java-codebase-rag 0.11.2__tar.gz → 0.12.1__tar.gz

java_codebase_rag-0.12.1/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: java-codebase-rag
+Version: 0.12.1
+Summary: Renamed to jrag-cli; this package only depends on jrag-cli. New setups: pip install jrag-cli.
+Author: HumanBean17
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/HumanBean17/jrag
+Project-URL: Repository, https://github.com/HumanBean17/jrag
+Project-URL: Issues, https://github.com/HumanBean17/jrag/issues
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: jrag-cli==0.12.1
+
+# java-codebase-rag (renamed to `jrag-cli`)
+
+This package has been **renamed to [`jrag-cli`](https://github.com/HumanBean17/jrag)**.
+
+`java-codebase-rag` remains on PyPI as a thin compatibility shim that depends
+on `jrag-cli` and ships no code of its own. Upgrading an existing install
+pulls `jrag-cli` in transparently:
+
+```bash
+pip install -U java-codebase-rag   # installs jrag-cli behind the scenes
+```
+
+For new setups, install the canonical package directly:
+
+```bash
+pip install jrag-cli
+```
+
+The CLI entry points, MCP server, and module layout are unchanged — `jrag`
+and `jrag-mcp` (plus the legacy `java-codebase-rag` / `java-codebase-rag-mcp`
+aliases) are all provided by `jrag-cli`. See
+[HumanBean17/jrag](https://github.com/HumanBean17/jrag) for documentation.

java_codebase_rag-0.12.1/README.md

@@ -0,0 +1,22 @@
+# java-codebase-rag (renamed to `jrag-cli`)
+
+This package has been **renamed to [`jrag-cli`](https://github.com/HumanBean17/jrag)**.
+
+`java-codebase-rag` remains on PyPI as a thin compatibility shim that depends
+on `jrag-cli` and ships no code of its own. Upgrading an existing install
+pulls `jrag-cli` in transparently:
+
+```bash
+pip install -U java-codebase-rag   # installs jrag-cli behind the scenes
+```
+
+For new setups, install the canonical package directly:
+
+```bash
+pip install jrag-cli
+```
+
+The CLI entry points, MCP server, and module layout are unchanged — `jrag`
+and `jrag-mcp` (plus the legacy `java-codebase-rag` / `java-codebase-rag-mcp`
+aliases) are all provided by `jrag-cli`. See
+[HumanBean17/jrag](https://github.com/HumanBean17/jrag) for documentation.

java_codebase_rag-0.12.1/java_codebase_rag.egg-info/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: java-codebase-rag
+Version: 0.12.1
+Summary: Renamed to jrag-cli; this package only depends on jrag-cli. New setups: pip install jrag-cli.
+Author: HumanBean17
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/HumanBean17/jrag
+Project-URL: Repository, https://github.com/HumanBean17/jrag
+Project-URL: Issues, https://github.com/HumanBean17/jrag/issues
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: jrag-cli==0.12.1
+
+# java-codebase-rag (renamed to `jrag-cli`)
+
+This package has been **renamed to [`jrag-cli`](https://github.com/HumanBean17/jrag)**.
+
+`java-codebase-rag` remains on PyPI as a thin compatibility shim that depends
+on `jrag-cli` and ships no code of its own. Upgrading an existing install
+pulls `jrag-cli` in transparently:
+
+```bash
+pip install -U java-codebase-rag   # installs jrag-cli behind the scenes
+```
+
+For new setups, install the canonical package directly:
+
+```bash
+pip install jrag-cli
+```
+
+The CLI entry points, MCP server, and module layout are unchanged — `jrag`
+and `jrag-mcp` (plus the legacy `java-codebase-rag` / `java-codebase-rag-mcp`
+aliases) are all provided by `jrag-cli`. See
+[HumanBean17/jrag](https://github.com/HumanBean17/jrag) for documentation.

java_codebase_rag-0.12.1/java_codebase_rag.egg-info/SOURCES.txt

@@ -0,0 +1,7 @@
+README.md
+pyproject.toml
+java_codebase_rag.egg-info/PKG-INFO
+java_codebase_rag.egg-info/SOURCES.txt
+java_codebase_rag.egg-info/dependency_links.txt
+java_codebase_rag.egg-info/requires.txt
+java_codebase_rag.egg-info/top_level.txt

java_codebase_rag-0.12.1/java_codebase_rag.egg-info/requires.txt

@@ -0,0 +1 @@
+jrag-cli==0.12.1

java_codebase_rag-0.12.1/pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "java-codebase-rag"
+version = "0.12.1"
+description = "Renamed to jrag-cli; this package only depends on jrag-cli. New setups: pip install jrag-cli."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "MIT"
+authors = [
+    { name = "HumanBean17" },
+]
+dependencies = ["jrag-cli==0.12.1"]
+
+[project.urls]
+Homepage = "https://github.com/HumanBean17/jrag"
+Repository = "https://github.com/HumanBean17/jrag"
+Issues = "https://github.com/HumanBean17/jrag/issues"
+
+# Metadata-only shim: explicitly ship no modules so setuptools does not perform
+# auto-discovery (a `[tool.setuptools.packages*]` section would imply a module
+# tree the shim does not have). Every console script and importable module
+# lives in the canonical `jrag-cli` dist, pulled in via the dependency above.
+[tool.setuptools]
+py-modules = []

java_codebase_rag-0.11.2/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2025 HumanBean17
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

java_codebase_rag-0.11.2/PKG-INFO

@@ -1,331 +0,0 @@
-Metadata-Version: 2.4
-Name: java-codebase-rag
-Version: 0.11.2
-Summary: MCP server for semantic + structural search over Java codebases
-Author: HumanBean17
-License-Expression: MIT
-Project-URL: Homepage, https://github.com/HumanBean17/java-codebase-rag
-Project-URL: Repository, https://github.com/HumanBean17/java-codebase-rag
-Project-URL: Issues, https://github.com/HumanBean17/java-codebase-rag/issues
-Keywords: mcp,java,rag,code-search,graph,lancedb,ladybug
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Operating System :: POSIX :: Linux
-Classifier: Operating System :: MacOS :: MacOS X
-Classifier: Operating System :: Microsoft :: Windows
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: cocoindex[lancedb]<2,>=1.0.15; sys_platform != "darwin" or platform_machine != "x86_64"
-Requires-Dist: ladybug<0.18,>=0.17.1
-Requires-Dist: lancedb<0.36,>=0.34; sys_platform != "darwin" or platform_machine != "x86_64"
-Requires-Dist: mcp<2,>=1.27.0
-Requires-Dist: numpy<2.5,>=1.26.4
-Requires-Dist: pathspec<2,>=1.0.4
-Requires-Dist: pyarrow<26,>=23.0.1
-Requires-Dist: pydantic<3,>=2.0
-Requires-Dist: PyYAML<7,>=6.0.3
-Requires-Dist: questionary<3,>=2.0
-Requires-Dist: rich<16,>=14
-Requires-Dist: sentence-transformers<6,>=5.4.0; sys_platform != "darwin" or platform_machine != "x86_64"
-Requires-Dist: tree-sitter<0.26,>=0.25.2
-Requires-Dist: tree-sitter-java<0.24,>=0.23.5
-Requires-Dist: unidiff<1,>=0.7.3
-Requires-Dist: watchdog<7,>=6
-Provides-Extra: dev
-Requires-Dist: pytest>=7; extra == "dev"
-Requires-Dist: pytest-asyncio>=0.21; extra == "dev"
-Requires-Dist: pytest-xdist>=3; extra == "dev"
-Requires-Dist: ruff>=0.4; extra == "dev"
-Dynamic: license-file
-
-# java-codebase-rag
-
-A graph-native code intelligence layer for Java microservice estates, surfaced through the **`jrag` CLI** — one command per engineering intent. A **legacy MCP server** (`search` / `find` / `describe` / `neighbors` / `resolve`) is also available for existing setups. Both are thin surfaces over the same **AST Graph**: a deterministic property graph extracted from Java source with tree-sitter, stored **locally** in **LadybugDB** (graph) alongside a **LanceDB** vector index (chunks). There is no server to host and no cloud round-trip — the index lives on your disk and your source never leaves the machine. Both surfaces collapse onto three primitive operations: **locate**, **inspect**, **walk**.
-
-> **What this is: a GPS for code navigation**, not a reasoning engine.
-> Agents use a simple loop:
->
-> 1. **Locate** entry nodes (`jrag find`, `jrag search`, or identifier-shaped lookup)
-> 2. **Inspect** what a node is (`jrag inspect`)
-> 3. **Walk** one hop at a time (`jrag callers` / `callees` / `hierarchy` / …) until enough evidence is gathered
->
-> The tool exposes structure and adjacency; the agent owns multi-hop reasoning and stop conditions.
-
-For the design rationale, the GPS metaphor, and the full ontology, see [`docs/paper/paper.pdf`](./docs/paper/paper.pdf) (architecture report).
-
----
-
-## Why this exists
-
-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 + AST Graph, not either-or.** Semantic recall (LanceDB chunk vectors) and structural navigation (the LadybugDB AST Graph) are composed in one surface. `search` finds candidate nodes by meaning; `neighbors` walks the exact edge you care about (`CALLS`, `IMPLEMENTS`, `INJECTS`, `EXPOSES`, …). 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`, `COMPONENT`, `CONFIG`, `ENTITY`, `CLIENT`, `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.
-
-- **Ranking specialized for Java codebases.** The composite ranker is aware of role, microservice, and FQN structure — not a generic BM25. A search for `"chat ingress"` surfaces controllers before utility classes; a search scoped to one microservice doesn't drown in matches from the other 19. Defaults are tuned on the bank-chat fixture and exposed in `docs/CONFIGURATION.md` for per-repo overrides.
-
-- **Cross-service resolution + system-level navigation.** `HTTP_CALLS` and `ASYNC_CALLS` edges connect Clients and Producers in one microservice to Routes and Handlers in another, resolved at index time from URL/topic strings + Spring `@FeignClient` / `RestTemplate` conventions. `/who-hits-route`, `/trace-request-flow`, and `/impact-of` use these to answer questions a single-service tool fundamentally can't — "who calls this REST endpoint from outside this service", "trace this Kafka message end-to-end", "if I change this DTO, which services break".
-
-- **Brownfield annotations as a first-class override.** Real Java estates have hand-rolled HTTP clients, dynamic topic names, reflection-heavy routing. `@CodebaseHttpRoute`, `@CodebaseAsyncRoute`, `@CodebaseHttpClient`, and `@CodebaseProducer` let you pin the truth in source. They have **exclusive priority** — when a symbol is annotated, framework-convention inference is skipped entirely. You get a correct graph on legacy code without rewriting it.
-
-The rest of this README is the install, the tool/command orientation, and the reference for putting that to work.
-
----
-
-## Install
-
-```bash
-pip install java-codebase-rag
-```
-
-Python **3.11+** required, on **Linux, macOS, and Windows**. On Linux, Windows, and **Apple Silicon** Macs every native dependency (LanceDB, LadybugDB, CocoIndex) ships a wheel and you get the full semantic + graph search. **Intel Macs (x86_64) install graph-only**: PyTorch ≥2.3 and LanceDB ≥0.26 dropped macOS Intel wheels, so the vector stack is auto-excluded via PEP 508 markers — `pip install java-codebase-rag` works out of the box, the graph layer (`find` / `describe` / `neighbors` / `resolve`) is fully usable, and the `search` tool falls back to **lexical search** over the symbol graph — BM25-ranked over a LadybugDB full-text index (same tool contract, keyword-ranked instead of semantic; an advisory notes the mode). Semantic/vector search needs Apple Silicon, Linux, or Windows. After install, `java-codebase-rag --help` should print the CLI groups.
-The package includes the CocoIndex lifecycle dependency used by `init`, `increment`, `reprocess`, and `erase` on platforms that have it (it is absent on Intel Mac).
-
-### Interactive setup (recommended)
-
-Run `java-codebase-rag install` from your Java project root to launch an interactive setup wizard that:
-
-1. Detects Java source directories (Maven/Gradle modules)
-2. Configures the embedding model (auto-downloads ~90MB or uses a local path)
-3. Selects agent hosts (Claude Code, Qwen Code, GigaCode)
-4. Deploys MCP registration, skill, and agent artifacts
-5. Generates `.java-codebase-rag.yml` configuration
-6. Runs `init` to build the index
-
-```bash
-# Interactive mode
-java-codebase-rag install
-
-# Non-interactive mode (for CI/automation)
-java-codebase-rag install --non-interactive --agent claude-code
-```
-
-After `pip install --upgrade java-codebase-rag`, run `java-codebase-rag update` to refresh shipped artifacts and catch up the index (Lance + graph).
-
-All indexing lifecycle commands (`init`, `increment`, `reprocess`, `install`, `update`) show a unified `Vectors → Optimize → Graph` progress bar on stderr during the index build (powered by `rich`); pass `--quiet` to suppress it.
-
-### Manual registration
-
-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/LadybugDB schemas, config files, and Python APIs may change without a deprecation period. Track `main` and rebuild indexes when ontology or embedding settings change.
-
----
-
-## Tools & commands at a glance
-
-`jrag` is the default and recommended surface (`java-codebase-rag install --surface cli`). The **MCP server** (`--surface mcp`) is kept as a **legacy** option for existing setups. Both surfaces walk the same LanceDB vectors + LadybugDB **AST Graph**. Switch an existing install later with `java-codebase-rag update --surface mcp|cli`.
-
-**CLI surface — `jrag`, one command per engineering intent**
-
-```bash
-# Orientation
-jrag status                    # index health (ontology version, freshness, counts)
-jrag microservices             # microservices with resolved type counts
-jrag map                       # counts per kind per service/module
-jrag map --by module           # group by module instead (--module filters)
-jrag conventions               # dominant roles + framework tallies
-jrag overview chat-core        # bundle for a microservice
-jrag overview /chat/assign     # route flow (inbound callers + outbound CALLS)
-jrag overview banking.chat     # topic producers + consumers
-jrag overview chat-core --as microservice  # override auto-detection
-
-# Locate
-jrag find ChatService          # exact name/FQN lookup (symbols)
-jrag find --role CONTROLLER    # filter mode (NodeFilter flags)
-jrag inspect ChatService       # full node details + edge_summary
-jrag outline src/main/.../Foo.java  # all symbols declared in a file
-jrag imports src/main/.../Foo.java   # imports resolved to graph nodes
-
-# Listings
-jrag http-routes               # HTTP routes
-jrag http-clients              # HTTP clients (Feign / RestTemplate / WebClient)
-jrag producers                 # async message producers (Kafka / StreamBridge)
-jrag topics                    # message topics grouped by producer
-jrag jobs                      # scheduled tasks (@Scheduled)
-jrag listeners                 # message listeners (@KafkaListener etc.)
-jrag entities                  # JPA entities
-
-# Traversals (all resolve-first)
-jrag callers ChatService#assign(Request)   # who calls me?
-jrag callers ChatIngressController         # controller: also lists its EXPOSES routes
-jrag callees ChatService#assign(Request)   # what do I call?
-jrag hierarchy AbstractBase               # type tree (parents + children)
-jrag implementations PaymentProcessor     # classes implementing an interface
-jrag subclasses AbstractRepository        # classes extending a type
-jrag overrides Impl#run()                 # methods this overrides (dispatch UP)
-jrag overridden-by Iface#run()            # methods overriding this (dispatch DOWN)
-jrag dependents PaymentGateway            # who injects this type?
-jrag dependencies ChatService             # types this injects
-jrag impact PaymentGateway                # fleet-wide blast radius
-jrag decompose ChatIngressController#assign   # role-waterfall flow
-jrag flow /chat/assign                    # request flow through a route
-jrag connection chat-core                 # cross-service connections
-
-# Semantic search
-jrag search "assign a chat agent"         # semantic over Lance (java table)
-jrag search "kafka" --table all           # java + sql + yaml tables
-jrag search "audit" --hybrid              # vector + keyword hybrid
-jrag search "audit" --offset 5            # paginated
-```
-
-Every `<query>` command takes human-readable identifiers (FQN / simple name / route path / topic) — never raw node IDs. Output contract, flags, and the resolve-first rule are in [`jrag` — agent CLI](#jrag--agent-cli) below.
-
-**MCP surface — five tools over stdio (legacy)**
-
-| Tool | Purpose | Required args |
-|---|---|---|
-| `search` | Locate nodes by NL / code text. | `query` |
-| `find` | Locate nodes by structured filter. | `kind`, `filter` |
-| `describe` | Full record + edge counts for one node. | `id` |
-| `resolve` | Identifier-shaped lookup (FQN-collision-safe). Returns `one` / `many` / `none`. | `identifier` |
-| `neighbors` | Graph walk, one hop. | `ids`, `direction`, `edge_types` |
-
-Full schemas, `NodeFilter` / `EdgeFilter` semantics, and the hints contract live in [`docs/AGENT-GUIDE.md`](./docs/AGENT-GUIDE.md). Edge types and traversal directions are listed in [`docs/EDGE-NAVIGATION.md`](./docs/EDGE-NAVIGATION.md).
-
-### Three-layer architecture
-
-Layer 1 (storage) → Layer 2 (the `jrag` CLI, **or** the legacy 5-tool MCP) → Layer 3 (skill). The CLI-surface skill **[`/explore-codebase-cli`](./skills/explore-codebase-cli/SKILL.md)** documents the `jrag` CLI; the MCP-surface skill **[`/explore-codebase`](./skills/explore-codebase/SKILL.md)** documents the legacy 5-tool MCP (PR-JRAG-5). See the [architecture diagram in `skills/README.md`](./skills/README.md#three-layer-architecture).
-
----
-
-## Configuration
-
-The operator-facing surface is small: pick an index dir, pick an embedding model, optionally drop a `.java-codebase-rag.yml` at your project root for microservice layout and brownfield overrides.
-
-| If you want to… | See |
-|---|---|
-| Set env vars and override precedence | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) §1 |
-| Configure microservice roots and embeddings via YAML | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) §2 |
-| Understand the graph (nodes, edges, capabilities, ranking) | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) §3 |
-| Steer a brownfield Java tree (custom stereotypes, non-Spring stacks) | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) §4 |
-| Control which files the indexer walks | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) §5 |
-| Check whether your repo fits this tool's assumptions | [`docs/CODEBASE_REQUIREMENTS.md`](./docs/CODEBASE_REQUIREMENTS.md) |
-
----
-
-## CLI cheat sheet
-
-Run `java-codebase-rag --help` to list grouped subcommands. Operator playbook with workflows, exit codes, and env alignment lives in [`docs/JAVA-CODEBASE-RAG-CLI.md`](./docs/JAVA-CODEBASE-RAG-CLI.md).
-
-| Group | Subcommand | What it does |
-|---|---|---|
-| Setup | `install` | Interactive setup wizard: config, MCP registration, skill/agent deployment, indexing. |
-| Setup | `update` | Refresh shipped artifacts (skill, agent, MCP entry) + incremental Lance/graph catch-up after pip upgrade. |
-| Lifecycle | `init` | First-time index. Refuses if artifacts already exist. |
-| 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. |
-
----
-
-## jrag — agent CLI
-
-`jrag` is a separate console script (alongside `java-codebase-rag`) built for AI
-coding agents. It gives the agent **one command per engineering intent** and
-takes human-readable identifiers (FQN / simple name / route path / topic) —
-never raw node IDs. Every `<query>` command resolves the identifier via
-`resolve_v2` as the first step; on `many` it returns candidates and stops, on
-`none` it returns `not_found`. Auto-pick is forbidden.
-
-The default output is compact text (a deliberate divergence from the operator
-CLI's TTY heuristic — `jrag` is agent-facing/non-TTY). `--format json` emits the
-shared envelope verbatim. Every command emits the same envelope shape:
-
-```json
-{
-  "status": "ok",
-  "nodes": {"com.example.Foo": {"kind": "symbol", "fqn": "com.example.Foo"}},
-  "edges": [{"edge_type": "CALLS", "confidence": 0.9, "target": "com.example.Bar#baz()"}],
-  "root": "com.example.Foo",
-  "agent_next_actions": ["jrag callees com.example.Foo#bar()"],
-  "truncated": false
-}
-```
-
-No raw graph node id ever appears on either surface: `nodes` is keyed by each
-node's natural identifier (FQN for symbols, `METHOD path` for routes,
-`member_fqn->target` for clients, `topic:<name>` for topics), `root` is the
-root's natural identifier, and each edge carries `target` (the referenced node's
-identifier) instead of a graph id. The agent reuses these identifiers directly
-as the next command's `<query>` — there is nothing else to pass.
-
-`agent_next_actions` carries up to 5 contextual next-step hints (e.g. after
-`inspect`, the agent sees `jrag callers <fqn>`, `jrag callees <fqn>`, etc. for
-the edges the root actually has). Omitted from JSON when empty.
-
-The full command catalog lives in [Tools & commands at a glance](#tools--commands-at-a-glance).
-
-### Flags
-
-| Flag | Scope | Effect |
-|------|-------|--------|
-| `--format text\|json` | all | output format (default: text) |
-| `--service <name>` | listings/traversals | filter by microservice |
-| `--module <name>` | listings/traversals | filter by module |
-| `--limit <n>` | listings/traversals | cap results (default 20; `limit+1` fetch detects truncation) |
-| `--offset <n>` | `find`, `search` only | paginate (other commands reject it) |
-| `--kind symbol\|route\|client\|producer` | `<query>` commands | resolve hint |
-| `--java-kind`, `--role`, `--fqn-contains` | `<query>` commands | client-side post-filters |
-| `--index-dir <path>` | all | override index directory |
-
-`--offset` is intentionally NOT a global flag: only `find` and `search` route
-through backends that accept it. Every other command rejects it.
-
-A missing or stale index produces an actionable `status: error` envelope (exit
-2) rather than a traceback:
-
-```
-error: No index at /path/to/code_graph.lbug. Run: java-codebase-rag init --source-root <root>
-```
-
-See [`plans/active/PLAN-JRAG-CLI.md`](./plans/active/PLAN-JRAG-CLI.md) for the
-full design and per-PR breakdown.
-
----
-
-## Further reading
-
-| Document | What's in it |
-|---|---|
-| [`docs/paper/paper.pdf`](./docs/paper/paper.pdf) | Architecture report — design rationale, GPS metaphor, three-layer architecture, design principles, future work. |
-| [`docs/AGENT-GUIDE.md`](./docs/AGENT-GUIDE.md) | Agent-facing guide. Copy-paste into `QWEN.md` / `CLAUDE.md` / `AGENTS.md`. |
-| [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) | Environment variables, project YAML, graph ontology, brownfield overrides, ignore patterns. |
-| [`docs/JAVA-CODEBASE-RAG-CLI.md`](./docs/JAVA-CODEBASE-RAG-CLI.md) | CLI operator playbook: workflows, exit codes, env alignment. |
-| [`docs/EDGE-NAVIGATION.md`](./docs/EDGE-NAVIGATION.md) | MCP-traversable edges, directions, dot-key composition. |
-| [`skills/`](./skills/) | `/explore-codebase-cli` (CLI surface) + `/explore-codebase` (legacy MCP surface) skills — operating manuals for hosts with skill discovery (alternative to copy-pasting AGENT-GUIDE). See [`skills/README.md`](./skills/README.md). |
-| [`docs/MANUAL-VERIFICATION-CHECKLIST.md`](./docs/MANUAL-VERIFICATION-CHECKLIST.md) | 7-phase agent-driven verification after indexing your project. |
-| [`docs/CODEBASE_REQUIREMENTS.md`](./docs/CODEBASE_REQUIREMENTS.md) | Assumptions about your Java repo + per-file edit map for non-conforming codebases. |
-| [`docs/PRODUCT-VISION.md`](./docs/PRODUCT-VISION.md) | Long-term product direction. |
-
----
-
-## Install from source (contributors)
-
-```bash
-git clone https://github.com/HumanBean17/java-codebase-rag
-cd java-codebase-rag
-python3 -m venv .venv
-.venv/bin/pip install -e ".[dev]"
-```
-
-The `cocoindex` package powers lifecycle commands that run the indexer (`init`, `increment`, `reprocess`, `erase`). Search and MCP navigation do not invoke it directly.
-
-The default embedding model is `sentence-transformers/all-MiniLM-L6-v2` (downloaded on first `init`). Override via the `SBERT_MODEL` env var — see [`docs/CONFIGURATION.md` §1](./docs/CONFIGURATION.md#1-environment-variables).
-
----
-
-## Roadmap (graph layer)
-
-- `get_service_topology` — microservice-level summary aggregating `HTTP_CALLS` / `ASYNC_CALLS`.
-- Agentic routing layer (query classifier → vector / graph / both).
-- Optional `codegraph_nodes` LanceDB table embedding symbol summaries so the graph itself is vector-searchable.