code-graph-rag 0.0.534__tar.gz → 0.0.589__tar.gz

{code_graph_rag-0.0.534/code_graph_rag.egg-info → code_graph_rag-0.0.589}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: code-graph-rag
-Version: 0.0.534
+Version: 0.0.589
 Summary: The ultimate RAG for your monorepo. Query, understand, and edit multi-language codebases with the power of AI and knowledge graphs
 License-Expression: MIT
 Keywords: rag,retrieval-augmented-generation,knowledge-graph,code-analysis,tree-sitter,mcp,mcp-server,llm,graph-database,semantic-search,codebase,memgraph,developer-tools,monorepo
@@ -20,7 +20,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: loguru>=0.7.3
 Requires-Dist: mcp>=1.28.1
-Requires-Dist: pydantic-ai>=1.102.0
+Requires-Dist: pydantic-ai>=2.0.0
 Requires-Dist: pydantic-settings>=2.12.0
 Requires-Dist: pymgclient>=1.5.1
 Requires-Dist: python-dotenv>=1.2.1
@@ -37,7 +37,6 @@ Requires-Dist: click>=8.3.1
 Requires-Dist: protobuf>=6.33.5
 Requires-Dist: defusedxml>=0.7.1
 Requires-Dist: huggingface-hub[hf-xet]>=1.7.2
-Requires-Dist: griffe<2,>=1.0
 Requires-Dist: pathspec>=1.0.4
 Provides-Extra: test
 Requires-Dist: pytest>=8.4.1; extra == "test"
@@ -256,8 +255,8 @@ print(f"Embedding dimension: {len(embedding)}")
 ```python
 from cgr import settings
 
-settings.set_orchestrator("openai", "gpt-4o", api_key="sk-...")
-settings.set_cypher("google", "gemini-2.5-flash", api_key="your-key")
+settings.set_orchestrator("openai", "gpt-5.6-terra", api_key="sk-...")
+settings.set_cypher("google", "gemini-3.5-flash-lite", api_key="your-key")
 ```
 
 ## Environment Variables
@@ -269,10 +268,10 @@ Configure via `.env` or environment variables:
 | `MEMGRAPH_HOST` | `localhost` | Memgraph hostname |
 | `MEMGRAPH_PORT` | `7687` | Memgraph port |
 | `ORCHESTRATOR_PROVIDER` | | Provider: `google`, `openai`, `anthropic`, `azure`, `ollama`, `minimax`, `litellm_proxy` |
-| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-4o`, `gemini-2.5-pro`) |
+| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-5.6-terra`, `gemini-3.6-flash`, `claude-sonnet-5`, `qwen2.5-coder`) |
 | `ORCHESTRATOR_API_KEY` | | API key for the provider (not needed for `ollama`) |
 | `CYPHER_PROVIDER` | | Provider for Cypher generation |
-| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `codellama`, `gpt-4o-mini`) |
+| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `qwen2.5-coder`, `gpt-5.6-luna`, `gemini-3.5-flash-lite`) |
 | `CYPHER_API_KEY` | | API key for Cypher provider (not needed for `ollama`) |
 | `TARGET_REPO_PATH` | `.` | Default repository path |
 

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/PYPI_README.md

@@ -180,8 +180,8 @@ print(f"Embedding dimension: {len(embedding)}")
 ```python
 from cgr import settings
 
-settings.set_orchestrator("openai", "gpt-4o", api_key="sk-...")
-settings.set_cypher("google", "gemini-2.5-flash", api_key="your-key")
+settings.set_orchestrator("openai", "gpt-5.6-terra", api_key="sk-...")
+settings.set_cypher("google", "gemini-3.5-flash-lite", api_key="your-key")
 ```
 
 ## Environment Variables
@@ -193,10 +193,10 @@ Configure via `.env` or environment variables:
 | `MEMGRAPH_HOST` | `localhost` | Memgraph hostname |
 | `MEMGRAPH_PORT` | `7687` | Memgraph port |
 | `ORCHESTRATOR_PROVIDER` | | Provider: `google`, `openai`, `anthropic`, `azure`, `ollama`, `minimax`, `litellm_proxy` |
-| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-4o`, `gemini-2.5-pro`) |
+| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-5.6-terra`, `gemini-3.6-flash`, `claude-sonnet-5`, `qwen2.5-coder`) |
 | `ORCHESTRATOR_API_KEY` | | API key for the provider (not needed for `ollama`) |
 | `CYPHER_PROVIDER` | | Provider for Cypher generation |
-| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `codellama`, `gpt-4o-mini`) |
+| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `qwen2.5-coder`, `gpt-5.6-luna`, `gemini-3.5-flash-lite`) |
 | `CYPHER_API_KEY` | | API key for Cypher provider (not needed for `ollama`) |
 | `TARGET_REPO_PATH` | `.` | Default repository path |
 

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/README.md

@@ -129,10 +129,16 @@ You also need Docker (for Memgraph), `cmake`, and `ripgrep`. Full prerequisites,
 cgr daemon up
 
 # Parse a repository into the graph, then query it
-cgr start --repo-path /path/to/repo --update-graph --clean
+cgr start --repo-path /path/to/repo --update-graph
 cgr start --repo-path /path/to/repo
 ```
 
+Repeat the first command for each repository you want indexed; the graph is
+shared, and syncing one project leaves the others alone. To start over from an
+empty graph, add `--clean` — it deletes **every** project in the shared graph,
+not just this one, and asks for confirmation first when other
+projects would be destroyed.
+
 The [Quick Start](docs/getting-started/quickstart.md) guide walks through parsing, querying, and exporting in five minutes.
 
 ## MCP Server

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589/code_graph_rag.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: code-graph-rag
-Version: 0.0.534
+Version: 0.0.589
 Summary: The ultimate RAG for your monorepo. Query, understand, and edit multi-language codebases with the power of AI and knowledge graphs
 License-Expression: MIT
 Keywords: rag,retrieval-augmented-generation,knowledge-graph,code-analysis,tree-sitter,mcp,mcp-server,llm,graph-database,semantic-search,codebase,memgraph,developer-tools,monorepo
@@ -20,7 +20,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: loguru>=0.7.3
 Requires-Dist: mcp>=1.28.1
-Requires-Dist: pydantic-ai>=1.102.0
+Requires-Dist: pydantic-ai>=2.0.0
 Requires-Dist: pydantic-settings>=2.12.0
 Requires-Dist: pymgclient>=1.5.1
 Requires-Dist: python-dotenv>=1.2.1
@@ -37,7 +37,6 @@ Requires-Dist: click>=8.3.1
 Requires-Dist: protobuf>=6.33.5
 Requires-Dist: defusedxml>=0.7.1
 Requires-Dist: huggingface-hub[hf-xet]>=1.7.2
-Requires-Dist: griffe<2,>=1.0
 Requires-Dist: pathspec>=1.0.4
 Provides-Extra: test
 Requires-Dist: pytest>=8.4.1; extra == "test"
@@ -256,8 +255,8 @@ print(f"Embedding dimension: {len(embedding)}")
 ```python
 from cgr import settings
 
-settings.set_orchestrator("openai", "gpt-4o", api_key="sk-...")
-settings.set_cypher("google", "gemini-2.5-flash", api_key="your-key")
+settings.set_orchestrator("openai", "gpt-5.6-terra", api_key="sk-...")
+settings.set_cypher("google", "gemini-3.5-flash-lite", api_key="your-key")
 ```
 
 ## Environment Variables
@@ -269,10 +268,10 @@ Configure via `.env` or environment variables:
 | `MEMGRAPH_HOST` | `localhost` | Memgraph hostname |
 | `MEMGRAPH_PORT` | `7687` | Memgraph port |
 | `ORCHESTRATOR_PROVIDER` | | Provider: `google`, `openai`, `anthropic`, `azure`, `ollama`, `minimax`, `litellm_proxy` |
-| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-4o`, `gemini-2.5-pro`) |
+| `ORCHESTRATOR_MODEL` | | Model ID (e.g. `gpt-5.6-terra`, `gemini-3.6-flash`, `claude-sonnet-5`, `qwen2.5-coder`) |
 | `ORCHESTRATOR_API_KEY` | | API key for the provider (not needed for `ollama`) |
 | `CYPHER_PROVIDER` | | Provider for Cypher generation |
-| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `codellama`, `gpt-4o-mini`) |
+| `CYPHER_MODEL` | | Model ID for Cypher generation (e.g. `qwen2.5-coder`, `gpt-5.6-luna`, `gemini-3.5-flash-lite`) |
 | `CYPHER_API_KEY` | | API key for Cypher provider (not needed for `ollama`) |
 | `TARGET_REPO_PATH` | `.` | Default repository path |
 

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/code_graph_rag.egg-info/SOURCES.txt

@@ -22,6 +22,7 @@ codebase_rag/decorators.py
 codebase_rag/docker-compose.yaml
 codebase_rag/embedder.py
 codebase_rag/exceptions.py
+codebase_rag/flow_verdict.py
 codebase_rag/function_registry.py
 codebase_rag/graph_audit.py
 codebase_rag/graph_loader.py
@@ -251,6 +252,7 @@ codebase_rag/tools/shell_command.py
 codebase_rag/tools/structural_editor.py
 codebase_rag/tools/structural_search.py
 codebase_rag/tools/tool_descriptions.py
+codebase_rag/tools/web_search.py
 codebase_rag/utils/__init__.py
 codebase_rag/utils/dependencies.py
 codebase_rag/utils/fqn_resolver.py

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/code_graph_rag.egg-info/requires.txt

@@ -1,6 +1,6 @@
 loguru>=0.7.3
 mcp>=1.28.1
-pydantic-ai>=1.102.0
+pydantic-ai>=2.0.0
 pydantic-settings>=2.12.0
 pymgclient>=1.5.1
 python-dotenv>=1.2.1
@@ -17,7 +17,6 @@ click>=8.3.1
 protobuf>=6.33.5
 defusedxml>=0.7.1
 huggingface-hub[hf-xet]>=1.7.2
-griffe<2,>=1.0
 pathspec>=1.0.4
 
 [ast-grep]

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/cli.py

@@ -2,6 +2,7 @@
 
 import asyncio
 import json
+import sys
 import time
 from collections.abc import Callable
 from fnmatch import fnmatch
@@ -199,6 +200,78 @@ def _capture_selection(capture: list[str] | None) -> CaptureSelection:
     return resolve_capture([*split_spec(settings.CGR_CAPTURE), *(capture or [])])
 
 
+def _stdin_is_interactive() -> bool:
+    try:
+        return sys.stdin.isatty()
+    except (AttributeError, ValueError):
+        return False
+
+
+def _projects_in_graph(ingestor: MemgraphIngestor) -> list[str] | None:
+    """Every project in the graph, or None when the graph cannot be read.
+
+    None is NOT an empty graph: treating a failed enumeration as "no other
+    projects" would skip the confirmation and wipe every project precisely
+    when we cannot say what would be lost.
+    """
+    try:
+        return sorted(ingestor.list_projects())
+    except Exception as exc:
+        logger.warning(ls.MG_LIST_PROJECTS_FAILED.format(error=exc))
+        return None
+
+
+def _confirm_destructive_clean(
+    ingestor: MemgraphIngestor, project_name: str, assume_yes: bool
+) -> None:
+    """Abort unless the user accepts losing every other project in the graph."""
+    if assume_yes:
+        return
+
+    # `--clean` deletes the whole graph, so the prompt counts every project in
+    # it. Deriving that count from `others` would understate it by one whenever
+    # this project has not been synced yet and so is not in the graph.
+    projects = _projects_in_graph(ingestor)
+    if projects is None:
+        # Fail closed: an unreadable project list cannot show what the wipe
+        # would destroy, so it must not be read as an empty graph.
+        app_context.console.print(
+            style(cs.CLI_ERR_CLEAN_UNKNOWN_PROJECTS, cs.Color.RED)
+        )
+        raise typer.Exit(1)
+
+    others = [name for name in projects if name != project_name]
+    if not others:
+        return
+
+    app_context.console.print(
+        style(
+            cs.CLI_WARN_CLEAN_OTHER_PROJECTS.format(
+                project_name=project_name,
+                count=len(others),
+                projects=", ".join(others),
+            ),
+            cs.Color.YELLOW,
+        )
+    )
+
+    if not _stdin_is_interactive():
+        app_context.console.print(
+            style(
+                cs.CLI_ERR_CLEAN_NEEDS_CONFIRMATION.format(project_name=project_name),
+                cs.Color.RED,
+            )
+        )
+        raise typer.Exit(1)
+
+    confirmed = typer.confirm(
+        cs.CLI_PROMPT_CLEAN_CONFIRM.format(count=len(projects)), default=False
+    )
+    if not confirmed:
+        app_context.console.print(style(cs.CLI_MSG_CLEAN_ABORTED, cs.Color.CYAN))
+        raise typer.Exit(1)
+
+
 def _run_graph_sync(
     repo: Path,
     project_name: str,
@@ -209,6 +282,7 @@ def _run_graph_sync(
     output: str | None = None,
     capture: list[str] | None = None,
     skip_embeddings: bool | None = None,
+    assume_yes: bool = False,
 ) -> None:
     cgrignore = load_ignore_patterns(repo)
     cli_excludes = frozenset(exclude) if exclude else frozenset()
@@ -222,6 +296,7 @@ def _run_graph_sync(
     elapsed = time.monotonic()
     with connect_memgraph(batch_size) as ingestor:
         if clean:
+            _confirm_destructive_clean(ingestor, project_name, assume_yes)
             _info(style(cs.CLI_MSG_CLEANING_DB, cs.Color.YELLOW))
             ingestor.clean_database()
             _delete_hash_cache(repo)
@@ -336,6 +411,12 @@ def start(
         "--clean",
         help=ch.HELP_CLEAN_DB,
     ),
+    yes: bool = typer.Option(
+        False,
+        "--yes",
+        "-y",
+        help=ch.HELP_ASSUME_YES,
+    ),
     output: str | None = typer.Option(
         None,
         "-o",
@@ -452,6 +533,7 @@ def start(
     if clean and not update_graph:
         repo_to_clean = Path(target_repo_path)
         with connect_memgraph(effective_batch_size) as ingestor:
+            _confirm_destructive_clean(ingestor, resolved_project_name, yes)
             _info(style(cs.CLI_MSG_CLEANING_DB, cs.Color.YELLOW))
             ingestor.clean_database()
 
@@ -481,6 +563,7 @@ def start(
             output=output,
             capture=capture,
             skip_embeddings=no_embeddings or None,
+            assume_yes=yes,
         )
         _info(style(cs.CLI_MSG_GRAPH_UPDATED, cs.Color.GREEN))
         return

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/cli_help.py

@@ -124,7 +124,7 @@ HELP_MEMGRAPH_HOST = "Memgraph host."
 HELP_MEMGRAPH_PORT = "Memgraph port."
 HELP_ORCHESTRATOR = (
     "Model for the planning assistant, in provider:model form "
-    "(for example openai:gpt-4 or ollama:llama3.2)."
+    "(for example openai:gpt-5.6-terra or ollama:qwen2.5-coder)."
 )
 HELP_CYPHER_MODEL = "Model used to generate Cypher, in provider:model form."
 HELP_NO_CONFIRM = "Skip edit confirmation prompts."
@@ -146,8 +146,13 @@ HELP_MAX_WAIT = (
 
 HELP_UPDATE_GRAPH = "Parse the repository and sync its graph before continuing."
 HELP_CLEAN_DB = (
-    "Delete every project from the shared graph and clear the selected repository's "
-    "sync cache. With --update-graph, rebuild after deletion."
+    "DESTRUCTIVE: Delete every project from the shared graph and clear the selected "
+    "repository's sync cache. With --update-graph, rebuild after deletion. Asks for "
+    "confirmation when other projects would be destroyed; use --yes to skip the prompt."
+)
+HELP_ASSUME_YES = (
+    "Answer yes to destructive confirmations, such as the one --clean asks before "
+    "deleting other projects from the shared graph."
 )
 HELP_OUTPUT_GRAPH = "Write the updated graph to PATH as JSON. Requires --update-graph."
 HELP_OUTPUT_PATH = "Write the exported graph to PATH."

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/ast_java.py

@@ -238,3 +238,8 @@ JAVA_SRC_FOLDERS = frozenset(
         JAVA_PATH_TEST,
     }
 )
+
+JAVA_MAVEN_SOURCE_ROOTS = (
+    (JAVA_PATH_SRC, JAVA_PATH_MAIN, JAVA_PATH_JAVA),
+    (JAVA_PATH_SRC, JAVA_PATH_TEST, JAVA_PATH_JAVA),
+)

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/ast_js.py

@@ -215,8 +215,19 @@ JS_SHORT_CIRCUIT_OPERATORS: frozenset[str] = frozenset({"||", "??", "&&"})
 # (`[Symbol.iterator]`, `[Symbol.toStringTag]`) as the definition pass
 # registers it; user symbol keys register without the `Symbol.` path.
 JS_WELL_KNOWN_SYMBOL_NAME_PREFIX = "[Symbol."
+JS_COMPUTED_NAME_PREFIX = "["
 JS_COMPUTED_NAME_SUFFIX = "]"
 JS_WELL_KNOWN_SYMBOL_BRACKET_PREFIX = "[Symbol["
+JS_SYMBOL_FOR_PREFIX = "for("
+JS_STRING_QUOTES = "'\""
+# Registry symbols whose members RUNTIMES invoke themselves; an
+# application-defined Symbol.for(...) key is reached only by visible code.
+JS_RUNTIME_REGISTRY_SYMBOL_KEYS = frozenset(
+    {
+        "nodejs.util.inspect.custom",
+        "nodejs.rejection",
+    }
+)
 # `&&` alone among them cannot yield its LEFT operand as a function value.
 JS_OPERATOR_LOGICAL_AND = "&&"
 TS_JS_ELSE_CLAUSE = "else_clause"

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/ast_rust.py

@@ -4,6 +4,7 @@ from .ast_java import TS_GENERIC_TYPE
 from .ast_nodes import TS_IDENTIFIER, TS_SCOPED_IDENTIFIER, TS_TYPE_IDENTIFIER
 from .ast_scala import TS_GENERIC_FUNCTION
 from .core import KEYWORD_SELF, KEYWORD_SUPER
+from .graph import NodeLabel
 
 TS_RS_SCOPED_TYPE_IDENTIFIER = "scoped_type_identifier"
 TS_RS_PRIMITIVE_TYPE = "primitive_type"
@@ -26,6 +27,13 @@ TS_RS_IMPL_ITEM = "impl_item"
 TS_RS_FUNCTION_SIGNATURE_ITEM = "function_signature_item"
 TS_RS_CLOSURE_EXPRESSION = "closure_expression"
 TS_RS_UNION_ITEM = "union_item"
+TS_RS_TYPE_PARAMETERS = "type_parameters"
+TS_RS_TYPE_PARAMETER = "type_parameter"
+TS_RS_WHERE_CLAUSE = "where_clause"
+TS_RS_WHERE_PREDICATE = "where_predicate"
+# Items whose generic parameter lists and where clauses put trait bounds in
+# scope for the calls beneath them.
+RS_GENERIC_SCOPE_ITEMS = (TS_RS_FUNCTION_ITEM, TS_RS_IMPL_ITEM, TS_RS_TRAIT_ITEM)
 TS_RS_USE_DECLARATION = "use_declaration"
 TS_RS_EXTERN_CRATE_DECLARATION = "extern_crate_declaration"
 TS_RS_CALL_EXPRESSION = "call_expression"
@@ -176,6 +184,12 @@ RS_USE_LIST_DELIMITERS = frozenset({"{", "}", ","})
 RS_ENCODING_UTF8 = "utf8"
 
 RS_WILDCARD_PREFIX = "*"
+# Marks a `use path::{self}` entry, whose name the base path supplies rather
+# than the source. Rust keeps types and values in separate namespaces while
+# the import map holds one slot per name, so such a binding is WEAK: it never
+# displaces a name another `use` in the same scope already claimed (#1054).
+# No Rust identifier can contain the marker character.
+RS_SELF_MODULE_PREFIX = "@"
 
 RS_FIELD_ARGUMENT = "argument"
 
@@ -191,3 +205,119 @@ RS_MANIFEST_TARGET_SECTIONS = ("bin", "lib", "example", "test", "bench")
 RS_MANIFEST_PATH_KEY = "path"
 RS_MANIFEST_PACKAGE_KEY = "package"
 RS_MANIFEST_BUILD_KEY = "build"
+RS_MANIFEST_AUTOLIB_KEY = "autolib"
+RS_MANIFEST_AUTOBINS_KEY = "autobins"
+RS_MANIFEST_AUTOEXAMPLES_KEY = "autoexamples"
+RS_MANIFEST_AUTOTESTS_KEY = "autotests"
+RS_MANIFEST_AUTOBENCHES_KEY = "autobenches"
+RS_MANIFEST_AUTO_KEYS = (
+    RS_MANIFEST_AUTOLIB_KEY,
+    RS_MANIFEST_AUTOBINS_KEY,
+    RS_MANIFEST_AUTOEXAMPLES_KEY,
+    RS_MANIFEST_AUTOTESTS_KEY,
+    RS_MANIFEST_AUTOBENCHES_KEY,
+)
+RS_AUTO_DIR_KEYS = {
+    "examples": RS_MANIFEST_AUTOEXAMPLES_KEY,
+    "tests": RS_MANIFEST_AUTOTESTS_KEY,
+    "benches": RS_MANIFEST_AUTOBENCHES_KEY,
+}
+# Candidate locations of a PATHLESS manifest target table, matched against
+# the files that actually exist (cargo errors on an ambiguous pair, so only
+# a single existing candidate resolves). [lib] is fixed at src/lib.rs; a bin
+# whose name equals the package name may be src/main.rs.
+RS_DEFAULT_LIB_PATH = "src/lib.rs"
+RS_DEFAULT_MAIN_PATH = "src/main.rs"
+RS_MANIFEST_BIN_SECTION = "bin"
+RS_MANIFEST_KIND_DIRS = {
+    "bin": "src/bin",
+    "example": "examples",
+    "test": "tests",
+    "bench": "benches",
+}
+RS_MANIFEST_WORKSPACE_KEY = "workspace"
+RS_MANIFEST_MEMBERS_KEY = "members"
+RS_MANIFEST_NAME_KEY = "name"
+RS_MANIFEST_LIB_SECTION = "lib"
+RS_MANIFEST_DEP_SECTIONS = ("dependencies", "dev-dependencies", "build-dependencies")
+RS_MANIFEST_TARGET_TABLE_KEY = "target"
+# Crates shipped with the toolchain: external by construction, no
+# manifest needed to know a use head naming one is outside the project.
+RS_STDLIB_CRATES = frozenset({"std", "core", "alloc", "proc_macro"})
+
+# Node labels a Rust qn segment carries when it is a TYPE the caller sits
+# inside (an impl block), not an inline `mod`. An impl adds no module level,
+# so `super::` inside a method counts from the file module's parent (#1093).
+RS_TYPE_SCOPE_LABELS = frozenset(
+    {
+        NodeLabel.CLASS.value,
+        NodeLabel.INTERFACE.value,
+        NodeLabel.ENUM.value,
+        NodeLabel.TYPE.value,
+        NodeLabel.UNION.value,
+    }
+)
+
+# Traits the Rust prelude puts in scope with no `use`: an impl naming one
+# without importing it and without a same-named first-party declaration
+# implements the standard trait, whose dispatch lives outside the graph
+# (issue #1048). Marker traits with no methods are omitted as pointless.
+RS_PRELUDE_TRAITS = frozenset(
+    {
+        "AsMut",
+        "AsRef",
+        "Clone",
+        "Default",
+        "DoubleEndedIterator",
+        "Drop",
+        "ExactSizeIterator",
+        "Extend",
+        "Fn",
+        "FnMut",
+        "FnOnce",
+        "From",
+        "FromIterator",
+        "Into",
+        "IntoIterator",
+        "Iterator",
+        "Ord",
+        "PartialEq",
+        "PartialOrd",
+        "ToOwned",
+        "ToString",
+        "TryFrom",
+        "TryInto",
+    }
+)
+
+# Iterator-adaptor closure typing (issue #1045): a closure argument of one
+# of these adaptors receives the sequence's element (by value or
+# reference, indistinguishable for method binding), so its parameter can
+# type from the iterated collection's element type.
+RS_ITER_ADAPTORS = frozenset(
+    {
+        "map",
+        "filter",
+        "for_each",
+        "inspect",
+        "take_while",
+        "skip_while",
+        "filter_map",
+        "find",
+        "position",
+        "any",
+        "all",
+    }
+)
+# Chain hops between the collection and the adaptor that preserve the
+# element type. Element-changing adaptors (enumerate, zip, flat_map) are
+# deliberately absent: crossing one loses the element.
+RS_ITER_NEUTRAL_HOPS = frozenset(
+    {"iter", "into_iter", "iter_mut", "by_ref", "rev", "cloned", "copied", "filter"}
+)
+# Sequence containers whose FIRST generic argument is the element type.
+RS_ELEMENT_CONTAINERS = frozenset({"Vec", "VecDeque"})
+RS_ITER_MAP = "map"
+RS_ITER_COLLECT = "collect"
+TS_RS_ARRAY_TYPE = "array_type"
+RS_FIELD_ELEMENT = "element"

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/cli.py

@@ -76,6 +76,22 @@ CLI_MSG_SYNC_DONE = "Knowledge graph sync done for '{project}' in {elapsed:.2f}s
 CLI_MSG_CLEANING_DB = "Cleaning database..."
 CLI_MSG_CLEANING_HASH_CACHE = "Removing hash cache: {path}"
 CLI_MSG_CLEAN_DONE = "Clean completed successfully!"
+CLI_WARN_CLEAN_OTHER_PROJECTS = (
+    "--clean deletes EVERY project from the shared graph, not just "
+    "'{project_name}'.\n{count} other project(s) would be destroyed: {projects}"
+)
+CLI_PROMPT_CLEAN_CONFIRM = "Delete all {count} project(s) from the shared graph?"
+CLI_ERR_CLEAN_NEEDS_CONFIRMATION = (
+    "Refusing to run --clean without a terminal to confirm on. "
+    "Re-run with --yes to delete every project in the shared graph, or drop "
+    "--clean to update '{project_name}' in place."
+)
+CLI_ERR_CLEAN_UNKNOWN_PROJECTS = (
+    "Refusing to run --clean: the existing projects could not be listed, so "
+    "there is no way to show what the wipe would destroy. Fix the graph "
+    "connection, or pass --yes to delete everything regardless."
+)
+CLI_MSG_CLEAN_ABORTED = "Aborted: the graph was left untouched."
 CLI_MSG_DELETING_PROJECT = "Deleting project '{project_name}' from the graph..."
 CLI_MSG_PROJECT_DELETED = "Project '{project_name}' deleted successfully."
 CLI_ERR_PROJECT_NOT_FOUND = (

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/core.py

@@ -21,6 +21,10 @@ SEPARATOR_SLASH = "/"
 # Disambiguates definitions that share one qualified name (if/else import
 # fallbacks, typing.overload, try/except fallbacks): "<qn>@<start_line>".
 DUP_QN_MARKER = "@"
+# Joined after the line when a same-named definition already holds that line,
+# so same-line twins stay distinct (issue #1071). Every consumer splits on
+# DUP_QN_MARKER and keeps the base, so nothing reads the suffix back.
+DUP_QN_COLUMN_MARKER = "_"
 
 PATH_CURRENT_DIR = "."
 PATH_PARENT_DIR = ".."

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/deadcode_roots.py

@@ -330,3 +330,26 @@ PY_ENUM_HOOK_METHOD_NAMES: frozenset[str] = frozenset(
         "_missing_",
     }
 )
+
+# (H) ES well-known symbols (incl. Explicit Resource Management: dispose/asyncDispose)
+# (H) These are invoked implicitly by the runtime (e.g. [Symbol.iterator] by for..of)
+# (H) and never called by name, so they are dead-code liveness roots.
+JS_WELL_KNOWN_SYMBOLS: frozenset[str] = frozenset(
+    {
+        "asyncIterator",
+        "hasInstance",
+        "isConcatSpreadable",
+        "iterator",
+        "match",
+        "matchAll",
+        "replace",
+        "search",
+        "species",
+        "split",
+        "toPrimitive",
+        "toStringTag",
+        "unscopables",
+        "dispose",
+        "asyncDispose",
+    }
+)

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/fqn_specs.py

@@ -140,6 +140,7 @@ from .ast_python import (
 from .ast_rust import (
     TS_RS_CALL_EXPRESSION,
     TS_RS_CLOSURE_EXPRESSION,
+    TS_RS_CONST_ITEM,
     TS_RS_ENUM_ITEM,
     TS_RS_EXTERN_CRATE_DECLARATION,
     TS_RS_FUNCTION_ITEM,
@@ -149,6 +150,7 @@ from .ast_rust import (
     TS_RS_MACRO_INVOCATION,
     TS_RS_MOD_ITEM,
     TS_RS_SOURCE_FILE,
+    TS_RS_STATIC_ITEM,
     TS_RS_STRUCT_ITEM,
     TS_RS_TRAIT_ITEM,
     TS_RS_TYPE_ITEM,
@@ -410,6 +412,16 @@ RS_TYPE_NODE_TYPES = (
 )
 RS_IDENT_NODE_TYPES = (TS_RS_FUNCTION_ITEM, TS_RS_MOD_ITEM)
 
+# Nodes whose body holds items no path from another module can name.
+RS_BODY_LOCAL_CONTAINERS = frozenset(
+    {
+        TS_RS_FUNCTION_ITEM,
+        TS_RS_CLOSURE_EXPRESSION,
+        TS_RS_CONST_ITEM,
+        TS_RS_STATIC_ITEM,
+    }
+)
+
 CPP_NAME_NODE_TYPES = (
     CppNodeType.CLASS_SPECIFIER,
     TS_STRUCT_SPECIFIER,

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/graph.py

@@ -30,6 +30,10 @@ KEY_START_LINE = "start_line"
 KEY_END_LINE = "end_line"
 KEY_PATH = "path"
 KEY_ABSOLUTE_PATH = "absolute_path"
+# Whether flow analysis covered a Module: its language is in the source/sink
+# registry AND the FLOWS_TO capture group was enabled at indexing. Read by
+# the three-verdict flow reachability query (issue #1050).
+KEY_FLOW_COVERED = "flow_covered"
 KEY_EXTENSION = "extension"
 KEY_MODULE_TYPE = "module_type"
 KEY_IMPLEMENTS_MODULE = "implements_module"

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/mcp.py

@@ -19,6 +19,7 @@ class MCPToolName(StrEnum):
     STRUCTURAL_SEARCH = "structural_search"
     STRUCTURAL_REPLACE = "structural_replace"
     ASK_AGENT = "ask_agent"
+    FLOW_VERDICT = "flow_verdict"
 
 
 class MCPTransport(StrEnum):
@@ -64,6 +65,8 @@ class MCPParamName(StrEnum):
     PATTERN = "pattern"
     REWRITE = "rewrite"
     LANGUAGE = "language"
+    SOURCE_QN = "source_qualified_name"
+    SINK_QN = "sink_qualified_name"
     DRY_RUN = "dry_run"
 
 

{code_graph_rag-0.0.534 → code_graph_rag-0.0.589}/codebase_rag/constants/providers.py

@@ -96,6 +96,8 @@ DEFAULT_CONTEXT_WINDOW = 200_000
 MODEL_CONTEXT_WINDOWS: dict[str, int] = {
     "MiniMax-M3": 1_000_000,
     "MiniMax-M2.7": 204_800,
+    "claude-opus-5": 1_000_000,
+    "claude-sonnet-5": 1_000_000,
     "claude-opus-4-8": 1_000_000,
     "claude-opus-4-7": 1_000_000,
     "claude-opus-4-6": 200_000,