codegraph-brain 0.20.0__tar.gz → 0.21.0__tar.gz

codegraph_brain-0.21.0/.github/test-count-baseline

@@ -0,0 +1 @@
+2459

codegraph_brain-0.21.0/.release-please-manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "0.21.0"
+}

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/CHANGELOG.md

@@ -1,5 +1,25 @@
 # Changelog
 
+## [0.21.0](https://github.com/zaebee/codegraph-brain/compare/codegraph-brain-v0.20.0...codegraph-brain-v0.21.0) (2026-09-16)
+
+
+### Features
+
+* **resolver:** resolve JS/TS runtime globals into js_builtins.* ([#111](https://github.com/zaebee/codegraph-brain/issues/111)) ([#453](https://github.com/zaebee/codegraph-brain/issues/453)) ([84e790b](https://github.com/zaebee/codegraph-brain/commit/84e790b404f7a515e048f7a2370b8865b71912ff))
+
+
+### Bug Fixes
+
+* **cli:** a full ingest into a database records file hashes ([#461](https://github.com/zaebee/codegraph-brain/issues/461)) ([e0a4a5e](https://github.com/zaebee/codegraph-brain/commit/e0a4a5ec34f8b0b34220f3f318ce0edc99ed1d9b))
+* **pipeline:** rebuild when a change alters what other files resolve against ([#38](https://github.com/zaebee/codegraph-brain/issues/38)) ([#458](https://github.com/zaebee/codegraph-brain/issues/458)) ([8126fd6](https://github.com/zaebee/codegraph-brain/commit/8126fd6377c82613f9f8a76f33253a8cd9e636f0))
+* **resolver:** Python stdlib names are STDLIB only in Python sources ([#454](https://github.com/zaebee/codegraph-brain/issues/454)) ([#457](https://github.com/zaebee/codegraph-brain/issues/457)) ([15e7ba1](https://github.com/zaebee/codegraph-brain/commit/15e7ba17ae49e2e3c10a2ef9f6cf1f11e663edfb))
+
+
+### Documentation
+
+* auto-sync architecture graph and MCP reference ([#456](https://github.com/zaebee/codegraph-brain/issues/456)) ([ae24054](https://github.com/zaebee/codegraph-brain/commit/ae24054361935dbb1a1f9471eea7b4b949ab8a10))
+* auto-sync architecture graph and MCP reference ([#460](https://github.com/zaebee/codegraph-brain/issues/460)) ([a341063](https://github.com/zaebee/codegraph-brain/commit/a3410631511802bdc9851decadbbbf25b40d8d22))
+
 ## [0.20.0](https://github.com/zaebee/codegraph-brain/compare/codegraph-brain-v0.19.0...codegraph-brain-v0.20.0) (2026-09-11)
 
 

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: codegraph-brain
-Version: 0.20.0
+Version: 0.21.0
 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
@@ -202,31 +202,36 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
         models_Node["Node (models.py:85)"]:::classNode
     end
     subgraph sg_pipeline["pipeline.py"]
-        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:252)"]:::methodNode
-        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:192)"]:::methodNode
-        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:211)"]:::methodNode
-        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:157)"]:::methodNode
-        pipeline_IngestionPipeline_run["run (pipeline.py:53)"]:::methodNode
+        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (pipeline.py:249)"]:::methodNode
+        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:384)"]:::methodNode
+        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:310)"]:::methodNode
+        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:334)"]:::methodNode
+        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:212)"]:::methodNode
+        pipeline_IngestionPipeline_run["run (pipeline.py:99)"]:::methodNode
+        pipeline_IngestionPipeline_workspace_root["workspace_root (pipeline.py:82)"]:::methodNode
     end
     subgraph sg_engine["engine.py"]
-        engine_ResolverEngine["ResolverEngine (engine.py:19)"]:::classNode
-        engine_ResolverEngine_resolve["resolve (engine.py:36)"]:::methodNode
+        engine_ResolverEngine["ResolverEngine (engine.py:20)"]:::classNode
+        engine_ResolverEngine_resolve["resolve (engine.py:37)"]:::methodNode
     end
     subgraph sg_uplift["uplift.py"]
         uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:66)"]:::classNode
         uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:91)"]:::methodNode
     end
     subgraph sg_sqlite_store["sqlite_store.py"]
-        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:40)"]:::classNode
+        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:42)"]:::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_IngestionPipeline_workspace_root
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_get_extractor
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_process_file
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_is_noop_incremental
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine_resolve
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_cross_file_inputs_changed
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_run
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_persist_incremental
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine_execute_uplift
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine
@@ -236,16 +241,18 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
 |--------|------|------|
 | `Node` | CLASS | [`models.py:85`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L85) |
 | `Edge` | CLASS | [`models.py:142`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L142) |
-| `run` | METHOD | [`pipeline.py:53`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L53) |
-| `_process_file` | METHOD | [`pipeline.py:157`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L157) |
-| `_is_noop_incremental` | METHOD | [`pipeline.py:192`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L192) |
-| `_persist_incremental` | METHOD | [`pipeline.py:211`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L211) |
-| `_get_extractor` | METHOD | [`pipeline.py:252`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L252) |
-| `ResolverEngine` | CLASS | [`engine.py:19`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L19) |
-| `resolve` | METHOD | [`engine.py:36`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L36) |
+| `workspace_root` | METHOD | [`pipeline.py:82`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L82) |
+| `run` | METHOD | [`pipeline.py:99`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L99) |
+| `_process_file` | METHOD | [`pipeline.py:212`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L212) |
+| `_cross_file_inputs_changed` | METHOD | [`pipeline.py:249`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L249) |
+| `_is_noop_incremental` | METHOD | [`pipeline.py:310`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L310) |
+| `_persist_incremental` | METHOD | [`pipeline.py:334`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L334) |
+| `_get_extractor` | METHOD | [`pipeline.py:384`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L384) |
+| `ResolverEngine` | CLASS | [`engine.py:20`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L20) |
+| `resolve` | METHOD | [`engine.py:37`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L37) |
 | `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:40`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L40) |
+| `SQLiteStore` | CLASS | [`sqlite_store.py:42`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L42) |
 <!-- END_CGIS_GRAPH -->
 
 ---

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/README.md

@@ -152,31 +152,36 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
         models_Node["Node (models.py:85)"]:::classNode
     end
     subgraph sg_pipeline["pipeline.py"]
-        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:252)"]:::methodNode
-        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:192)"]:::methodNode
-        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:211)"]:::methodNode
-        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:157)"]:::methodNode
-        pipeline_IngestionPipeline_run["run (pipeline.py:53)"]:::methodNode
+        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (pipeline.py:249)"]:::methodNode
+        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:384)"]:::methodNode
+        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:310)"]:::methodNode
+        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:334)"]:::methodNode
+        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:212)"]:::methodNode
+        pipeline_IngestionPipeline_run["run (pipeline.py:99)"]:::methodNode
+        pipeline_IngestionPipeline_workspace_root["workspace_root (pipeline.py:82)"]:::methodNode
     end
     subgraph sg_engine["engine.py"]
-        engine_ResolverEngine["ResolverEngine (engine.py:19)"]:::classNode
-        engine_ResolverEngine_resolve["resolve (engine.py:36)"]:::methodNode
+        engine_ResolverEngine["ResolverEngine (engine.py:20)"]:::classNode
+        engine_ResolverEngine_resolve["resolve (engine.py:37)"]:::methodNode
     end
     subgraph sg_uplift["uplift.py"]
         uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:66)"]:::classNode
         uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:91)"]:::methodNode
     end
     subgraph sg_sqlite_store["sqlite_store.py"]
-        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:40)"]:::classNode
+        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:42)"]:::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_IngestionPipeline_workspace_root
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_get_extractor
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_process_file
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_is_noop_incremental
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine_resolve
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_cross_file_inputs_changed
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_run
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_persist_incremental
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine_execute_uplift
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine
@@ -186,16 +191,18 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
 |--------|------|------|
 | `Node` | CLASS | [`models.py:85`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L85) |
 | `Edge` | CLASS | [`models.py:142`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/core/models.py#L142) |
-| `run` | METHOD | [`pipeline.py:53`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L53) |
-| `_process_file` | METHOD | [`pipeline.py:157`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L157) |
-| `_is_noop_incremental` | METHOD | [`pipeline.py:192`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L192) |
-| `_persist_incremental` | METHOD | [`pipeline.py:211`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L211) |
-| `_get_extractor` | METHOD | [`pipeline.py:252`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L252) |
-| `ResolverEngine` | CLASS | [`engine.py:19`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L19) |
-| `resolve` | METHOD | [`engine.py:36`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L36) |
+| `workspace_root` | METHOD | [`pipeline.py:82`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L82) |
+| `run` | METHOD | [`pipeline.py:99`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L99) |
+| `_process_file` | METHOD | [`pipeline.py:212`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L212) |
+| `_cross_file_inputs_changed` | METHOD | [`pipeline.py:249`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L249) |
+| `_is_noop_incremental` | METHOD | [`pipeline.py:310`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L310) |
+| `_persist_incremental` | METHOD | [`pipeline.py:334`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L334) |
+| `_get_extractor` | METHOD | [`pipeline.py:384`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/pipeline.py#L384) |
+| `ResolverEngine` | CLASS | [`engine.py:20`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L20) |
+| `resolve` | METHOD | [`engine.py:37`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/resolver/engine.py#L37) |
 | `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:40`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L40) |
+| `SQLiteStore` | CLASS | [`sqlite_store.py:42`](https://github.com/zaebee/codegraph-brain/blob/main/src/cgis/storage/sqlite_store.py#L42) |
 <!-- END_CGIS_GRAPH -->
 
 ---

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/docs/architecture/diagrams/pipeline_flow.mermaid

@@ -12,31 +12,36 @@ classDef externalNode fill:#fff3e0,stroke:#e65100,stroke-width:1px,stroke-dashar
         models_Node["Node (models.py:85)"]:::classNode
     end
     subgraph sg_pipeline["pipeline.py"]
-        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:252)"]:::methodNode
-        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:192)"]:::methodNode
-        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:211)"]:::methodNode
-        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:157)"]:::methodNode
-        pipeline_IngestionPipeline_run["run (pipeline.py:53)"]:::methodNode
+        pipeline_IngestionPipeline_cross_file_inputs_changed["_cross_file_inputs_changed (pipeline.py:249)"]:::methodNode
+        pipeline_IngestionPipeline_get_extractor["_get_extractor (pipeline.py:384)"]:::methodNode
+        pipeline_IngestionPipeline_is_noop_incremental["_is_noop_incremental (pipeline.py:310)"]:::methodNode
+        pipeline_IngestionPipeline_persist_incremental["_persist_incremental (pipeline.py:334)"]:::methodNode
+        pipeline_IngestionPipeline_process_file["_process_file (pipeline.py:212)"]:::methodNode
+        pipeline_IngestionPipeline_run["run (pipeline.py:99)"]:::methodNode
+        pipeline_IngestionPipeline_workspace_root["workspace_root (pipeline.py:82)"]:::methodNode
     end
     subgraph sg_engine["engine.py"]
-        engine_ResolverEngine["ResolverEngine (engine.py:19)"]:::classNode
-        engine_ResolverEngine_resolve["resolve (engine.py:36)"]:::methodNode
+        engine_ResolverEngine["ResolverEngine (engine.py:20)"]:::classNode
+        engine_ResolverEngine_resolve["resolve (engine.py:37)"]:::methodNode
     end
     subgraph sg_uplift["uplift.py"]
         uplift_SemanticUpliftEngine["SemanticUpliftEngine (uplift.py:66)"]:::classNode
         uplift_SemanticUpliftEngine_execute_uplift["execute_uplift (uplift.py:91)"]:::methodNode
     end
     subgraph sg_sqlite_store["sqlite_store.py"]
-        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:40)"]:::classNode
+        sqlite_store_SQLiteStore["SQLiteStore (sqlite_store.py:42)"]:::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_IngestionPipeline_workspace_root
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_get_extractor
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_process_file
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_is_noop_incremental
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine
     pipeline_IngestionPipeline_run -->|CALLS| engine_ResolverEngine_resolve
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_cross_file_inputs_changed
+    pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_run
     pipeline_IngestionPipeline_run -->|CALLS| pipeline_IngestionPipeline_persist_incremental
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine_execute_uplift
     pipeline_IngestionPipeline_run -->|CALLS| uplift_SemanticUpliftEngine

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/docs/how-to/MCP_REFERENCE.md

@@ -237,9 +237,11 @@ Scan a local directory, extract all symbols, resolve links, and build the graph
 
     By default the ingest is **incremental**: only changed/new files are
     re-scanned, and the summary reports both what changed this run and the
-    whole-graph total. Set ``full_rebuild=True`` to re-scan every file and
-    overwrite the database from scratch — use this to drop nodes for files that
-    were deleted or renamed, which an incremental run leaves behind.
+    whole-graph total. When a change alters what other files resolve against — a
+    renamed, removed or added symbol, a deleted or new file, a changed base class
+    or re-export — the incremental run rebuilds the whole graph itself, so edges
+    in unchanged files never point at symbols that no longer exist. Set
+    ``full_rebuild=True`` to force a re-scan of every file from scratch.
 
 | Argument | Type | Required | Description |
 | :--- | :--- | :---: | :--- |

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/pyproject.toml

@@ -7,7 +7,7 @@ packages = ["src/cgis"]
 
 [project]
 name = "codegraph-brain"
-version = "0.20.0"
+version = "0.21.0"
 description = "Semantic code graph for AI agents — deterministic FQN resolution, impact analysis and architectural drift gates, exposed over MCP."
 readme = "README.md"
 requires-python = ">=3.12"

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/src/cgis/api/mcp_server.py

@@ -260,9 +260,11 @@ def cgis_ingest(project_path: str, db_path: str = _DEFAULT_DB, full_rebuild: boo
 
     By default the ingest is **incremental**: only changed/new files are
     re-scanned, and the summary reports both what changed this run and the
-    whole-graph total. Set ``full_rebuild=True`` to re-scan every file and
-    overwrite the database from scratch — use this to drop nodes for files that
-    were deleted or renamed, which an incremental run leaves behind.
+    whole-graph total. When a change alters what other files resolve against — a
+    renamed, removed or added symbol, a deleted or new file, a changed base class
+    or re-export — the incremental run rebuilds the whole graph itself, so edges
+    in unchanged files never point at symbols that no longer exist. Set
+    ``full_rebuild=True`` to force a re-scan of every file from scratch.
     """
     refusal = _reject_db_path(db_path)
     if refusal is not None:
@@ -272,13 +274,12 @@ def cgis_ingest(project_path: str, db_path: str = _DEFAULT_DB, full_rebuild: boo
     pipeline = IngestionPipeline(_EXTRACTORS)
     try:
         with SQLiteStore(db_path) as store:
-            if full_rebuild:
-                # Clear first, then run incrementally over an empty DB: this drops
-                # deleted-file nodes, repopulates files_state correctly, and runs
-                # uplift inside the pipeline (store provided) — all in one path.
-                store.clear()
-            _nodes, _raw, resolved = pipeline.run(project_path, store=store)
-            store.record_ingest(project_path)
+            # A rebuild replaces the stored graph in the transaction that writes the
+            # new one: deleted-file nodes and stale hashes go, uplift runs inside
+            # the pipeline, and a failure part-way leaves the old graph intact.
+            nodes, _raw, resolved = pipeline.run(project_path, store=store, rebuild=full_rebuild)
+            if nodes:
+                store.record_ingest(project_path)
             total_nodes = store.get_node_count()
             total_edges = store.get_edge_count()
     except Exception as exc:
@@ -292,8 +293,14 @@ def cgis_ingest(project_path: str, db_path: str = _DEFAULT_DB, full_rebuild: boo
         total_edges=total_edges,
         db=db_path,
     )
-    lines = [f"✅ Ingested: {project_path} (mode: {mode})"]
-    if not full_rebuild and not resolved:
+    if not nodes:
+        # Nothing extracted: a rebuild kept the stored graph, and neither mode
+        # records this path as the graph's fresh root.
+        kept = "the stored graph was kept" if full_rebuild else "the graph now holds none"
+        lines = [f"⚠️ No source files extracted from {project_path} (mode: {mode}); {kept}."]
+    else:
+        lines = [f"✅ Ingested: {project_path} (mode: {mode})"]
+    if nodes and not full_rebuild and not resolved:
         # Incremental no-op: an empty resolved set means no files changed. Say so
         # explicitly so the stable total below doesn't read as a shrunken graph (#192).
         lines.append("No files changed since the last ingest.")

{codegraph_brain-0.20.0 → codegraph_brain-0.21.0}/src/cgis/cli.py

@@ -54,7 +54,6 @@ from cgis.query.fqn import resolve_fqn
 from cgis.query.render.graph_json import graph_to_json
 from cgis.query.render.mermaid import MermaidCompiler
 from cgis.query.render.metrics import ArchitectureReport, DuckDBAnalyzer
-from cgis.resolver.uplift import SemanticUpliftEngine
 from cgis.storage.sqlite_store import RAW_CALL_PREFIX, SQLiteStore
 
 _DEFAULT_DB = "graph.db"
@@ -144,33 +143,27 @@ def main(
     """CGIS — Code Graph Intelligence System CLI."""
 
 
-def _write_graph_output(
+def _write_json_graph(
     output: str,
     source_path: str,
     nodes: list[Node],
     resolved_edges: list[Edge],
-    domains: str | None,
 ) -> None:
-    """Persist the ingestion result to the given output path (.db or .json)."""
-    if output.endswith(".json"):
-        enriched_nodes = HealthScorer(nodes, resolved_edges).enrich()
-        graph_data = {
-            "metadata": {
-                "source_path": source_path,
-                "node_count": len(enriched_nodes),
-                "edge_count": len(resolved_edges),
-            },
-            "nodes": [n.model_dump() for n in enriched_nodes],
-            "edges": [e.model_dump() for e in resolved_edges],
-        }
-        output_path = Path(output)
-        output_path.parent.mkdir(parents=True, exist_ok=True)
-        with output_path.open("w", encoding="utf-8") as f:
-            _json.dump(graph_data, f, indent=2)
-    else:
-        with SQLiteStore(output) as store:
-            store.save_graph(nodes, resolved_edges, overwrite=True)
-            SemanticUpliftEngine(store, domains).execute_uplift()
+    """Write the ingestion result as a health-enriched graph.json."""
+    enriched_nodes = HealthScorer(nodes, resolved_edges).enrich()
+    graph_data = {
+        "metadata": {
+            "source_path": source_path,
+            "node_count": len(enriched_nodes),
+            "edge_count": len(resolved_edges),
+        },
+        "nodes": [n.model_dump() for n in enriched_nodes],
+        "edges": [e.model_dump() for e in resolved_edges],
+    }
+    output_path = Path(output)
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    with output_path.open("w", encoding="utf-8") as f:
+        _json.dump(graph_data, f, indent=2)
 
 
 @app.command()
@@ -225,11 +218,22 @@ def ingest(
         )
         incremental = False
 
+    # Anything but JSON is a database. A full ingest into one runs the
+    # store-backed pipeline as a rebuild — the path MCP `full_rebuild` takes — so
+    # the file hashes the next --incremental compares against are written, and
+    # stale hashes and deleted files' nodes go, in the one transaction that writes
+    # the new graph. Writing it with save_graph afterwards left files_state as it was.
+    to_database = not output.endswith(".json")
     try:
-        if incremental:
+        if to_database:
+            # A bad path must not create or touch the database.
+            IngestionPipeline.workspace_root(path)
             with SQLiteStore(output) as store:
-                nodes, raw_edges, resolved_edges = pipeline.run(path, store=store)
-                store.record_ingest(path)
+                nodes, raw_edges, resolved_edges = pipeline.run(
+                    path, store=store, rebuild=not incremental
+                )
+                if nodes:
+                    store.record_ingest(path)
         else:
             nodes, raw_edges, resolved_edges = pipeline.run(path)
 
@@ -240,14 +244,8 @@ def ingest(
             )
             return
 
-        if not incremental:
-            _write_graph_output(output, path, nodes, resolved_edges, domains)
-            # Anything but JSON is a database — `_write_graph_output` branches on
-            # exactly that, and gating on `.db` alone left `-o graph.sqlite`
-            # advising a re-ingest that would take the same branch again.
-            if not output.endswith(".json"):
-                with SQLiteStore(output) as store:
-                    store.record_ingest(path)
+        if not to_database:
+            _write_json_graph(output, path, nodes, resolved_edges)
 
         table = Table(title="Ingestion Summary")
         table.add_column("Metric", style="cyan")

codegraph_brain-0.21.0/src/cgis/core/js_globals.py

@@ -0,0 +1,116 @@
+"""The names a JavaScript runtime provides without an import (#111).
+
+Plain data in `core` because two layers read it: the TypeScript extractor, to
+record which of these names a file rebinds, and the resolver, to rewrite calls
+on the ones it does not.
+"""
+
+#: ECMAScript standard globals plus the browser and Node host objects a UI or
+#: server codebase calls directly. A receiver is matched by its root segment only,
+#: so `Math.max` and `document.body.append` both qualify; `arr.map` does not.
+JS_GLOBALS: frozenset[str] = frozenset(
+    {
+        # ECMAScript value/function globals
+        "globalThis",
+        "isFinite",
+        "isNaN",
+        "parseFloat",
+        "parseInt",
+        "encodeURI",
+        "encodeURIComponent",
+        "decodeURI",
+        "decodeURIComponent",
+        "structuredClone",
+        "queueMicrotask",
+        # ECMAScript constructors and namespaces
+        "Array",
+        "ArrayBuffer",
+        "Atomics",
+        "BigInt",
+        "Boolean",
+        "DataView",
+        "Date",
+        "Error",
+        "EvalError",
+        "Float32Array",
+        "Float64Array",
+        "Function",
+        "Int8Array",
+        "Int16Array",
+        "Int32Array",
+        "Intl",
+        "JSON",
+        "Map",
+        "Math",
+        "Number",
+        "Object",
+        "Promise",
+        "Proxy",
+        "RangeError",
+        "ReferenceError",
+        "Reflect",
+        "RegExp",
+        "Set",
+        "String",
+        "Symbol",
+        "SyntaxError",
+        "TypeError",
+        "Uint8Array",
+        "Uint8ClampedArray",
+        "Uint16Array",
+        "Uint32Array",
+        "URIError",
+        "WeakMap",
+        "WeakRef",
+        "WeakSet",
+        # Host globals shared by browsers and Node
+        "console",
+        "setTimeout",
+        "clearTimeout",
+        "setInterval",
+        "clearInterval",
+        "fetch",
+        "URL",
+        "URLSearchParams",
+        "AbortController",
+        "TextEncoder",
+        "TextDecoder",
+        "Blob",
+        "FormData",
+        "Headers",
+        "Request",
+        "Response",
+        "crypto",
+        "performance",
+        # Browser globals
+        "window",
+        "document",
+        "navigator",
+        "location",
+        "history",
+        "localStorage",
+        "sessionStorage",
+        "requestAnimationFrame",
+        "cancelAnimationFrame",
+        "getComputedStyle",
+        "matchMedia",
+        "alert",
+        "confirm",
+        "prompt",
+        "ResizeObserver",
+        "IntersectionObserver",
+        "MutationObserver",
+        "CustomEvent",
+        "Event",
+        "WebSocket",
+        "Worker",
+        "Image",
+        # Node globals
+        "global",
+        "process",
+        "Buffer",
+        "require",
+        "setImmediate",
+        "clearImmediate",
+    }
+)