java-codebase-rag 0.9.5__tar.gz → 0.9.7__tar.gz

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7}/PKG-INFO

@@ -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-0.9.5 → java_codebase_rag-0.9.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "java-codebase-rag"
-version = "0.9.5"
+version = "0.9.7"
 description = "MCP server for semantic + structural search over Java codebases"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -64,36 +64,11 @@ Issues = "https://github.com/HumanBean17/java-codebase-rag/issues"
 
 [project.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"
 
-[tool.setuptools]
-packages = ["java_codebase_rag"]
-py-modules = [
-    "absence_types",
-    "absence_vocab",
-    "absence_diagnosis",
-    "ast_java",
-    "brownfield_events",
-    "build_ast_graph",
-    "chunk_heuristics",
-    "graph_enrich",
-    "graph_types",
-    "index_common",
-    "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",
-]
+[tool.setuptools.packages.find]
+where = ["src"]
 
 [tool.ruff]
 line-length = 100

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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__)
 

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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",

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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 ""

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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",

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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-0.9.5 → java_codebase_rag-0.9.7/src}/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"})

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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:

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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",

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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,

{java_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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_codebase_rag-0.9.5 → java_codebase_rag-0.9.7/src/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-0.9.5 → java_codebase_rag-0.9.7/src}/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-0.9.5 → java_codebase_rag-0.9.7/src}/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-0.9.5 → java_codebase_rag-0.9.7/src}/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"})