Migrate graph storage from KuzuDB to LadybugDB

This commit replaces the KuzuDB dependency with LadybugDB, the maintained fork by the same core team. This is a mechanical rename with no logic changes.

Changes:
- Dependency swap: kuzu>=0.11.3,<0.12 → ladybug>=0.17.1,<0.18
- File rename: kuzu_queries.py → ladybug_queries.py
- Class rename: KuzuGraph → LadybugGraph
- Function renames: resolve_kuzu_path → resolve_ladybug_path, etc.
- CLI arg rename: --kuzu-path → --ladybug-path
- Database file extension: code_graph.kuzu → code_graph.lbug
- Ontology field rename: kuzu_type → graph_type (engine-agnostic)
- Updated all imports, references, and documentation

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

AGENTS.md

@@ -74,8 +74,8 @@ when needed.
 |------|------|
 | `server.py` | MCP stdio server. Every `@mcp.tool` lives here. |
 | `search_lancedb.py` | Vector / hybrid / graph-expanded search; ranking. |
-| `build_ast_graph.py` | Tree-sitter → Kuzu graph builder (full rebuild). Owns `pass1`–`pass6` (`pass5` emits `HTTP_CALLS` / `ASYNC_CALLS` caller edges; `pass6_match_edges` resolves cross-service / intra-service / ambiguous / phantom / unresolved match outcomes — ontology 7). |
-| `kuzu_queries.py` | Read-only Cypher helpers used by the server. Includes `meta()` decoder for the Kuzu MAP-as-STRING JSON-blob columns. |
+| `build_ast_graph.py` | Tree-sitter → LadybugDB graph builder (full rebuild). Owns `pass1`–`pass6` (`pass5` emits `HTTP_CALLS` / `ASYNC_CALLS` caller edges; `pass6_match_edges` resolves cross-service / intra-service / ambiguous / phantom / unresolved match outcomes — ontology 7). |
+| `ladybug_queries.py` | Read-only Cypher helpers used by the server. Includes `meta()` decoder for the LadybugDB MAP-as-STRING JSON-blob columns. |
 | `ast_java.py` | Tree-sitter Java parsing, role/capability inference, `_string_value_atoms` helper (shared by route/client/producer extractors), `_collect_outgoing_calls` for caller-side detection. |
 | `graph_enrich.py` | `module` / `microservice` resolution, `BrownfieldOverrides` (route + role + capability + http client + async producer), meta-annotation walk, `resolve_routes_for_method` / `resolve_http_client_for_method` / `resolve_async_producer_for_method`. |
 | `java_ontology.py` | Source of truth for `VALID_ROLES`, `VALID_CAPABILITIES`, `VALID_CLIENT_KINDS`, `VALID_HTTP_CALL_STRATEGIES`, `VALID_ASYNC_CALL_STRATEGIES`, `VALID_HTTP_CALL_MATCHES`. |
@@ -90,7 +90,7 @@ when needed.
 
 ## Test layout
 
-- `tests/conftest.py` — session-scoped Kuzu graph fixture.
+- `tests/conftest.py` — session-scoped LadybugDB graph fixture.
 - `tests/bank-chat-system/` — deterministic Java corpus (fixture, not production model).
 - `tests/fixtures/call_graph_smoke/` — mini Maven tree calibrated against the call-graph resolver.
 - `tests/fixtures/brownfield_route_stubs/` — `@CodebaseRoute` / `@CodebaseRoutes` source stubs (PR-A3).
@@ -188,7 +188,7 @@ template):
   `VALID_ASYNC_CALL_STRATEGIES`, `VALID_HTTP_CALL_MATCHES`,
   `VALID_ROUTE_FRAMEWORKS`, `VALID_ROUTE_KINDS`, `VALID_PRODUCER_KINDS`,
   `VALID_RESOLVE_REASONS`, `VALID_UNRESOLVED_CALL_REASONS`.
-- Schema changes that affect the Lance index or Kuzu graph need a
+- Schema changes that affect the Lance index or LadybugDB graph need a
   matching update to the README "Re-index required" callout. Bump
   `ontology_version` when enrichment semantics change (currently **17**).
 - Brownfield is a first-class surface: any new auto-detection (route,
@@ -199,10 +199,10 @@ template):
   union when any brownfield layer fires on a method (single network packet
   → single edge). See `plans/completed/PLAN-TIER1B-COMPLETION.md` §
   "Caller-side composition divergence".
-- Kuzu's Python binder rejects `dict` for `MAP` columns. Store all
+- LadybugDB's Python binder rejects `dict` for `MAP` columns. Store all
   map-shaped graph_meta data (`routes_by_framework`, `routes_by_layer`,
   `http_calls_by_strategy`, `async_calls_by_strategy`, etc.) as `STRING`
-  JSON blobs and decode in `kuzu_queries.meta()`.
+  JSON blobs and decode in `ladybug_queries.meta()`.
 - `server.py` is a stdio MCP server: anything reachable from a tool
   handler must not write to **stdout** (that's the JSON-RPC transport).
   Diagnostics go to stderr.
@@ -216,10 +216,10 @@ template):
   support. `BrownfieldOverrides` already holds route, role, capability,
   http client, and async producer dicts — extend it in place.
 
-## Kuzu Cypher pitfalls
+## LadybugDB Cypher pitfalls
 
-When adding or editing Cypher run against Kuzu (for example in
-`kuzu_queries.py`, `mcp_v2.py`, or any `KuzuGraph._rows` caller):
+When adding or editing Cypher run against LadybugDB (for example in
+`ladybug_queries.py`, `mcp_v2.py`, or any `LadybugGraph._rows` caller):
 
 - **Do not filter relationship types with** `label(e) IN $list` **or**
   `label(e) IN ["A","B"]` **in** `WHERE`. On supported versions this can
@@ -252,7 +252,7 @@ When adding or editing Cypher run against Kuzu (for example in
   ```bash
   rm -rf /tmp/check && .venv/bin/python build_ast_graph.py \
     --source-root tests/bank-chat-system \
-    --kuzu-path /tmp/check/code_graph.kuzu --verbose
+    --ladybug-path /tmp/check/code_graph.lbug --verbose
   ```
 
 ## Commit and PR
@@ -289,7 +289,7 @@ When adding or editing Cypher run against Kuzu (for example in
 ## Cursor Cloud specific instructions
 
 This is a self-contained Python project — no external services
-(no Postgres, Kafka, Docker) are needed. All storage (Kuzu, LanceDB,
+(no Postgres, Kafka, Docker) are needed. All storage (LadybugDB, LanceDB,
 CocoIndex state) is embedded/file-based.
 
 ### Environment
@@ -317,12 +317,12 @@ first run. They are not required for normal development.
 
 ### Hello-world verification
 
-Build the Kuzu graph from the test fixture and inspect it:
+Build the LadybugDB graph from the test fixture and inspect it:
 
 ```bash
 rm -rf /tmp/check && .venv/bin/python build_ast_graph.py \
   --source-root tests/bank-chat-system \
-  --kuzu-path /tmp/check/code_graph.kuzu --verbose
+  --ladybug-path /tmp/check/code_graph.lbug --verbose
 .venv/bin/java-codebase-rag meta \
   --source-root tests/bank-chat-system --index-dir /tmp/check
 ```

README.md

@@ -2,7 +2,7 @@
 
 A graph-native code intelligence layer for Java microservice estates, exposed to LLM agents via the **Model Context Protocol (MCP)**.
 
-The system extracts a deterministic property graph from Java source (tree-sitter), stores it in **Kuzu** (graph) alongside a **LanceDB** vector index (chunks), and exposes a deliberately small MCP surface — **five tools**: `search`, `find`, `describe`, `neighbors`, `resolve` — that collapse onto three primitive agent operations: **locate**, **inspect**, **walk**.
+The system extracts a deterministic property graph from Java source (tree-sitter), stores it in **LadybugDB** (graph) alongside a **LanceDB** vector index (chunks), and exposes a deliberately small MCP surface — **five tools**: `search`, `find`, `describe`, `neighbors`, `resolve` — that collapse onto three primitive agent operations: **locate**, **inspect**, **walk**.
 
 > **What this MCP is:** a **GPS for code navigation**, not a reasoning engine.
 > Agents use a simple loop:
@@ -21,7 +21,7 @@ For the design rationale, the GPS metaphor, and the full ontology, see [`docs/pa
 
 Generic code-search tools (grep, ctags, vector-only RAG) hit a ceiling on real Java microservice estates: they find files but lose the structure that makes a Spring/JAX-RS system navigable. This project is built around five choices that target that gap.
 
-- **Hybrid RAG + GraphRAG, not either-or.** Semantic recall (LanceDB chunk vectors) and structural navigation (Kuzu property graph) are composed in one surface. `search` finds candidate nodes by meaning; `neighbors` walks the exact edge you care about (`CALLS`, `IMPLEMENTS`, `INJECTS`, `DECLARES_ROUTE`, …). The agent picks the right primitive per step instead of being forced into pure-vector or pure-symbol search.
+- **Hybrid RAG + GraphRAG, not either-or.** Semantic recall (LanceDB chunk vectors) and structural navigation (LadybugDB property graph) are composed in one surface. `search` finds candidate nodes by meaning; `neighbors` walks the exact edge you care about (`CALLS`, `IMPLEMENTS`, `INJECTS`, `DECLARES_ROUTE`, …). The agent picks the right primitive per step instead of being forced into pure-vector or pure-symbol search.
 
 - **A Java-tuned role model.** Symbols are labelled with stereotypes inferred from Spring and JAX-RS conventions — `CONTROLLER`, `SERVICE`, `REPOSITORY`, `CLIENT`, `PRODUCER`, `MAPPER`, `DTO`. Agents can ask "list controllers" or "who injects this repository" directly, instead of grep-ing for `@RestController` and hoping for the best. Roles drive both filtering (`find` with a `NodeFilter`) and ranking.
 
@@ -69,7 +69,7 @@ After `pip install --upgrade java-codebase-rag`, run `java-codebase-rag update`
 
 If you prefer manual configuration, see [`docs/JAVA-CODEBASE-RAG-CLI.md`](./docs/JAVA-CODEBASE-RAG-CLI.md) for the full CLI reference.
 
-> **Stability disclaimer.** This package does **not** promise backward compatibility. MCP tool contracts, env vars, Lance/Kuzu schemas, config files, and Python APIs may change without a deprecation period. Track `main` and rebuild indexes when ontology or embedding settings change.
+> **Stability disclaimer.** This package does **not** promise backward compatibility. MCP tool contracts, env vars, Lance/LadybugDB schemas, config files, and Python APIs may change without a deprecation period. Track `main` and rebuild indexes when ontology or embedding settings change.
 
 ---
 
@@ -82,7 +82,7 @@ This repo ships a small multi-module Spring fixture under [`tests/bank-chat-syst
 git clone https://github.com/HumanBean17/java-codebase-rag
 cd java-codebase-rag
 
-# 2. Build the index (Lance vectors + Kuzu graph). First run downloads the
+# 2. Build the index (Lance vectors + LadybugDB graph). First run downloads the
 #    embedding model (~90 MB) and takes ~30-60s on the fixture.
 java-codebase-rag init --source-root tests/bank-chat-system --index-dir /tmp/bank-chat-index
 
@@ -97,7 +97,7 @@ Smoke-test the index with two checks (`search_lancedb` ships with the package):
 JAVA_CODEBASE_RAG_INDEX_DIR=/tmp/bank-chat-index \
   python -m search_lancedb "chat ingress controller" --table java --limit 3
 
-# Vector + graph expansion — proves Kuzu is wired in
+# Vector + graph expansion — proves LadybugDB is wired in
 JAVA_CODEBASE_RAG_INDEX_DIR=/tmp/bank-chat-index \
   python -m search_lancedb "chat ingress controller" --table java --limit 3 \
     --graph-expand --expand-depth 2
@@ -197,8 +197,8 @@ Run `java-codebase-rag --help` to list grouped subcommands. Operator playbook wi
 | Setup | `install` | Interactive setup wizard: config, MCP registration, skill/agent deployment, indexing. |
 | Setup | `update` | Refresh shipped artifacts (skill, agent, MCP entry) after pip upgrade. |
 | Lifecycle | `init` | First-time index. Refuses if artifacts already exist. |
-| 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 | `increment` | CocoIndex catch-up + incremental LadybugDB update. `--vectors-only` for Lance only. |
+| Lifecycle | `reprocess` | Full Lance + LadybugDB 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. |
 | Analysis | `analyze-pr` | Blast-radius / risk from a unified diff. |