codegraph-brain 0.29.0__tar.gz → 0.30.0__tar.gz

codegraph_brain-0.30.0/.github/test-count-baseline

@@ -0,0 +1 @@
+3252

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/.github/workflows/ci.yml

@@ -162,6 +162,20 @@ jobs:
           # this exemption hides it — that is the cost, and it is the reason the
           # rule stays on for src/.
           #
+          # pythonsecurity:S8706 (connection-string injection) is the same
+          # finding at sqlite3.connect: graph_identity.py opens a database named
+          # on its own command line. `dump()` requires an existing .db/.sqlite/
+          # .sqlite3 regular file before connecting, and passes no `uri=True`, so
+          # the argument is a file name and never a connection string. Exempted
+          # for scripts/ on the S2083 reasoning above — the engine does not model
+          # the check — and kept on for src/.
+          #
+          # tests/fixtures/ is excluded from test analysis
+          # (`sonar.test.exclusions`; it sits under `sonar.tests`, so
+          # `sonar.exclusions` would not reach it): it holds input corpora, not
+          # code. Its package.json files exist to be parsed by cgis, and a lock
+          # file next to them (text:S8564) would be a fixture nothing reads.
+          #
           # `sonar.newCode.referenceBranch` overrides the server-side new-code
           # definition for this analysis. The instance default is
           # `previous_version` (confirmed: sonar.leak.period=previous_version,
@@ -218,13 +232,16 @@ jobs:
             -Dsonar.newCode.referenceBranch=main
             -Dsonar.sources=src,scripts,.github
             -Dsonar.tests=tests
+            -Dsonar.test.exclusions=tests/fixtures/**
             -Dsonar.python.version=3.12
             -Dsonar.python.coverage.reportPaths=coverage.xml
-            -Dsonar.issue.ignore.multicriteria=e1,e2,e3,e4
+            -Dsonar.issue.ignore.multicriteria=e1,e2,e3,e4,e5
             -Dsonar.issue.ignore.multicriteria.e1.ruleKey=pythonsecurity:S8707
             -Dsonar.issue.ignore.multicriteria.e1.resourceKey=scripts/**/*.py
             -Dsonar.issue.ignore.multicriteria.e4.ruleKey=pythonsecurity:S2083
             -Dsonar.issue.ignore.multicriteria.e4.resourceKey=scripts/**/*.py
+            -Dsonar.issue.ignore.multicriteria.e5.ruleKey=pythonsecurity:S8706
+            -Dsonar.issue.ignore.multicriteria.e5.resourceKey=scripts/**/*.py
             -Dsonar.issue.ignore.multicriteria.e2.ruleKey=githubactions:S8541
             -Dsonar.issue.ignore.multicriteria.e2.resourceKey=.github/workflows/*.yml
             -Dsonar.issue.ignore.multicriteria.e3.ruleKey=githubactions:S8544

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/.gitignore

@@ -15,6 +15,8 @@ downloads/
 eggs/
 .eggs/
 lib/
+# The graph-identity corpus has lib/ directories that are inputs, not build output.
+!tests/fixtures/graph_identity/corpus/**/lib/
 lib64/
 parts/
 sdist/

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/.pre-commit-config.yaml

@@ -40,6 +40,7 @@ repos:
           - tree-sitter>=0.25.2
           - tree-sitter-python>=0.25.0
           - tree-sitter-typescript>=0.23.2
+          - tree-sitter-go>=0.25.0
           - pytest>=9.0.3
           - "mcp[cli]>=2"  # must match the pyproject bound
           - duckdb>=1.1.0

codegraph_brain-0.30.0/.release-please-manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "0.30.0"
+}

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog
 
+## [0.30.0](https://github.com/zaebee/codegraph-brain/compare/codegraph-brain-v0.29.0...codegraph-brain-v0.30.0) (2026-10-15)
+
+
+### Features
+
+* **languages:** Go field and call-result types resolve receiver calls ([#608](https://github.com/zaebee/codegraph-brain/issues/608)) ([#614](https://github.com/zaebee/codegraph-brain/issues/614)) ([96ec5f3](https://github.com/zaebee/codegraph-brain/commit/96ec5f380d52ba1560c63b8b84af673627bc88d0))
+* **languages:** step 7b — the Go pilot ([#607](https://github.com/zaebee/codegraph-brain/issues/607)) ([4a62703](https://github.com/zaebee/codegraph-brain/commit/4a62703f41a4dfb74d1f96bee132b3f78f84c895))
+* **pipeline:** a graph built by other extraction code is rebuilt in full ([#617](https://github.com/zaebee/codegraph-brain/issues/617)) ([dc33153](https://github.com/zaebee/codegraph-brain/commit/dc331531556cc2dc49c8adfacbec079584953eb8))
+* **python:** FastAPI handlers play the ROUTE_HANDLER role ([#566](https://github.com/zaebee/codegraph-brain/issues/566)) ([#616](https://github.com/zaebee/codegraph-brain/issues/616)) ([9098ccd](https://github.com/zaebee/codegraph-brain/commit/9098ccd87ef08fbb3139243fda426b62e8d1b32b))
+
+
+### Bug Fixes
+
+* **docs:** coverage claims name Go — the MCP instructions are built from the registry ([#615](https://github.com/zaebee/codegraph-brain/issues/615)) ([8ea6362](https://github.com/zaebee/codegraph-brain/commit/8ea636239122b24c4a42b2a65517ebb12dad1b03))
+
+
+### Documentation
+
+* auto-sync architecture graph and MCP reference ([#598](https://github.com/zaebee/codegraph-brain/issues/598)) ([3feb1ac](https://github.com/zaebee/codegraph-brain/commit/3feb1ac40b1896acb0e57109c9bd1f2bf941d7bc))
+* auto-sync architecture graph and MCP reference ([#620](https://github.com/zaebee/codegraph-brain/issues/620)) ([3f36e15](https://github.com/zaebee/codegraph-brain/commit/3f36e15c30dca7280b57bebd70a8793764cd872e))
+* **spec:** language packs and a two-plane topology ([#593](https://github.com/zaebee/codegraph-brain/issues/593)) ([d9e7d85](https://github.com/zaebee/codegraph-brain/commit/d9e7d852b17d4cab4a2a4a0f2519f11f8de9236e))
+
 ## [0.29.0](https://github.com/zaebee/codegraph-brain/compare/codegraph-brain-v0.28.0...codegraph-brain-v0.29.0) (2026-10-14)
 
 

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/CLAUDE.md

@@ -45,21 +45,24 @@ make coverage-html   # same, writes htmlcov/
 The pipeline runs in three phases: **Extract → Resolve → Store**.
 
 ```
-IngestionPipeline (pipeline.py)
-  ├── BaseExtractor subclasses (extractors/)   ← language-specific AST → Nodes+Edges
-  │     └── PythonExtractor                    ← only language implemented so far
+IngestionPipeline (pipeline/__init__.py)
+  ├── cgis.languages (registry)                ← lazy: a pack is imported when its first file is met
+  │     ├── languages/python/                  ← PythonExtractor + PACK
+  │     ├── languages/typescript/              ← TypeScriptExtractor (.ts/.tsx) + PACK
+  │     └── languages/go/                      ← GoExtractor (.go) + go.mod reader + PACK (pilot)
   ├── ResolverEngine (resolver/engine.py)      ← raw_call: targets → resolved FQN edges
-  └── SQLiteStore (storage/sqlite_store.py)    ← persists graph; WAL mode
+  ├── SQLiteStore (storage/sqlite_store.py)    ← persists graph; WAL mode
+  └── post-write passes (pipeline/)            ← refresh_dispatch, SemanticUpliftEngine (pipeline/uplift.py)
         └── QueryEngine (query/engine.py)      ← BFS traversals (impact / flow)
 ```
 
-**Node FQN format**: `module.ClassName.method_name` — fully dot-separated, derived from the file path (e.g., `src/cgis/pipeline.py` → `src.cgis.pipeline.IngestionPipeline.run`). Use `file_path_to_module_fqn(path)` from `extractors/python_extractor.py` to convert paths. `__init__.py` strips the `/__init__` suffix.
+**Node FQN format**: `module.ClassName.method_name` — fully dot-separated, derived from the file path (e.g., `src/cgis/pipeline.py` → `src.cgis.pipeline.IngestionPipeline.run`). Use `cgis.languages.scope_of(path, source_root)` to convert paths (it picks the file's own pack; the Python rule lives in `languages/python/extractor.py`). `__init__.py` strips the `/__init__` suffix.
 
 **Raw call convention**: Extractors emit edges with `target = "raw_call:<name>"`. The `ResolverEngine` then resolves these to actual FQNs or leaves them unresolved (keeps the `raw_call:` prefix in output).
 
 **`ResolverEngine` resolution order** for a call to `name`:
 1. `self.method` → look up `method` on the enclosing class via `_class_methods` index
-2. Unqualified call → `_global_symbols` by name; if ambiguous, prefer same-file candidate via `_file_global_symbols`
+2. Unqualified call → `_global_symbols` by name; if ambiguous, prefer the same-scope candidate via `file_global_symbols` (a file's scope is its path, or the `metadata["scope"]` its FILE node declares — a Go package)
 
 ## Core Models (`src/cgis/core/models.py`)
 
@@ -68,12 +71,30 @@ IngestionPipeline (pipeline.py)
 - `NodeType` — structural (`FILE`, `MODULE`, `CLASS`, `FUNCTION`, `METHOD`…), runtime (`API_ENDPOINT`, `DB_TABLE`…), semantic (`DOMAIN_CONCEPT`).
 - `EdgeType` — structural (`CONTAINS`, `DECLARES`, `IMPORTS`), behavioral (`CALLS`, `REFERENCES`), semantic (`HANDLES`, `PERSISTS`, `AUTHORIZES`).
 
-## Adding a New Language Extractor
-
-1. Subclass `BaseExtractor` in `src/cgis/extractors/`.
-2. Implement `parse(code: str, file_path: str) -> tuple[list[Node], list[Edge]]`.
-3. Emit `CALLS` edges with `target="raw_call:<name>"` — the resolver handles the rest.
-4. Register the extractor in `cli.py`'s `extractors` dict with the file extension key.
+## Adding a Language Pack
+
+1. Create `src/cgis/languages/<name>/` with an extractor subclassing `cgis.core.extractor.BaseExtractor`
+   (`parse(code, file_path) -> tuple[list[Node], list[Edge]]`; emit `CALLS` edges with
+   `target="raw_call:<name>"`, set `Node.language = "<name>"`).
+2. In its `__init__.py`, define `PACK`, subclassing `cgis.core.extractor.LanguagePack` (mark methods `@override`)
+   (`name`, `extensions`, `code_fence`, `is_test`, `scope_of`, `extractor`, `project_reader`,
+   `index_facts`, `classify`, `resolution`). `resolution()` returns `ResolutionRules`
+   (`cgis.core.resolution`): type normalizers, steps at a position (`after:import_map`), a
+   fallback with its confidence, `reconcile_import` — all reading the index as `ResolutionView`.
+   Metadata other files resolve against goes in the manifest's `cross_file_metadata`. `classify` answers for references from the pack's own files and
+   runs the whole chain; a source with no pack gets the generic tail in `SymbolIndex.classify_fqn`.
+3. Add one `Manifest` to `MANIFESTS` in `src/cgis/languages/__init__.py`, with a `load` function that
+   imports the pack statically inside it (lazy, yet visible to the review-fingerprint walk). Nothing
+   else names the pack: CLI, MCP server, guardian and scripts all go through the registry, and the
+   `surface-packs` forbidden-edge gate fails if a surface imports a pack directly.
+4. A pack never imports another pack or `cgis.storage` (`cross-pack`, `pack-isolation` gates).
+5. A pack's `__init__` imports no grammar: import the extractor inside `extractor()`. Config reading
+   goes in a `ProjectReader` (`cgis.core.project`) whose facts are data keyed by `ingest_state`
+   key — the collector (`cgis.import_names`), not the pack, writes them. A key other than the four
+   built-ins (`_FACT_SHAPES`) travels as `ImportNames.extra`: recorded, compared, and merged into the
+   `state` the pack's `index_facts` reads. Its value must read back equal from JSON (no tuples).
+6. A FILE node's id comes from `file_node_id`, its definitions' namespace from `scope_of`; they differ
+   only where several files share a scope (Go), which the FILE node declares as `metadata["scope"]`.
 
 ## Type Discipline
 

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: codegraph-brain
-Version: 0.29.0
+Version: 0.30.0
 Summary: Semantic code graph for AI agents — deterministic FQN resolution, impact analysis and architectural drift gates, exposed over MCP.
 Project-URL: Homepage, https://github.com/zaebee/codegraph-brain
 Project-URL: Repository, https://github.com/zaebee/codegraph-brain
@@ -29,6 +29,7 @@ Requires-Dist: pydantic>=2.13.4
 Requires-Dist: pyyaml>=6.0.2
 Requires-Dist: rich>=15.0.0
 Requires-Dist: structlog>=25.5.0
+Requires-Dist: tree-sitter-go>=0.25.0
 Requires-Dist: tree-sitter-python>=0.25.0
 Requires-Dist: tree-sitter-typescript>=0.23.2
 Requires-Dist: tree-sitter>=0.25.2
@@ -60,7 +61,7 @@ Description-Content-Type: text/markdown
 
 CGIS parses a repository with tree-sitter into a graph of fully qualified symbols and the calls, imports and containment between them, stores it in SQLite, and serves it to AI agents over MCP. An agent that would otherwise grep and read whole files asks the graph instead.
 
-- **Languages:** Python · TypeScript / TSX
+- **Languages:** Python · TypeScript / TSX · Go (pilot)
 - **Runs:** locally — no account, no telemetry; the graph never leaves your disk ([the one opt-in exception](https://github.com/zaebee/codegraph-brain/blob/main/PRIVACY.md))
 
 ```console

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/README.md

@@ -10,7 +10,7 @@
 
 CGIS parses a repository with tree-sitter into a graph of fully qualified symbols and the calls, imports and containment between them, stores it in SQLite, and serves it to AI agents over MCP. An agent that would otherwise grep and read whole files asks the graph instead.
 
-- **Languages:** Python · TypeScript / TSX
+- **Languages:** Python · TypeScript / TSX · Go (pilot)
 - **Runs:** locally — no account, no telemetry; the graph never leaves your disk ([the one opt-in exception](https://github.com/zaebee/codegraph-brain/blob/main/PRIVACY.md))
 
 ```console

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/AUDIT.md

@@ -57,7 +57,7 @@ The graph is static structure. That boundary is real, and it is better stated he
 - **Not a penetration test.** Authorisation *coverage* means every handler has a static path to a guard. It does not mean the guard is correct, that the logic behind it is sound, or that the endpoint is unexploitable.
 - **Not a runtime analysis.** Nothing is executed. Behaviour that only appears under load, concurrency or real data is out of scope.
 - **Not a business-logic review.** The report says how your code is wired, not whether the wiring implements the right rules.
-- **Not language-complete.** Extractors cover Python and TypeScript. Vue, Astro, Go, Rust and everything else are invisible to the graph, and the report will say which parts of your codebase it could not see.
+- **Not language-complete.** Extractors cover Python and TypeScript, with Go as a pilot outside this offer. Vue, Astro, Rust and everything else are invisible to the graph, and the report will say which parts of your codebase it could not see.
 - **Not a substitute for judgement.** An empty impact result means *no static callers found*, not *safe to delete*. Dynamic dispatch, registries and framework decorators do not appear in any static graph. The report flags where this matters instead of asserting a safety it cannot see.
 
 Roughly a tenth of call edges in a typical Python codebase cannot be resolved statically at all — they are calls on objects typed at runtime. That number is in the report too, because it tells you how much of the analysis to trust.

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/architecture/HOW_IT_WORKS.md

@@ -188,35 +188,37 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
         models_Node["Node (models.py:89)"]:::classNode
     end
     subgraph sg_import_names["import_names.py"]
-        import_names_ImportNameCollector["ImportNameCollector (import_names.py:96)"]:::classNode
-        import_names_ImportNameCollector_collect["collect (import_names.py:151)"]:::methodNode
-        import_names_ImportNameCollector_note["note (import_names.py:143)"]:::methodNode
+        import_names_ImportNameCollector["ImportNameCollector (import_names.py:147)"]:::classNode
+        import_names_ImportNameCollector_collect["collect (import_names.py:168)"]:::methodNode
+        import_names_ImportNameCollector_note["note (import_names.py:163)"]:::methodNode
     end
-    subgraph sg_pipeline["pipeline.py"]
-        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (pipeline.py:314)"]:::methodNode
-        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:449)"]:::methodNode
-        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:375)"]:::methodNode
-        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:399)"]:::methodNode
-        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:274)"]:::methodNode
-        pipeline_IngestionPipeline_run["run (pipeline.py:135)"]:::methodNode
-        pipeline_IngestionPipeline_workspace_root["workspace_root (pipeline.py:118)"]:::methodNode
-        pipeline_observe["_observe (pipeline.py:76)"]:::funcNode
-        pipeline_refresh_dispatch["refresh_dispatch (pipeline.py:40)"]:::funcNode
-    end
-    subgraph sg_engine["engine.py"]
-        engine_ResolverEngine["ResolverEngine (engine.py:49)"]:::classNode
-        engine_ResolverEngine_resolve["resolve (engine.py:87)"]:::methodNode
+    subgraph sg_init["__init__.py"]
+        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (__init__.py:394)"]:::methodNode
+        pipeline_IngestionPipeline_get_extractor["_get_extractor (__init__.py:532)"]:::methodNode
+        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (__init__.py:455)"]:::methodNode
+        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (__init__.py:479)"]:::methodNode
+        pipeline_IngestionPipeline_process_file["_process_file (__init__.py:354)"]:::methodNode
+        pipeline_IngestionPipeline_run["run (__init__.py:209)"]:::methodNode
+        pipeline_IngestionPipeline_workspace_root["workspace_root (__init__.py:192)"]:::methodNode
+        pipeline_needs_rebuild["_needs_rebuild (__init__.py:138)"]:::funcNode
+        pipeline_observe["_observe (__init__.py:72)"]:::funcNode
+        pipeline_refresh_dispatch["refresh_dispatch (__init__.py:36)"]:::funcNode
     end
     subgraph sg_uplift["uplift.py"]
-        uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:66)"]:::classNode
-        uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:91)"]:::methodNode
+        uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:67)"]:::classNode
+        uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:92)"]:::methodNode
+    end
+    subgraph sg_engine["engine.py"]
+        engine_ResolverEngine["ResolverEngine (engine.py:63)"]:::classNode
+        engine_ResolverEngine_resolve["resolve (engine.py:109)"]:::methodNode
     end
     subgraph sg_sqlite_store["sqlite_store.py"]
-        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:65)"]:::classNode
+        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:81)"]:::classNode
     end
     pipeline_IngestionPipeline_run -->|REFERENCES| models_Node
     pipeline_IngestionPipeline_run -->|REFERENCES| models_Edge
     pipeline_IngestionPipeline_run -->|REFERENCES| sqlite_store_SQLiteStore
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_needs_rebuild
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_workspace_root
     pipeline_IngestionPipeline_run -->|CALLS| import_names_ImportNameCollector
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_observe
@@ -239,21 +241,22 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
 |--------|------|------|
 | `Node` | CLASS | [`models.py:89`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L89) |
 | `Edge` | CLASS | [`models.py:146`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L146) |
-| `ImportNameCollector` | CLASS | [`import_names.py:96`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L96) |
-| `note` | METHOD | [`import_names.py:143`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L143) |
-| `collect` | METHOD | [`import_names.py:151`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L151) |
-| `refresh_dispatch` | FUNCTION | [`pipeline.py:40`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L40) |
-| `_observe` | FUNCTION | [`pipeline.py:76`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L76) |
-| `workspace_root` | METHOD | [`pipeline.py:118`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L118) |
-| `run` | METHOD | [`pipeline.py:135`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L135) |
-| `_process_file` | METHOD | [`pipeline.py:274`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L274) |
-| `_cross_file_inputs_changed` | METHOD | [`pipeline.py:314`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L314) |
-| `_is_noop_incremental` | METHOD | [`pipeline.py:375`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L375) |
-| `_persist_incremental` | METHOD | [`pipeline.py:399`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L399) |
-| `_get_extractor` | METHOD | [`pipeline.py:449`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L449) |
-| `ResolverEngine` | CLASS | [`engine.py:49`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L49) |
-| `resolve` | METHOD | [`engine.py:87`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L87) |
-| `SemanticUpliftEngine` | CLASS | [`uplift.py:66`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/uplift.py#L66) |
-| `execute_uplift` | METHOD | [`uplift.py:91`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/uplift.py#L91) |
-| `SQLiteStore` | CLASS | [`sqlite_store.py:65`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L65) |
+| `ImportNameCollector` | CLASS | [`import_names.py:147`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L147) |
+| `note` | METHOD | [`import_names.py:163`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L163) |
+| `collect` | METHOD | [`import_names.py:168`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/import_names.py#L168) |
+| `refresh_dispatch` | FUNCTION | [`__init__.py:36`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L36) |
+| `_observe` | FUNCTION | [`__init__.py:72`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L72) |
+| `_needs_rebuild` | FUNCTION | [`__init__.py:138`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L138) |
+| `workspace_root` | METHOD | [`__init__.py:192`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L192) |
+| `run` | METHOD | [`__init__.py:209`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L209) |
+| `_process_file` | METHOD | [`__init__.py:354`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L354) |
+| `_cross_file_inputs_changed` | METHOD | [`__init__.py:394`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L394) |
+| `_is_noop_incremental` | METHOD | [`__init__.py:455`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L455) |
+| `_persist_incremental` | METHOD | [`__init__.py:479`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L479) |
+| `_get_extractor` | METHOD | [`__init__.py:532`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/__init__.py#L532) |
+| `SemanticUpliftEngine` | CLASS | [`uplift.py:67`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/uplift.py#L67) |
+| `execute_uplift` | METHOD | [`uplift.py:92`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline/uplift.py#L92) |
+| `ResolverEngine` | CLASS | [`engine.py:63`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L63) |
+| `resolve` | METHOD | [`engine.py:109`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L109) |
+| `SQLiteStore` | CLASS | [`sqlite_store.py:81`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L81) |
 <!-- END_CGIS_GRAPH -->

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/architecture/ONTOLOGY.md

@@ -129,4 +129,4 @@ domains:
         - "*storage.*"
 ```
 
-**Ontology compliance rule:** Any PR that adds a new `NodeType`, `EdgeType`, or modifies `domains.yaml` must update this document and the `_ONTOLOGY_CLASS` mapping in `src/cgis/resolver/uplift.py`.
+**Ontology compliance rule:** Any PR that adds a new `NodeType`, `EdgeType`, or modifies `domains.yaml` must update this document and the `_ONTOLOGY_CLASS` mapping in `src/cgis/pipeline/uplift.py`.

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/architecture/diagrams/pipeline_flow.mermaid

@@ -12,35 +12,37 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
         models_Node["Node (models.py:89)"]:::classNode
     end
     subgraph sg_import_names["import_names.py"]
-        import_names_ImportNameCollector["ImportNameCollector (import_names.py:96)"]:::classNode
-        import_names_ImportNameCollector_collect["collect (import_names.py:151)"]:::methodNode
-        import_names_ImportNameCollector_note["note (import_names.py:143)"]:::methodNode
+        import_names_ImportNameCollector["ImportNameCollector (import_names.py:147)"]:::classNode
+        import_names_ImportNameCollector_collect["collect (import_names.py:168)"]:::methodNode
+        import_names_ImportNameCollector_note["note (import_names.py:163)"]:::methodNode
     end
-    subgraph sg_pipeline["pipeline.py"]
-        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (pipeline.py:314)"]:::methodNode
-        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:449)"]:::methodNode
-        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:375)"]:::methodNode
-        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:399)"]:::methodNode
-        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:274)"]:::methodNode
-        pipeline_IngestionPipeline_run["run (pipeline.py:135)"]:::methodNode
-        pipeline_IngestionPipeline_workspace_root["workspace_root (pipeline.py:118)"]:::methodNode
-        pipeline_observe["_observe (pipeline.py:76)"]:::funcNode
-        pipeline_refresh_dispatch["refresh_dispatch (pipeline.py:40)"]:::funcNode
-    end
-    subgraph sg_engine["engine.py"]
-        engine_ResolverEngine["ResolverEngine (engine.py:49)"]:::classNode
-        engine_ResolverEngine_resolve["resolve (engine.py:87)"]:::methodNode
+    subgraph sg_init["__init__.py"]
+        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (__init__.py:394)"]:::methodNode
+        pipeline_IngestionPipeline_get_extractor["_get_extractor (__init__.py:532)"]:::methodNode
+        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (__init__.py:455)"]:::methodNode
+        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (__init__.py:479)"]:::methodNode
+        pipeline_IngestionPipeline_process_file["_process_file (__init__.py:354)"]:::methodNode
+        pipeline_IngestionPipeline_run["run (__init__.py:209)"]:::methodNode
+        pipeline_IngestionPipeline_workspace_root["workspace_root (__init__.py:192)"]:::methodNode
+        pipeline_needs_rebuild["_needs_rebuild (__init__.py:138)"]:::funcNode
+        pipeline_observe["_observe (__init__.py:72)"]:::funcNode
+        pipeline_refresh_dispatch["refresh_dispatch (__init__.py:36)"]:::funcNode
     end
     subgraph sg_uplift["uplift.py"]
-        uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:66)"]:::classNode
-        uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:91)"]:::methodNode
+        uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:67)"]:::classNode
+        uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:92)"]:::methodNode
+    end
+    subgraph sg_engine["engine.py"]
+        engine_ResolverEngine["ResolverEngine (engine.py:63)"]:::classNode
+        engine_ResolverEngine_resolve["resolve (engine.py:109)"]:::methodNode
     end
     subgraph sg_sqlite_store["sqlite_store.py"]
-        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:65)"]:::classNode
+        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:81)"]:::classNode
     end
     pipeline_IngestionPipeline_run -->|REFERENCES| models_Node
     pipeline_IngestionPipeline_run -->|REFERENCES| models_Edge
     pipeline_IngestionPipeline_run -->|REFERENCES| sqlite_store_SQLiteStore
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_needs_rebuild
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_workspace_root
     pipeline_IngestionPipeline_run -->|CALLS| import_names_ImportNameCollector
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_observe

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/how-to/MCP_REFERENCE.md

@@ -55,8 +55,9 @@ Reachability/authorization audit — which sources never reach a checkpoint.
     NOT transitively reach an ownership check. Reachability follows behavioral edges
     (CALLS *and* FastAPI ``Depends()`` DEPENDS_ON), so a guard wired via DI counts.
 
-    Select sources with ``from_type`` (a NodeType like ``ROUTE_HANDLER`` /
-    ``API_ENDPOINT`` / ``FUNCTION``) and/or ``from_prefix`` (FQN prefix) — at least
+    Select sources with ``from_type`` (the ``ROUTE_HANDLER`` role — FastAPI handlers on
+    a router built in the same module — or a NodeType like ``FUNCTION``) and/or
+    ``from_prefix`` (FQN prefix) — at least
     one is required. Returns JSON ``{target, covered, gaps}`` where each gap carries
     ``fqn``/``file``/``line``. Generalizes to validators, event tracking, or
     service-layer-boundary rules by pointing ``target`` at the required node.
@@ -68,7 +69,7 @@ Reachability/authorization audit — which sources never reach a checkpoint.
 | :--- | :--- | :---: | :--- |
 | `target` | `string` | ✓ | FQN of the checkpoint every source must reach, e.g. an ownership check. A unique dot-boundary suffix also resolves. |
 | `db_path` | `string` |  | SQLite graph built by cgis_ingest. A relative path resolves against the MCP server's working directory, not the agent's — prefer an absolute path. |
-| `from_type` | `any` |  | NodeType of the sources to audit, e.g. ROUTE_HANDLER, API_ENDPOINT or FUNCTION (any case). Give this, from_prefix, or both. |
+| `from_type` | `any` |  | NodeType or role of the sources to audit (any case): ROUTE_HANDLER selects FastAPI handlers on a router built in the same module; a structural type such as FUNCTION selects by type. Give this, from_prefix, or both. |
 | `from_prefix` | `any` |  | Only audit sources at or under this FQN prefix, matched on whole dot-segments. A selection matching no source is an error naming the whole-segment prefixes it may have meant. Combined with from_type when both are given. |
 | `depth` | `integer` |  | Maximum reachability depth; a longer path is reported as a gap. |
 

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/ontology/domains.yaml

@@ -6,10 +6,10 @@ domains:
     description: "Source code parsing and AST extraction"
     heuristics:
       file_path_patterns:
-        - "*extractors/*"
+        - "*languages/*"
       fqn_patterns:
         - "*.Extractor*"
-        - "*extractors.*"
+        - "*languages.*"
 
   StorageLayer:
     description: "Database storage, schemas, and persistence"
@@ -21,7 +21,7 @@ domains:
         - "*storage.*"
 
   SemanticEngine:
-    description: "Symbol resolution, linkage, and semantic uplift"
+    description: "Symbol resolution and linkage"
     heuristics:
       file_path_patterns:
         - "*resolver/*"
@@ -29,8 +29,6 @@ domains:
         - "*.Resolver*"
         - "*.ResolverEngine*"
         - "*resolver.*"
-        - "*.uplift*"
-        - "*.SemanticUplift*"
 
   QueryLayer:
     description: "Graph traversal and query operations"
@@ -53,12 +51,13 @@ domains:
         - "*.EdgeType*"
 
   Pipeline:
-    description: "Ingestion pipeline orchestration"
+    description: "Ingestion pipeline orchestration and its post-write passes (semantic uplift, dispatch)"
     heuristics:
       file_path_patterns:
-        - "*pipeline.py"
+        - "*pipeline/*"
       fqn_patterns:
         - "*.IngestionPipeline*"
+        - "*pipeline"
         - "*pipeline.*"
 
   APILayer:

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/ontology/patterns.yaml

@@ -114,22 +114,47 @@ patterns:
 # measurement (see plan: docs/specs/plans/2026-06-10-motif-basis-part-b.md).
 project_domains:
   # Python graph (ingest root: src/ → FQNs carry the cgis. prefix)
-  - name: "extraction"
-    fqn_prefix: "cgis.extractors"
+  # Language packs (spec: Drift gates, Domains) — one domain per pack, one shared
+  # bar (ruling G2), so a new pack is measured against it from its first commit;
+  # tests/unit/test_patterns_yaml.py fails for a pack without one.
+  # Was the single "extraction" domain over cgis.extractors / cgis.languages
+  # (#116, #183, steps 1-5). Measured at step 6 (main ca32430): python layered_dag
+  # 0.393 (best fit funnel 0.328), typescript layered_dag 0.184. Shared
+  # tolerance = loosest + headroom.
+  - name: "languages.python"
+    fqn_prefix: "cgis.languages.python"
     expected_pattern: layered_dag
     profile: python
-    # Re-negotiated in #116: PythonExtractor was decomposed from a God Object into a
-    # layered package (orchestrator python_extractor → handlers → _python_ast core),
-    # so the domain is no longer pure_utility. Best-fit is now layered_dag (same
-    # pattern as cgis.query).
-    # Re-baselined in #183 (≈0.32 → 0.37): the resolver stopped fabricating phantom
-    # `module.list.append`-style internal FQNs for builtin-method calls (e.g. `edges.append`
-    # where `edges: list[Edge]`). Those fake intra-domain CALLS edges had been artificially
-    # deflating this domain's drift; 0.37 is the honest census of the real structure (no real
-    # edges lost — verified by edge-diff). Correctness-driven re-baseline, not ratchet loosening.
-    drift_tolerance: 0.40
+    drift_tolerance: 0.42
     hygiene_baseline:
-      unresolved_ratio: 0.37 # measured 0.3604 when the gate came alive (#149)
+      unresolved_ratio: 0.37 # measured 0.356 at step 6 (the old extraction baseline)
+
+  - name: "languages.typescript"
+    fqn_prefix: "cgis.languages.typescript"
+    expected_pattern: layered_dag
+    profile: python
+    drift_tolerance: 0.42
+    hygiene_baseline:
+      unresolved_ratio: 0.31 # measured 0.295 at step 6
+
+  - name: "languages.go"
+    fqn_prefix: "cgis.languages.go"
+    expected_pattern: layered_dag
+    profile: python
+    drift_tolerance: 0.42
+    hygiene_baseline:
+      unresolved_ratio: 0.26 # measured 0.242 at step 7b (drift 0.285)
+
+  # The pack contract and the model (spec: Core). layered_dag, not the spec's
+  # pure_utility — measured 0.215 vs 0.554 at step 6: since steps 1-4 the contract
+  # is layered (extractor/index/resolution/project -> models) (ruling G1).
+  - name: "core"
+    fqn_prefix: "cgis.core"
+    expected_pattern: layered_dag
+    profile: python
+    drift_tolerance: 0.25
+    hygiene_baseline:
+      unresolved_ratio: 0.21 # measured 0.191 at step 6
 
   - name: "resolution"
     fqn_prefix: "cgis.resolver"
@@ -137,7 +162,12 @@ project_domains:
     profile: python
     drift_tolerance: 0.40 # v2 measured ≈0.25 post-#115 split (tv_imp 0.00 — real 021C chain engine→symbols→indices; residual is tv_calls)
     hygiene_baseline:
-      unresolved_ratio: 0.45 # measured 0.4451 when the gate came alive (#149)
+      # Re-baselined 0.45 -> 0.46 in language-packs step 5 (user decision): moving
+      # resolver/uplift.py into cgis/pipeline/ took 70 calls, 28 of them unresolved
+      # (0.40), out of a domain at 0.44 — 136/309 became 108/239 = 0.452 with no
+      # unresolved edge added and the moved code unchanged. A denominator effect,
+      # not a resolution regression; 0.46 keeps the ratchet's usual small headroom.
+      unresolved_ratio: 0.46 # measured 0.4519 after step 5 (was 0.4451 at #149)
 
   - name: "pipeline"
     fqn_prefix: "cgis.pipeline"
@@ -252,15 +282,9 @@ project_domains:
     hygiene_baseline:
       unresolved_ratio: 0.79 # measured 0.7857 when the gate came alive (#149)
 
-# ── Project-level quotient binding (spec §3.4) — OBSERVE-ONLY burn-in ────────
-# Measured quotient IMPORTS census {021D .4, 021U .4, 030T .2}: the domain
-# graph is an orchestrator star out of `pipeline`, NOT the chain the spec
-# example claimed. enforce stays false until the burn-in settles whether to
-# rebind to orchestrator or restructure; flipping to true makes it a ratchet.
-project_level:
-  - name: "cgis-project"
-    fqn_prefix: "quotient"
-    expected_pattern: pipeline_stage
-    profile: python
-    drift_tolerance: 0.15
-    enforce: false
+# ── Project-level quotient ───────────────────────────────────────────────────
+# Retired in language-packs step 6 (#146). cgis's topology is enforced by the
+# forbidden-edge gate (tests/self_parsing/test_architecture.py, exact shrinking
+# allowlists); the build/read plane quotients are printed observe-only by
+# tests/self_parsing/test_drift.py. The `project_level` section remains a
+# supported feature for other repositories.

{codegraph_brain-0.29.0 → codegraph_brain-0.30.0}/docs/ontology/tolerances.lock

@@ -11,7 +11,10 @@
 # update the lock and justify it in the PR description.
 
 project_domains:
-  extraction: 0.40
+  languages.python: 0.42
+  languages.typescript: 0.42
+  languages.go: 0.42
+  core: 0.25
   resolution: 0.40
   pipeline: 0.25
   storage: 0.20
@@ -25,6 +28,3 @@ project_domains:
   store: 0.15
   providers: 0.17
   utils: 0.20
-
-project_level:
-  cgis-project: 0.15