codespine 0.5.3

Local Java code intelligence indexer backed by a graph database

CodeSpine

A code-intelligence layer for Java codebases — purpose-built for AI agents.

Instead of making your agent read hundreds of raw source files, CodeSpine maps your entire codebase into a live graph and exposes it through 24 structured MCP tools. Your agent asks a question, gets a precise answer — no file trawling, no wasted tokens, no hallucinated call chains.

Token efficiency in practice: a get_symbol_context call returns a fully-resolved call graph for a symbol in one round-trip. The equivalent "read every relevant file" approach typically costs 10-50× more tokens and still misses transitive edges.

---

How it works

Your Java codebase
       │
  codespine analyse          ← one-time (or on-demand) indexing
       │
  ~/.codespine_db            ← Kuzu graph DB (symbols, calls, communities, flows …)
       │
  codespine mcp              ← FastMCP server — 24 tools
       │
  Your AI agent (Claude, GPT, Cursor, Cline …)

Agents talk to the MCP server. They never need to open a .java file unless they are actually editing it.

---

Installation

pip install codespine

Optional: install sentence-transformers to enable semantic vector search (adds ~500 MB of model weight).

pip install sentence-transformers

---

Quick Start

1 — Index your codebase

# Fast (BM25 + fuzzy search, no embeddings — recommended first run)
codespine analyse /path/to/your/project

# Full (adds semantic vector search, takes longer)
codespine analyse /path/to/your/project --embed

# Deep (+ dead code, execution flows, communities, git coupling)
codespine analyse /path/to/your/project --deep

Example output:

$ codespine analyse .
Walking files...               142 files found
Parsing code...                142/142  (parallel, 4 workers)
Tracing calls...               847 calls resolved
Analyzing types...             234 type relationships
Detecting communities...       8 clusters found
Detecting execution flows...   34 processes found
Finding dead code...           12 unreachable symbols
Analyzing git history...       18 coupled file pairs

Done in 18s — 623 symbols, 1 847 edges, 8 clusters, 34 flows

2 — Wire up MCP

Add to your MCP config (~/.claude/mcp.json or equivalent):

{
  "mcpServers": {
    "codespine": {
      "command": "codespine",
      "args": ["mcp"]
    }
  }
}

3 — Let the agent explore

The agent can now call tools like:

search_hybrid("payment retry logic")
get_symbol_context("processPayment")
get_impact("com.example.PaymentService#charge")
detect_dead_code()
get_codebase_stats()

---

MCP Tools (24)

Connectivity & Discovery

Tool	What it does
ping()	Confirm the server is alive. Call this first.
get_capabilities()	Returns what is indexed right now — projects, symbol counts, which features are available, and whether watch mode is running. Call before other tools to avoid trial-and-error.
list_projects()	List every indexed project with path, symbol count, and file count.
get_codebase_stats()	Per-project breakdown: files, classes, methods, calls, embeddings, totals.

Search

Tool	What it does
search_hybrid(query, k, project)	BM25 + semantic vector + fuzzy, fused with RRF. Scope to a project with project=.
find_symbol(name, kind, project, limit)	Exact / prefix name lookup returning all matches grouped by project. Use this when the same class name exists in multiple projects to pick the right one.
list_packages(project, limit)	All Java packages with class count, grouped by project. Good for structural orientation before searching.

Analysis

Tool	What it does
get_symbol_context(query, max_depth, project)	Full call graph context for a symbol — callers, callees, types, up to max_depth hops.
get_impact(symbol, max_depth, project)	Depth-grouped impact analysis with confidence scores. Shows what breaks if this symbol changes.
detect_dead_code(limit, project)	Unreachable symbols after applying framework exemptions (Spring, JPA, …).
trace_execution_flows(entry_symbol, max_depth, project)	Execution paths from entry points (or a specific symbol).
get_symbol_community(symbol)	Which community cluster a symbol belongs to, with co-members.
get_change_coupling(months, min_strength, min_cochanges, project)	Git-derived file pairs that change together — useful for predicting collateral changes.

Git

Tool	What it does
git_log(file_path, limit, project)	Commit history for a file or the whole repo.
git_diff(ref, file_path, project)	Diff against a ref (default HEAD).
compare_branches(base_ref, head_ref)	Symbol-level diff between two branches — which classes/methods changed.

Watch Mode (live incremental reindex)

Tool	What it does
start_watch(path, global_interval)	Start incremental reindexing in the background. Watches for file changes and updates the graph within global_interval seconds. Recommended: keep this running during active development sessions so the graph stays fresh.
stop_watch()	Gracefully stop the background watcher.
get_watch_status()	Check if watch is running — uptime, path, interval.

On-demand Analysis (non-blocking)

Tool	What it does
analyse_project(path, full, deep, embed)	Trigger a full re-analysis as a background job. Returns immediately. Poll get_analyse_status() for progress.
get_analyse_status()	Check background analysis — running / done / failed, last log lines.

Index Management

Tool	What it does
reset_project(project_id)	Delete all graph data for one project (clean-slate re-index).
reset_index()	Wipe the entire index — all projects, communities, flows.

Power / Debug

Tool	What it does
run_cypher(query)	Execute a raw Cypher read query against the graph (Kuzu dialect). For advanced exploration.

---

CLI Reference

Indexing

codespine analyse <path>              # fast index (no embeddings)
codespine analyse <path> --embed      # + semantic vectors
codespine analyse <path> --full       # force full re-index (skip incremental)
codespine analyse <path> --deep       # + dead code, flows, communities, git coupling
codespine analyse <path> --deep --embed  # everything

Search & Analysis

codespine search "payment retry bug" [--k 20] [--json]
codespine context "processPayment"   [--max-depth 3] [--json]
codespine impact  "com.example.Service#processPayment(java.lang.String)" [--max-depth 4] [--json]
codespine deadcode [--limit 200] [--json]
codespine flow   [--entry <symbol>] [--max-depth 6] [--json]
codespine community [--symbol <symbol>] [--json]
codespine coupling  [--months 6] [--min-strength 0.3] [--min-cochanges 3] [--json]
codespine diff <base>..<head> [--json]

Stats

codespine stats           # per-project table: files, classes, methods, calls, embeddings
codespine stats --json    # machine-readable output

Watch

codespine watch [--path .] [--global-interval 30]

Index Management

codespine clear-project <project_id>   # remove one project from the graph
codespine clear-index                  # wipe the entire index

---

Workspace / Multi-Project Support

CodeSpine understands three levels of hierarchy:

~/IdeaProjects/              ← workspace  (a folder of independent projects)
├── payments-service/        ← project    (has its own .git / pom.xml)
│   ├── core/                ← module     (Maven <module> or Gradle subproject)
│   └── api/                 ← module
└── inventory-service/       ← project
    └── (single-module)

• Workspace detection: if the path you give to analyse has no .git or build file at its root, CodeSpine scans one level down for sub-projects and indexes them all.
• Project IDs: single-module → payments-service; multi-module → payments-service::core, payments-service::api.
• Scoped queries: every analysis and search tool accepts an optional project= parameter so agents can work within one project without noise from others.
• Cross-project search: omit project= to search across everything.

---

Embedding / Speed Trade-off

Flag	Index time	Search modes available
(no flag)	Fast (~seconds–minutes)	BM25, fuzzy, exact
--embed	Slower (minutes, depends on model)	BM25, fuzzy, exact + semantic vector

sentence-transformers must be installed for --embed to have any effect. If it is not installed, indexing always skips embeddings silently.

Most agent workflows work great without embeddings — BM25 + fuzzy covers keyword, partial-name, and typo-tolerant search. Add --embed when you need concept-level similarity ("find all classes related to retry logic").

---

Runtime Paths

Path	Purpose
~/.codespine_db	Kuzu graph database
~/.codespine.pid	Watch-mode PID file
~/.codespine.log	Watch-mode log
~/.codespine_embedding_cache.sqlite3	Embedding vector cache

---

Project Docs

• Contributing
• Security
• Code of Conduct