feat: incremental graph rebuild (3-PR sequence: G1+G2+G3)

AGENTS.md

@@ -43,7 +43,7 @@ when needed.
   variables, full `.java-codebase-rag.yml` reference, **graph layer**
   (node kinds, edges, capabilities, ranking, "Re-index required"
   callouts), brownfield overrides, ignore patterns. The current
-  `ontology_version` is **15** (`EDGE_SCHEMA` in `java_ontology.py`;
+  `ontology_version` is **17** (`EDGE_SCHEMA` in `java_ontology.py`;
   material `OVERRIDES` Symbol→Symbol edges: subtype instance method →
   supertype declaration with matching `signature`, one
   `IMPLEMENTS`/`EXTENDS` hop; valid `neighbors` `EdgeType`).
@@ -190,7 +190,7 @@ template):
   `VALID_RESOLVE_REASONS`, `VALID_UNRESOLVED_CALL_REASONS`.
 - Schema changes that affect the Lance index or Kuzu graph need a
   matching update to the README "Re-index required" callout. Bump
-  `ontology_version` when enrichment semantics change (currently **15**).
+  `ontology_version` when enrichment semantics change (currently **17**).
 - Brownfield is a first-class surface: any new auto-detection (route,
   role, capability, http client, async producer) must compose with the
   matching `BrownfieldOverrides` layer. Last writer wins (outermost layer

README.md

@@ -168,7 +168,7 @@ Run `java-codebase-rag --help` to list grouped subcommands. Operator playbook wi
 | Group | Subcommand | What it does |
 |---|---|---|
 | Lifecycle | `init` | First-time index. Refuses if artifacts already exist. |
-| Lifecycle | `increment` | CocoIndex catch-up (Lance only); Kuzu stays stale until `reprocess`. |
+| Lifecycle | `increment` | CocoIndex catch-up + incremental Kuzu update. `--vectors-only` for Lance only. |
 | Lifecycle | `reprocess` | Full Lance + Kuzu rebuild. `--vectors-only` / `--graph-only` for a single phase. |
 | Lifecycle | `erase` | Delete index artifacts. Requires `--yes` or TTY confirm. |
 | Introspection | `meta`, `tables`, `diagnose-ignore`, `unresolved-calls` | Health, table listing, ignore-layer diagnostics, receiver-failure call sites. |
@@ -212,5 +212,4 @@ The default embedding model is `sentence-transformers/all-MiniLM-L6-v2` (downloa
 
 - `get_service_topology` — microservice-level summary aggregating `HTTP_CALLS` / `ASYNC_CALLS`.
 - Agentic routing layer (query classifier → vector / graph / both).
-- Incremental Kuzu updates (per-changed-file).
 - Optional `codegraph_nodes` LanceDB table embedding symbol summaries so the graph itself is vector-searchable.

ast_java.py

@@ -83,7 +83,7 @@
 # Phase 11: `EDGE_SCHEMA` in `java_ontology.py` (canonical edge navigation schema; v14 re-index).
 # Phase 12: CALLS `callee_declaring_role`, supertype-walk dedup, pass3 unresolved counters (v15 re-index).
 # Bumps whenever extraction / enrichment semantics change.
-ONTOLOGY_VERSION = 16
+ONTOLOGY_VERSION = 17
 
 ROLE_ANNOTATIONS: dict[str, str] = {
     # Spring Web