict[str, Any]] = []
                 match_clause = "MATCH (a)-[e]->(b)" if direction == "out" else "MATCH (a)<-[e]-(b)"
                 for label in flat_labels:
@@ -1850,7 +1864,7 @@ def neighbors_v2(
 
 
 # Re-export resolve symbols from resolve_service.py (imported here to avoid circular import)
-from resolve_service import (  # noqa: E402
+from java_codebase_rag.analysis.resolve_service import (  # noqa: E402
     ResolveCandidate,
     ResolveOutput,
     ResolveStatus,

server.py → java_codebase_rag/mcp/server.py

@@ -9,13 +9,17 @@ import time
 from pathlib import Path
 from typing import Literal
 
-import mcp_v2
-import resolve_service
-from index_common import SBERT_MODEL
+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, vector_stack_installed
+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 (
@@ -25,13 +29,20 @@ from java_codebase_rag.config import (
     resolved_sbert_model_for_process_env,
     resolve_operator_config,
 )
-from ladybug_queries import LadybugGraph, resolve_ladybug_path
+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), "
@@ -114,7 +125,7 @@ class ScopeManager:
         self._log_detection()
 
     def _detect_scope(self) -> str | None:
-        from graph_enrich import detect_microservice_from_path
+        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:
@@ -300,7 +311,7 @@ def _graph_meta_output() -> GraphMetaOutput:
 
 def list_code_index_tables_payload() -> IndexInfoOutput:
     try:
-        from search_lancedb import TABLES
+        from java_codebase_rag.search.search_lancedb import TABLES
 
         tables = dict(TABLES)
     except ImportError:
@@ -333,7 +344,7 @@ async def _run_graph_phase(
     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 = Path(__file__).resolve().parent / "build_ast_graph.py"
+    builder = _BUILDER_FILE
     if not builder.is_file():
         return None, "", "", False
     try:
@@ -415,7 +426,15 @@ async def run_refresh_pipeline(
             phases_run=["graph"] if started else [],
             optimize_error=None,
         )
-    cocoindex_bin = Path(sys.executable).parent / "cocoindex"
+    # 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).
@@ -423,23 +442,21 @@ async def run_refresh_pipeline(
             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}",
+            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 = root / "java_index_flow_lancedb.py"
-    bundle_dir = Path(__file__).resolve().parent
+    flow_path = _FLOW_FILE
     if not flow_path.is_file():
-        fallback = bundle_dir / "java_index_flow_lancedb.py"
-        if fallback.is_file():
-            flow_path = fallback
-        else:
-            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 under {root} nor {bundle_dir}",
-                phases_run=[],
-            )
+        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

java_codebase_rag/pipeline.py

@@ -29,8 +29,17 @@ VECTORS_SKIPPED_GRAPH_ONLY = (
 )
 
 
-def bundle_dir() -> Path:
-    return Path(__file__).resolve().parent.parent
+# Package-internal locations of the cocoindex flow definition and the graph
+# builder. Both are executed *by file path* — cocoindex loads the flow via a
+# ``file:Class`` target (COCOINDEX_TARGET below) and the builder runs as
+# ``python <path>`` — so we must resolve their paths without importing them
+# (this module deliberately stays free of heavy ML imports at import time).
+# Derived from this file's location so they resolve under both editable and
+# wheel installs.
+_PKG_DIR = Path(__file__).resolve().parent
+_FLOW_DIR = _PKG_DIR / "index"
+_FLOW_FILE = _FLOW_DIR / "java_index_flow_lancedb.py"
+_BUILDER_FILE = _PKG_DIR / "graph" / "build_ast_graph.py"
 
 
 def cocoindex_bin() -> Path:
@@ -266,7 +275,7 @@ def _run_cocoindex_update_impl(
             stdout="",
             stderr=f"cocoindex not found: {exe}",
         )
-    bd = bundle_dir()
+    bd = _FLOW_DIR
     flow = bd / "java_index_flow_lancedb.py"
     if not flow.is_file():
         if on_progress is not None:
@@ -343,7 +352,7 @@ def run_cocoindex_drop(env: dict[str, str], *, quiet: bool) -> subprocess.Comple
             stdout="",
             stderr=f"cocoindex not found: {exe}",
         )
-    bd = bundle_dir()
+    bd = _FLOW_DIR
     cmd = [str(exe), "drop", COCOINDEX_TARGET, "-f"]
     if quiet:
         cmd.append("-q")
@@ -366,7 +375,7 @@ def run_build_ast_graph(
     on_progress: Callable[[ProgressEvent], None] | None = None,
     on_progress_console: object | None = None,
 ) -> subprocess.CompletedProcess[str]:
-    builder = bundle_dir() / "build_ast_graph.py"
+    builder = _BUILDER_FILE
     if not builder.is_file():
         return subprocess.CompletedProcess(
             args=[],
@@ -424,7 +433,7 @@ def run_incremental_graph(
     on_progress_console: object | None = None,
 ) -> subprocess.CompletedProcess[str]:
     """Run incremental graph rebuild by passing --incremental flag to build_ast_graph.py."""
-    builder = bundle_dir() / "build_ast_graph.py"
+    builder = _BUILDER_FILE
     if not builder.is_file():
         return subprocess.CompletedProcess(
             args=[],

search_lancedb.py → java_codebase_rag/search/search_lancedb.py

@@ -15,15 +15,15 @@ import lancedb
 import numpy as np
 from sentence_transformers import SentenceTransformer
 
-from chunk_heuristics import analyze_chunk, looks_like_code_identifier
-from index_common import SBERT_MODEL
+from java_codebase_rag.ast.chunk_heuristics import analyze_chunk, looks_like_code_identifier
+from java_codebase_rag.search.index_common import SBERT_MODEL
 from java_codebase_rag.config import maybe_expand_embedding_model_path, resolved_sbert_model_for_process_env
 
 # Scoring & dedup primitives live in `search_scoring` (dependency-free — no
 # lancedb/torch) so the lexical backend `search_lexical` can share them on
 # graph-only (macOS Intel) installs where this module is unimportable. Re-exported
 # here for backward compatibility (`from search_lancedb import _clamp01`, etc.).
-from search_scoring import (  # noqa: F401
+from java_codebase_rag.search.search_scoring import (  # noqa: F401
     DEDUP_OVERFETCH,
     _ACTION_VERB_BONUS,
     _ACTION_VERB_PREFIXES,
@@ -522,7 +522,7 @@ def _graph_expand_merge(
     """Expand vector top-k through the LadybugDB graph and fuse (RRF) with the original list."""
     # Lazy import so the module works without ladybug installed when graph_expand=False.
     try:
-        from ladybug_queries import LadybugGraph
+        from java_codebase_rag.graph.ladybug_queries import LadybugGraph
     except Exception:
         return vector_rows
 

search_lexical.py → java_codebase_rag/search/search_lexical.py

@@ -21,8 +21,8 @@ import os
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
-from ladybug_queries import LadybugGraph
-from search_scoring import (
+from java_codebase_rag.graph.ladybug_queries import LadybugGraph
+from java_codebase_rag.search.search_scoring import (
     _ROLE_SCORE_WEIGHTS,
     _TYPE_MATCH_BONUS_CAP,
     _TYPE_MATCH_BONUS_PER_HIT,
@@ -33,7 +33,7 @@ from search_scoring import (
 )
 
 if TYPE_CHECKING:
-    from mcp_v2 import NodeFilter
+    from java_codebase_rag.mcp.mcp_v2 import NodeFilter
 
 # Lexical relevance weights. The class/file name is the strongest discovery
 # signal (mirrors the type-name bonus rationale in search_scoring); fqn/package

{java_codebase_rag-0.9.5.dist-info → java_codebase_rag-0.9.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: java-codebase-rag
-Version: 0.9.5
+Version: 0.9.7
 Summary: MCP server for semantic + structural search over Java codebases
 Author: HumanBean17
 License-Expression: MIT

java_codebase_rag-0.9.7.dist-info/RECORD

@@ -0,0 +1,57 @@
+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/_version.py,sha256=Dnoh_a-c13fqPQ-HV9CsSPbFUkihUJl_z5CACW4qDyA,1365
+java_codebase_rag/cli.py,sha256=ttPjHgruxsNm69IAjy_UXNPPi-IYb0WjqKBVz7WHMPQ,45604
+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=VPs69os_3co3UPSoBVhpfoVnqDaPJ6Ycbk8A4AyXZOo,30548
+java_codebase_rag/installer.py,sha256=c-_tR1Ct_O3yhmruFRnDoM1Wilz-igD9qdkDPsNqLMI,79934
+java_codebase_rag/jrag.py,sha256=7-erzOy24tp6_iE0zx-3TQ7jqPaM46XQzS-NM-I30EM,199857
+java_codebase_rag/jrag_envelope.py,sha256=I5q7E3DmuJBnDl1iv7bW2NucPJ2YxlmNEtM2dau18Vw,48730
+java_codebase_rag/jrag_hints.py,sha256=aazBRI3pOeyq2IjQuoMzDkA-1cB_tTGbVcguX3BzOiQ,9286
+java_codebase_rag/jrag_render.py,sha256=lRbavEdq395hgZfDoqlKggvilddpJ98f5KNxw-iW-xU,34943
+java_codebase_rag/lance_optimize.py,sha256=HI3aFebP1fenLL6Cav1jMG5kLXSrHLndO_MIJY6qQVo,11977
+java_codebase_rag/pipeline.py,sha256=5xCCjjGE0bpA0q97yKipWAJIAkxDGPvGvhEExSTF4BQ,18891
+java_codebase_rag/progress.py,sha256=2IxdMALDM0wAQCyJrrfZ975zM_85C-4BfHxf4AtYifE,23212
+java_codebase_rag/absence/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/absence/absence_diagnosis.py,sha256=RJNlycQY28fL5h1e7Kupaff-xabLzfzbbXLM-VSReBc,27631
+java_codebase_rag/absence/absence_types.py,sha256=BHOwTVrUAiALFuh4CxX-1hHvxmoG2zYSAcMmJocGZAc,4244
+java_codebase_rag/absence/absence_vocab.py,sha256=t2OYhel70j6ZSlP01xh6kvlvTdygaF6IBEhuTThCiaw,16366
+java_codebase_rag/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/analysis/pr_analysis.py,sha256=b5VTur9_ffB_SCcZ-O8-cYWXwLc7BP-S02hSeTgz9hs,18418
+java_codebase_rag/analysis/resolve_service.py,sha256=vVnCRXDQlFhQfIZljh4Jk5lL63IXC7lEArRWk0Hcs34,28715
+java_codebase_rag/ast/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/ast/ast_java.py,sha256=8na7Sw7UBOMr6KmcQck1U_AMct2UShOn9Jx5o75Y_j8,99513
+java_codebase_rag/ast/brownfield_events.py,sha256=yxXkKDgMb3VPtaiakGzncHM_EGnda8xIue6w90yYp8s,2055
+java_codebase_rag/ast/chunk_heuristics.py,sha256=aQk2NOKxzUdqoUAJUO3G3LE0MN_bYZWNLQ0tkmj5uts,1813
+java_codebase_rag/graph/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/graph/build_ast_graph.py,sha256=xrTz_iGwRzJWWcS-0mPTCVyhsxuApWCkQnf7LOPnWT4,176547
+java_codebase_rag/graph/graph_enrich.py,sha256=51Q8aE0Mw09SVYBESd3H57IftsOpfkwgJV2ibt0RzwE,72598
+java_codebase_rag/graph/graph_types.py,sha256=pezEpYxws4degBmV6V0MHLyg5x9XhixfPgZ-7fhNrVM,4835
+java_codebase_rag/graph/java_ontology.py,sha256=Fa6iCsrBLPc2lCl-6VR2qHN4Q9Ix8Gps3thQhIEGjrM,17241
+java_codebase_rag/graph/ladybug_queries.py,sha256=E1m3VhCC4FfAefeuar8p-Slo_HldpTl5FybN9DO_CnM,100710
+java_codebase_rag/graph/path_filtering.py,sha256=R--XzI51LXBu5IBKMCnJWbkNr6I5d-SDmltyQQnWco0,17674
+java_codebase_rag/index/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/index/java_index_flow_lancedb.py,sha256=RX3NpWIUfghaxDIUBQvOGedtK7ebsJcqbABkD2z_B3Y,29770
+java_codebase_rag/index/java_index_v1_common.py,sha256=nF1KrSqboF_RRvWerG9knRRFmWwsrG_CvhgnsoZ8KqA,1154
+java_codebase_rag/install_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/install_data/agents/explorer-rag-cli.md,sha256=bVmmzrBSSamMz7hDIKxL5alAZOXsJ_Km8TQnCcxDad0,10292
+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=K2qwZqk2xPxjPxXtUHvax1Ug2J7nBYeMTIjRznO100g,10059
+java_codebase_rag/mcp/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/mcp/mcp_hints.py,sha256=eJzm_HpfaEKblT4-FW_9bgvDemZYs3E6exGeznflrXM,42536
+java_codebase_rag/mcp/mcp_v2.py,sha256=h5cvUcU4sDBQqoGFjIR5va8Cr_cIElhPzhx4EnDjFfk,77792
+java_codebase_rag/mcp/server.py,sha256=DJGlx8U5SD4Pe6Ro71OeFHi6HsYZ4r4uINn7R7uSKk4,40935
+java_codebase_rag/search/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+java_codebase_rag/search/index_common.py,sha256=HT6FKHFJ084eFvd3fR1j8z8gf4eWoPHVW8GXLpw464I,285
+java_codebase_rag/search/search_lancedb.py,sha256=1A_yDdZSn7MV7ybgErQvgOwLIoCC7ofZ2tfLk8hvWhE,34582
+java_codebase_rag/search/search_lexical.py,sha256=vXiZkOHMozZuq2aLLTttO1OrCt87aSV9TkmNUOC-pZA,14321
+java_codebase_rag/search/search_scoring.py,sha256=SSs2GLvHCB_gsKPo0N-YPGeAVNWx-TsXXPJO2JPsOOY,12321
+java_codebase_rag-0.9.7.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
+java_codebase_rag-0.9.7.dist-info/METADATA,sha256=FnWq4FTAO_VFNrrh0vpZ_wZeCuh0jHrUSQsq66xbEnQ,20331
+java_codebase_rag-0.9.7.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
+java_codebase_rag-0.9.7.dist-info/entry_points.txt,sha256=pa6yYHbHG7ZZ7G9ZJgYK1Fz6eR9okldPLo7qLY2THuo,190
+java_codebase_rag-0.9.7.dist-info/top_level.txt,sha256=u2i_IKLLOkYyNE32m4TIED0vtKtQDdPEVqRtNuhC1Hk,18
+java_codebase_rag-0.9.7.dist-info/RECORD,,

{java_codebase_rag-0.9.5.dist-info → java_codebase_rag-0.9.7.dist-info}/entry_points.txt

@@ -1,4 +1,4 @@
 [console_scripts]
 java-codebase-rag = java_codebase_rag.cli:_console_script_main
-java-codebase-rag-mcp = server:main
+java-codebase-rag-mcp = java_codebase_rag.mcp.server:main
 jrag = java_codebase_rag.jrag:_console_script_main

java_codebase_rag-0.9.7.dist-info/top_level.txt

@@ -0,0 +1 @@
+java_codebase_rag

java_codebase_rag-0.9.5.dist-info/RECORD

@@ -1,49 +0,0 @@
-absence_diagnosis.py,sha256=EorBpkVM5LRWxaTbmbQ3eo6Ew_V7r6enTgtXfcjqzfw,27533
-absence_types.py,sha256=ukDy1GKgebCYdM0OYJ7a5xoI82M2wd0i0KEJwxQFGlo,4220
-absence_vocab.py,sha256=yySRdonAR8hXv0YpTgvaUV0UzihvbvUuSoIXJa5WBiU,15897
-ast_java.py,sha256=1E5XU5lsc1Ltyv96kSv5VNhRl_KRTsYeHG_qDLgPMcc,99419
-brownfield_events.py,sha256=yxXkKDgMb3VPtaiakGzncHM_EGnda8xIue6w90yYp8s,2055
-build_ast_graph.py,sha256=scaC7TnmmmrjAv3R3qy_30kLb2DH4w7lznLxjDCntOs,176403
-chunk_heuristics.py,sha256=aQk2NOKxzUdqoUAJUO3G3LE0MN_bYZWNLQ0tkmj5uts,1813
-graph_enrich.py,sha256=CYc2K7Zw_CTefaJkL9h6nZmvw3uN8XbIkg4iYQ-ICY0,72528
-graph_types.py,sha256=bf8EEkvWSyRxFQgycTnxxZQwlikLZSU3B-U1Z1cFQtg,4789
-index_common.py,sha256=HT6FKHFJ084eFvd3fR1j8z8gf4eWoPHVW8GXLpw464I,285
-java_index_flow_lancedb.py,sha256=kZh8HgwtGV8Ul_pwdBS7g62hVvKkk8EXTk-qr6NNba8,29676
-java_index_v1_common.py,sha256=nF1KrSqboF_RRvWerG9knRRFmWwsrG_CvhgnsoZ8KqA,1154
-java_ontology.py,sha256=eUGFa96GV_09s2f2sWSMdqYmoxU3-1pyU2iipvcDjG0,17219
-ladybug_queries.py,sha256=SXXNcYxdXCHcQ6SBZdZyqAa-hv5_OFaKsfNx4zVtPgY,100688
-mcp_hints.py,sha256=zp-4cnOmbYD0YovmZiLS2oGcvWcWE7n8jKVz4_xifno,42512
-mcp_v2.py,sha256=Q69-0IOna1XRG06RcEFEsS-YucuBh60sAVIIDKoOnBc,76688
-path_filtering.py,sha256=R--XzI51LXBu5IBKMCnJWbkNr6I5d-SDmltyQQnWco0,17674
-pr_analysis.py,sha256=zrmZZD5yotJtM02Kif6_jgI_oeformOao793akp0N6Y,18394
-resolve_service.py,sha256=EAfWlGQ4U1qKoPCfZ7BZUUy8pm0w9tldga3Krw0_GO4,28543
-search_lancedb.py,sha256=LmratGpyEKcCYohXVTapjGd-rk_kryS93oD43foGZeQ,34486
-search_lexical.py,sha256=6U0SgRH36Qmh3IIPzMi553ztW7MCnCvg5cSlMpxIdu8,14250
-search_scoring.py,sha256=SSs2GLvHCB_gsKPo0N-YPGeAVNWx-TsXXPJO2JPsOOY,12321
-server.py,sha256=SWh7hZshzVuhYqEm6Leq1GS2VP6olml4dz9nrGwf-KM,39889
-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/_version.py,sha256=Dnoh_a-c13fqPQ-HV9CsSPbFUkihUJl_z5CACW4qDyA,1365
-java_codebase_rag/cli.py,sha256=LcNgfOS7r8_vTckuyUbUxI7bhUyYoU_iwzUb37nT5Ts,45296
-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=VPs69os_3co3UPSoBVhpfoVnqDaPJ6Ycbk8A4AyXZOo,30548
-java_codebase_rag/installer.py,sha256=c-_tR1Ct_O3yhmruFRnDoM1Wilz-igD9qdkDPsNqLMI,79934
-java_codebase_rag/jrag.py,sha256=XJN1ejEwxLpTrDJW4lyPjdhP21m7ZRv-JZh73aQDc14,199393
-java_codebase_rag/jrag_envelope.py,sha256=cTe-2lk8-Fvmo9_Ps6rN0QtBSw4muSD_UXvm_rkUc48,47984
-java_codebase_rag/jrag_hints.py,sha256=k2PFE4s3lZgBYHMdZcTjx1-w28nfQcBtQEVsSxI_DvE,9262
-java_codebase_rag/jrag_render.py,sha256=MYPyiB7JiQrSw_KHMjCdWg9JuaxpO3Pv_FI4W7bG8sQ,34917
-java_codebase_rag/lance_optimize.py,sha256=HI3aFebP1fenLL6Cav1jMG5kLXSrHLndO_MIJY6qQVo,11977
-java_codebase_rag/pipeline.py,sha256=OCqBVjkGZOCvzmBElKMes6ynYn9dSN9J1bhRFyEceVE,18355
-java_codebase_rag/progress.py,sha256=2IxdMALDM0wAQCyJrrfZ975zM_85C-4BfHxf4AtYifE,23212
-java_codebase_rag/install_data/agents/explorer-rag-cli.md,sha256=bVmmzrBSSamMz7hDIKxL5alAZOXsJ_Km8TQnCcxDad0,10292
-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=K2qwZqk2xPxjPxXtUHvax1Ug2J7nBYeMTIjRznO100g,10059
-java_codebase_rag-0.9.5.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
-java_codebase_rag-0.9.5.dist-info/METADATA,sha256=cxCb0ljrq1h-E0nS7d7WI8t8LTQwUpIcYNwZXgUkMjM,20331
-java_codebase_rag-0.9.5.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
-java_codebase_rag-0.9.5.dist-info/entry_points.txt,sha256=cj3QTc11UYVQnj9T3orc4daiIGaCYrXP149vKbH2R4U,168
-java_codebase_rag-0.9.5.dist-info/top_level.txt,sha256=gYhQnlcJKpqwIOTwAneruJrkeBzIjoC71LeHMGMZLAY,349
-java_codebase_rag-0.9.5.dist-info/RECORD,,

java_codebase_rag-0.9.5.dist-info/top_level.txt

@@ -1,24 +0,0 @@
-absence_diagnosis
-absence_types
-absence_vocab
-ast_java
-brownfield_events
-build_ast_graph
-chunk_heuristics
-graph_enrich
-graph_types
-index_common
-java_codebase_rag
-java_index_flow_lancedb
-java_index_v1_common
-java_ontology
-ladybug_queries
-mcp_hints
-mcp_v2
-path_filtering
-pr_analysis
-resolve_service
-search_lancedb
-search_lexical
-search_scoring
-server