chore: polish bundle — correctness/robustness nits (#359) (#370)

* chore: polish bundle — small correctness/robustness nits (#359)

- exclude_roles now disables role weighting (search_lancedb): skip_role_weight
  was bool(role or role_in), so an exclude_roles-only filter still applied role
  weights — asymmetric with role/role_in. Include exclude_roles.
- _parse_ladybug_json quotes only key positions (ladybug_queries): the old
  (\\w+): regex matched word-colon runs inside values too (e.g. a URL), corrupting
  them. Quote keys only after { , [ ; fix the misleading "counts_json" log label.
- resolve rejects wildcards consistently (mcp_v2): * / ? silently returned
  status='none'; search/find/neighbors reject them. Now success=False with a
  pointer to search(query=...). Updated the wildcard test accordingly.
- client-kind literals de-leaked: feign_method/rest_template/web_client emitted
  and matched directly; reference named CLIENT_KIND_* constants from
  java_ontology so a rename can't desync the emit/match sites.
- CALLS dedup key includes call_site_byte (build_ast_graph): two call sites of
  the same method on the same source line (same arg_count) no longer collapse
  into one edge. Regenerated the bank-chat baseline CALLS count (678 -> 684) and
  mirrored the byte-inclusive key in the dedup test.
- malformed YAML no longer silently swallowed (config): catch yaml.YAMLError and
  emit a stderr hint instead of a bare except returning {}.
- table_names() -> list_tables() (config, cli): the lancedb deprecation warning
  is gone (lance_optimize already preferred list_tables).

Deferred: the FastMCP run_stdio_async "coroutine never awaited" RuntimeWarning —
benign (the server runs; run_stdio_async is a clean coroutine awaited by
asyncio.run), root cause elusive without FastMCP stdio-transport internals, and
a speculative entry-point change risks destabilizing server startup.

Co-Authored-By: Claude <noreply@anthropic.com>

* fix(graph): count CALLS with the same 5-tuple key used to write them

_write_meta deduped CALLS with the pre-#370 4-tuple (no call_site_byte)
while _write_edges wrote edges with the 5-tuple, so counts['calls']
(678) diverged from the real CALLS edge count (684) and describe/stats
undercounted. Mirror the 5-tuple in _write_meta and bump the bank-chat
baseline's counts_json.calls to 684.

Verified red->green: with only the fixture bumped, the baseline test
fails (rebuild yields 678); with the _write_meta fix it passes.

Co-Authored-By: Claude <noreply@anthropic.com>

* fix(enrich): use CLIENT_KIND_REST_TEMPLATE at the synthesized-hint site

The client-kind literal de-leak missed graph_enrich.py, which still
emitted the bare "rest_template" default when synthesizing a brownfield
HttpClientHint with no anchor. Reference the named constant so a future
rename in VALID_CLIENT_KINDS cannot silently desync this emit site.

Co-Authored-By: Claude <noreply@anthropic.com>

* fix(config): keep load_yaml_mapping best-effort for read/decode errors

Narrowing the except to yaml.YAMLError let OSError (chmod 000,
stat/read TOCTOU) and UnicodeDecodeError (non-UTF-8 config) propagate
and abort startup, breaking the loader's return-{} contract. Catch all
three so an unreadable/malformed config degrades to defaults; keep the
stderr hint (generalized).

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

Author: HumanBean17

ast_java.py

@@ -1868,6 +1868,11 @@ def _collect_outgoing_calls(
     file_rel: str,
 ) -> list[OutgoingCallDecl]:
     del project_root
+    from java_ontology import (  # deferred: java_ontology imports ast_java
+        CLIENT_KIND_FEIGN_METHOD,
+        CLIENT_KIND_REST_TEMPLATE,
+        CLIENT_KIND_WEB_CLIENT,
+    )
     out: list[OutgoingCallDecl] = []
     method_fqn = f"{type_fqn}#{method_decl.signature}"
     type_mods = _find_modifiers_child(type_node) if type_node is not None else None
@@ -1899,7 +1904,7 @@ def _collect_outgoing_calls(
             OutgoingCallDecl(
                 method_fqn=method_fqn,
                 method_sig=method_decl.signature,
-                client_kind="feign_method",
+                client_kind=CLIENT_KIND_FEIGN_METHOD,
                 channel="http",
                 feign_target_name=feign_target_name,
                 feign_target_url=feign_target_url,
@@ -1998,7 +2003,7 @@ def visit(n: Node) -> None:
                     OutgoingCallDecl(
                         method_fqn=method_fqn,
                         method_sig=method_decl.signature,
-                        client_kind="rest_template",
+                        client_kind=CLIENT_KIND_REST_TEMPLATE,
                         channel="http",
                         feign_target_name="",
                         feign_target_url="",
@@ -2051,7 +2056,7 @@ def visit(n: Node) -> None:
                     OutgoingCallDecl(
                         method_fqn=method_fqn,
                         method_sig=method_decl.signature,
-                        client_kind="web_client",
+                        client_kind=CLIENT_KIND_WEB_CLIENT,
                         channel="http",
                         feign_target_name="",
                         feign_target_url="",

build_ast_graph.py

@@ -66,7 +66,13 @@
     symbol_id,
 )
 from path_filtering import LayeredIgnore, iter_java_source_files
-from java_ontology import VALID_CLIENT_KINDS, VALID_HTTP_CALL_MATCHES, VALID_PRODUCER_KINDS
+from java_ontology import (
+    CLIENT_KIND_FEIGN_METHOD,
+    CLIENT_KIND_REST_TEMPLATE,
+    VALID_CLIENT_KINDS,
+    VALID_HTTP_CALL_MATCHES,
+    VALID_PRODUCER_KINDS,
+)
 
 log = logging.getLogger(__name__)
 
@@ -2403,7 +2409,7 @@ def _phantom_async_route_id(call: OutgoingCallDecl) -> str:
                         )
                     rid = ""
                     strategy = call.resolution_strategy
-                    if call.client_kind == "feign_method":
+                    if call.client_kind == CLIENT_KIND_FEIGN_METHOD:
                         exposing = next((e for e in tables.exposes_rows if e.symbol_id == member.node_id), None)
                         if exposing is not None:
                             rid = exposing.route_id
@@ -2606,7 +2612,7 @@ def _match_call_edge(
         return "unresolved", []
 
     candidates: list[RouteRow] = []
-    if call.client_kind == "feign_method":
+    if call.client_kind == CLIENT_KIND_FEIGN_METHOD:
         # Prefer endpoint matching by target service + path/method for Feign declarations.
         path_value = call.path_template_call
         method_value = call.method_call
@@ -2735,7 +2741,7 @@ def _micro_factor(member: MemberEntry | None) -> float:
             if src_route is None and member is not None:
                 # Recover feign caller hints from persisted caller-side Client declarations.
                 for client in client_hints_by_member.get(member.node_id, ()):
-                    if client.client_kind != "feign_method":
+                    if client.client_kind != CLIENT_KIND_FEIGN_METHOD:
                         continue
                     path_template, path_regex = _normalize_path(client.path)
                     src_route = RouteRow(
@@ -2771,7 +2777,7 @@ def _micro_factor(member: MemberEntry | None) -> float:
             call = OutgoingCallDecl(
                 method_fqn=f"{member.parent_fqn}#{member.decl.signature}" if member else "",
                 method_sig=member.decl.signature if member else "",
-                client_kind="feign_method" if _feign_like else "rest_template",
+                client_kind=CLIENT_KIND_FEIGN_METHOD if _feign_like else CLIENT_KIND_REST_TEMPLATE,
                 channel="http",
                 feign_target_name=src_route.feign_name if src_route else "",
                 feign_target_url=src_route.feign_url if src_route else "",
@@ -3454,13 +3460,15 @@ def _write_edges(conn: ladybug.Connection, tables: GraphTables, _file_by_node_id
     _bulk_copy(conn, "OVERRIDES", _REL_OVERRIDES_COLUMNS, overrides_rows)
 
     # Stage CALLS rows with dedup and callee_declaring_role materialization
-    seen_calls: set[tuple[str, str, int, int]] = set()
+    seen_calls: set[tuple[str, str, int, int, int]] = set()
     calls_rows: list[dict] = []
     member_by_id = {m.node_id: m for m in tables.members}
     for row in tables.calls_rows:
         if row.src_id not in valid_ids or row.dst_id not in valid_ids:
             continue
-        key = (row.src_id, row.dst_id, row.arg_count, row.call_site_line)
+        # Include call_site_byte so two call sites of the same method on the same
+        # source line (same arg_count) are kept as distinct edges (issue #359).
+        key = (row.src_id, row.dst_id, row.arg_count, row.call_site_line, row.call_site_byte)
         if key in seen_calls:
             continue
         seen_calls.add(key)
@@ -3636,10 +3644,15 @@ def _write_routes_and_exposes(conn: ladybug.Connection, tables: GraphTables, _fi
 
 
 def _write_meta(conn: ladybug.Connection, tables: GraphTables, source_root: Path) -> None:
-    seen_calls: set[tuple[str, str, int, int]] = set()
+    # Dedup key MUST match _write_edges (build_ast_graph.py, _REL_CALLS writer): the
+    # 5-tuple includes call_site_byte so two call sites of the same method on the
+    # same source line are counted separately. A previous version used the 4-tuple
+    # here, which made counts['calls'] (678) diverge from the real CALLS edge count
+    # (684) that _write_edges actually persisted — describe/stats then undercounted.
+    seen_calls: set[tuple[str, str, int, int, int]] = set()
     calls_unique = 0
     for row in tables.calls_rows:
-        key = (row.src_id, row.dst_id, row.arg_count, row.call_site_line)
+        key = (row.src_id, row.dst_id, row.arg_count, row.call_site_line, row.call_site_byte)
         if key not in seen_calls:
             seen_calls.add(key)
             calls_unique += 1

graph_enrich.py

@@ -43,6 +43,7 @@
     _TYPE_ANN_TO_CAPABILITY,
 )
 from java_ontology import (
+    CLIENT_KIND_REST_TEMPLATE,
     VALID_CAPABILITIES,
     VALID_CLIENT_KINDS,
     VALID_PRODUCER_KINDS,
@@ -1301,7 +1302,7 @@ def resolve_http_client_for_method(
             hint = overrides.annotation_to_http_client_hint.get("CodebaseHttpClient")
             if hint is None:
                 hint = HttpClientHint(
-                    client_kind=anchor.client_kind if anchor else "rest_template",
+                    client_kind=anchor.client_kind if anchor else CLIENT_KIND_REST_TEMPLATE,
                     target_service=anchor.feign_target_name if anchor else "",
                     path=anchor.path_template_call if anchor else "",
                     method=anchor.method_call if anchor else "",

java_codebase_rag/cli.py

@@ -617,7 +617,7 @@ def _cmd_erase(args: argparse.Namespace) -> int:
             import lancedb
 
             db = lancedb.connect(str(cfg.index_dir.resolve()))
-            for name in db.table_names():
+            for name in db.list_tables():
                 to_describe.append(cfg.index_dir / name)
         except Exception:
             pass
@@ -665,7 +665,7 @@ def work(progress: "PipelineProgress | None") -> int:
                 import lancedb
 
                 db = lancedb.connect(str(cfg.index_dir.resolve()))
-                for name in list(db.table_names()):
+                for name in list(db.list_tables()):
                     try:
                         db.drop_table(name)
                     except Exception as exc:

java_codebase_rag/config.py

@@ -244,7 +244,17 @@ def load_yaml_mapping(source_root: Path) -> dict[str, Any]:
         return {}
     try:
         data = yaml.safe_load(path.read_text(encoding="utf-8"))
-    except Exception:
+    except (yaml.YAMLError, OSError, UnicodeDecodeError) as exc:
+        # Best-effort loader: a missing/unreadable/malformed config must NOT abort
+        # startup — return {} and proceed with defaults. Narrowing this to
+        # ``yaml.YAMLError`` alone let OSError (chmod 000, stat/read TOCTOU) and
+        # UnicodeDecodeError (non-UTF-8 config) propagate to the caller; the broader
+        # tuple restores the graceful-degradation contract while still surfacing the
+        # problem on stderr.
+        print(
+            f"java-codebase-rag: could not load config {path}: {exc}; ignoring config.",
+            file=sys.stderr,
+        )
         return {}
     return data if isinstance(data, dict) else {}
 
@@ -483,7 +493,7 @@ def index_dir_has_existing_artifacts(index_dir: Path) -> tuple[bool, list[str]]:
             import lancedb
 
             db = lancedb.connect(str(index_dir.resolve()))
-            for name in db.table_names():
+            for name in db.list_tables():
                 paths.append(str((index_dir / name).resolve()) + " (Lance table)")
         except Exception:
             pass

java_ontology.py

@@ -49,6 +49,11 @@
     "rest_template",
     "web_client",
 ))
+# Named members of VALID_CLIENT_KINDS — reference these at emit/match sites so a
+# rename in the set above cannot silently desync callers (issue #359).
+CLIENT_KIND_FEIGN_METHOD = "feign_method"
+CLIENT_KIND_REST_TEMPLATE = "rest_template"
+CLIENT_KIND_WEB_CLIENT = "web_client"
 
 VALID_PRODUCER_KINDS: frozenset[str] = frozenset((
     "kafka_send",
@@ -433,6 +438,9 @@ class EdgeSpec:
     "VALID_ROUTE_FRAMEWORKS",
     "VALID_ROUTE_KINDS",
     "VALID_CLIENT_KINDS",
+    "CLIENT_KIND_FEIGN_METHOD",
+    "CLIENT_KIND_REST_TEMPLATE",
+    "CLIENT_KIND_WEB_CLIENT",
     "VALID_PRODUCER_KINDS",
     "VALID_HTTP_CALL_STRATEGIES",
     "VALID_ASYNC_CALL_STRATEGIES",

ladybug_queries.py

@@ -30,21 +30,27 @@
 
 
 def _parse_ladybug_json(raw: str | None) -> dict[str, Any]:
-    """Parse JSON from LadybugDB which returns unquoted keys like {key: value}."""
+    """Parse JSON from LadybugDB which returns unquoted keys like {key: value}.
+
+    Only quote keys at key positions (after ``{``, ``,`` or ``[``) so values
+    containing word-colon patterns (e.g. a URL ``https://...`` inside a quoted
+    string) are not corrupted. The previous ``(\\w+):`` regex matched ``word:``
+    anywhere, including inside values (issue #359).
+    """
     if not raw:
         return {}
-    # LadybugDB returns JSON without quotes around keys: {packages: 1, files: 2}
-    # Convert to standard JSON: {"packages": 1, "files": 2}
-    # This regex matches word characters followed by ':' at the start of a key
-    quoted = re.sub(r'(\w+):', r'"\1":', raw)
+    # Quote unquoted keys only where a key is expected: preceded by '{', ',' or
+    # '[' (with optional whitespace). This leaves word-colon runs inside values
+    # untouched.
+    quoted = re.sub(r'([,{\[]\s*)(\w+):', lambda m: f'{m.group(1)}"{m.group(2)}":', raw)
     try:
         return json.loads(quoted)
     except Exception:
         try:
-            # Fallback: try parsing as-is (for standard JSON)
+            # Fallback: try parsing as-is (for standard JSON).
             return json.loads(raw)
         except Exception:
-            log.warning("Failed to parse counts_json: %s", raw[:100])
+            log.warning("Failed to parse graph_meta JSON blob: %s", raw[:100])
             return {}
 
 # Composed describe / neighbors dot-keys (not stored graph edge labels).

mcp_v2.py

@@ -1533,7 +1533,18 @@ def resolve_v2(
 
         assert trimmed is not None
         if "*" in trimmed or "?" in trimmed:
-            return _resolve_finalize_success(trimmed, hint_kind, [])
+            out = ResolveOutput(
+                success=False,
+                status="none",
+                message=(
+                    "Wildcards (* and ?) are not supported in resolve; "
+                    "use search(query=...) for ranked text search."
+                ),
+                advisories=[],
+                resolved_identifier=trimmed,
+            )
+            _resolve_assert_invariants(out)
+            return out
 
         g = graph or LadybugGraph.get()
         raw: list[tuple[NodeRef, ResolveReason, int]] = []

search_lancedb.py

@@ -853,7 +853,7 @@ def run_search(
         capability=capability, capability_in=capability_in,
     ) if "java" in table_keys else []
 
-    skip_role_weight = bool(role or role_in)
+    skip_role_weight = bool(role or role_in or exclude_roles)
     query_toks = _query_tokens(query)
 
     if len(table_keys) == 1:

tests/fixtures/graph_baseline_bank_chat.json

@@ -6,14 +6,14 @@
     "INJECTS": 94,
     "DECLARES": 606,
     "OVERRIDES": 38,
-    "CALLS": 678,
+    "CALLS": 684,
     "UNRESOLVED_AT": 227
   },
   "graph_meta": {
     "ontology_version": 17,
     "built_at": 1782110216,
     "source_root": "/Users/dmitry/Desktop/CursorProjects/java-enterprise-codebase-rag/tests/bank-chat-system",
-    "counts_json": "{packages: 29, files: 130, types: 140, members: 606, phantoms: 54, extends: 18, implements: 21, injects: 94, declares: 606, overrides: 38, calls: 678, routes: 29, exposes: 15, clients: 8, declares_client: 8, producers: 9, declares_producer: 9, http_calls: 8, async_calls: 9}"
+    "counts_json": "{packages: 29, files: 130, types: 140, members: 606, phantoms: 54, extends: 18, implements: 21, injects: 94, declares: 606, overrides: 38, calls: 684, routes: 29, exposes: 15, clients: 8, declares_client: 8, producers: 9, declares_producer: 9, http_calls: 8, async_calls: 9}"
   },
   "sampled_edges": {
     "EXTENDS": [