codespine 0.7.3

Local Java code intelligence indexer backed by a graph database

CodeSpine

CodeSpine cuts token burn for coding agents working on Java codebases.

Instead of having an agent open dozens of .java files to answer one question, CodeSpine indexes the codebase once and serves the structure over MCP. The agent asks for symbols, callers, impact, flows, dead code, and module boundaries directly, which means fewer file reads, fewer wasted context windows, and fewer hallucinated code paths.

It indexes classes, methods, calls, type relationships, cross-module links, git coupling, dead-code candidates, and execution flows so agents can work from graph answers first and source files second.

It also keeps a separate dirty overlay for uncommitted Java edits, so agents can query current work-in-progress without forcing the committed base index to churn on every save.

The MCP daemon and the indexer run independently. Querying while a full re-index is running no longer causes crashes or memory contention — reads go to an isolated snapshot that is atomically updated when indexing completes.

Why It Saves Tokens

• One MCP call can replace many file opens. get_symbol_context("PaymentService") returns a resolved neighborhood instead of forcing the agent to read every caller and callee file manually.
• Search is structure-aware. Agents can ask for a symbol, concept, impact radius, or dead-code candidate without scanning entire packages.
• Multi-module repos stay scoped. Project-aware IDs and project= parameters reduce noise from unrelated modules and workspaces.
• Repeat sessions get cheaper. Once indexed, the agent reuses the graph instead of re-discovering the same relationships every turn.
• Active edits stay smooth. Dirty files are kept in an overlay and merged into fast queries until you commit, instead of hammering the main graph DB on each change.

Install

pip install codespine

Optional semantic search:

pip install "codespine[ml]"

What It Does

• Hybrid search: BM25 + fuzzy by default, semantic vector search with --embed
• Impact analysis: callers, dependencies, and confidence-scored edges
• Dead code detection: Java-aware exemptions for tests, framework hooks, contracts, and common DI patterns
• Execution flows: traces from entry points through the call graph
• Community detection: structural clusters for architectural context
• Change coupling: git-history-based file relationships
• Multi-project and multi-module indexing: workspaces, Maven modules, Gradle subprojects
• Cross-module call linking: signature-based detection of calls between Maven/Gradle modules
• Concurrent read/write isolation: MCP queries run against a read replica; the indexer writes separately, with no memory contention
• MCP server: structured tools for Claude, Cursor, Cline, Copilot, and similar clients

Editing Without Stale Indexes

CodeSpine uses a two-layer model:

• Base index: last committed state
• Dirty overlay: uncommitted Java changes

Fast tools read merged base + overlay state by default:

• search
• context
• impact
• MCP search_hybrid
• MCP find_symbol
• MCP get_symbol_context
• MCP get_impact

Deep analyses stay committed-only until promotion:

• deadcode
• flow
• community
• coupling

codespine watch updates the dirty overlay after a debounce window, then promotes it into the base index when local HEAD changes.

Quick Start

Index a repo:

codespine analyse /path/to/project

Run a deeper pass:

codespine analyse /path/to/project --deep

Add embeddings for semantic search:

codespine analyse /path/to/project --embed

Typical output:

$ codespine analyse .
Walking files...               142 files found
Index mode...                  incremental (8 files to index, 0 deleted)
Parsing code...                8/8
Tracing calls...               847 calls resolved
Analyzing types...             234 type relationships
Cross-module linking...        skipped (single module)
Detecting communities...       loading symbols
Detecting communities...       623 symbols, 1204 structural edges
Detecting communities...       persisting 8/8 clusters
Detecting communities...       8 clusters found
Detecting execution flows...   34 entry points, tracing
Detecting execution flows...   34 processes found
Finding dead code...           12 unreachable symbols
Analyzing git history...       18 commits, computing co-changes
Analyzing git history...       18 coupled file pairs
Generating embeddings...       0 vectors stored

Done in 4.2s - 623 symbols, 1847 edges, 8 clusters, 34 flows (no embeddings; rerun with --embed for semantic search)
Publishing read replica...     MCP will reload automatically

Each analysis phase streams live progress in place. The final step publishes a read replica so the MCP daemon picks up the new index without restarting.

Search the index:

codespine search "retry payment"
codespine context "PaymentService"
codespine impact "com.example.PaymentService#charge(java.lang.String)"
codespine stats

MCP

Foreground MCP server:

codespine mcp

Minimal MCP config:

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

If the client launches the wrong Python environment, use the absolute binary path instead:

{
  "mcpServers": {
    "codespine": {
      "command": "/absolute/path/to/codespine",
      "args": ["mcp"]
    }
  }
}

Agent Onboarding

When an agent connects to CodeSpine for the first time, it should call:

1. guide() — returns a structured catalog of every tool, organized by category, with recommended workflows and tips.
2. get_capabilities() — returns what is indexed right now, which features are ready, and what's missing.

The same information is available from the CLI:

codespine guide          # tool catalog, workflows, tips
codespine guide --json   # structured JSON for tooling

MCP Tools

Discovery & Status

Tool	Description
guide()	Tool catalog, workflows, and tips. Call first if new to CodeSpine.
get_capabilities()	What is indexed and which features are available right now.
list_projects()	All indexed projects with symbol/file counts.
get_codebase_stats()	Per-project stats: files, classes, methods, call edges, embeddings.
list_packages(project)	Java packages in the index.
ping()	Verify the MCP server is alive.

Search & Lookup

Tool	Description
search_hybrid(query, k, project)	Ranked symbol search (BM25 + vector + fuzzy via RRF).
find_symbol(name, kind, project, limit)	Exact/prefix name lookup across all projects.
get_symbol_context(query, max_depth, project)	One-shot deep context: search + impact + community + flows.
get_neighborhood(symbol, project)	Callers, callees, siblings, and override/implements.

Analysis

Tool	Description
get_impact(symbol, max_depth, project)	Caller-tree impact analysis with confidence scores.
detect_dead_code(limit, project, strict)	Methods with no callers (Java-aware exemptions).
trace_execution_flows(entry_symbol, max_depth, project)	Execution paths from entry points.
get_symbol_community(symbol)	Architectural community cluster for a symbol.
get_change_coupling(months, min_strength, min_cochanges)	Files that historically change together.

Git

Tool	Description
git_log(file_path, limit, project)	Recent git commits.
git_diff(ref, file_path, project)	Git diff (working tree vs ref, or between refs).
compare_branches(base_ref, head_ref, project)	Symbol-level diff between two git refs.

Indexing & Watch

Tool	Description
analyse_project(path, full, deep, embed)	Index a Java project (background job).
get_analyse_status()	Poll analysis progress.
reindex_file(file_path, project)	Re-index a single .java file (<1 s).
start_watch(path)	Watch for .java changes and update overlay in real time.
stop_watch()	Stop the background watch process.
get_watch_status()	Watch mode status: running, path, uptime.

Overlay

Tool	Description
get_overlay_status(project)	Uncommitted overlay state by project/module.
promote_overlay(project)	Commit dirty overlay into the base index.
clear_overlay(project)	Discard dirty overlay without changing the base.

Reset

Tool	Description
reset_project(project_id)	Remove all data for one project.
reset_index()	Remove ALL data across every project.
force_reset_index()	Emergency: delete data files when normal reset fails.

Advanced

Tool	Description
run_cypher(query)	Run a raw Cypher query against the graph DB.

CLI

# Indexing
codespine analyse <path>                     # incremental index
codespine analyse <path> --full              # full re-index
codespine analyse <path> --deep              # + communities, flows, dead code, coupling
codespine analyse <path> --embed             # + vector embeddings
codespine watch --path .                     # live re-index on file changes

# Search & Analysis
codespine search "query"                     # hybrid search
codespine context "symbol"                   # one-shot deep context
codespine impact "symbol"                    # caller-tree impact
codespine deadcode                           # dead code candidates
codespine flow                               # execution flows
codespine community                          # architectural clusters
codespine coupling                           # git change coupling
codespine diff main..feature                 # symbol-level branch diff

# Status & Info
codespine stats                              # per-project statistics
codespine list                               # indexed projects
codespine status                             # service and database status
codespine guide                              # tool catalog and workflows

# Overlay
codespine overlay-status                     # dirty overlay state
codespine overlay-promote                    # commit overlay to base
codespine overlay-clear                      # discard overlay

# Server Management
codespine start                              # launch background MCP server
codespine stop                               # stop background MCP server
codespine mcp                                # foreground MCP (stdio, for IDE)

# Cleanup & Reset
codespine clear-project <project_id>         # remove one project
codespine clear-index                        # remove all indexed data
codespine force-reset                        # emergency: delete all data files
codespine setup                              # check dependencies

analyse defaults to incremental mode. Repeat runs are designed to be fast when files have not changed.

Workspace And Module Detection

CodeSpine can index:

• a single Java repo
• a multi-module Maven or Gradle repo
• a workspace directory containing multiple repos

Project IDs are:

• single-module repo: payments-service
• multi-module repo: payments-service::core, payments-service::api

That same project ID can be passed into MCP tools and CLI analysis calls that support project scoping.

Deep Analysis Trade-Offs

--deep enables the expensive graph-wide passes:

• communities
• execution flows
• dead code
• git coupling

Use it when you want architecture-level context. Skip it when you just need the graph refreshed for search, context, and impact.

When a dirty overlay exists, deep-analysis results intentionally exclude those uncommitted edits until promotion.

--embed is also optional. Without it, CodeSpine still supports exact, keyword, and fuzzy search. Add embeddings when you need concept-level retrieval.

Concurrent Indexing and Querying

The indexer (write) and the MCP daemon (read) use separate database paths:

• The indexer writes to ~/.codespine_db with a 512 MB buffer pool.
• When indexing completes, analyse atomically copies the database to ~/.codespine_db_read and touches a sentinel file.
• The MCP daemon and all read-only CLI commands open ~/.codespine_db_read with a 128 MB buffer pool.
• The MCP daemon watches the sentinel file and silently reloads from the new snapshot on the next tool call — no restart needed.

Running codespine analyse --deep --embed on one project while querying a different one no longer causes buffer pool OOM or lock contention.

Runtime Files

• ~/.codespine_db - graph database (write)
• ~/.codespine_db_read - read replica used by MCP and CLI queries
• ~/.codespine_db_read.updated - sentinel file; touched after each successful snapshot
• ~/.codespine.pid - MCP background server PID
• ~/.codespine.log - server log
• ~/.codespine_embedding_cache.json - embedding cache
• ~/.codespine_index_meta/ - incremental file metadata cache
• ~/.codespine_overlay/ - uncommitted dirty overlay state

Notes

• codespine start launches a background MCP server. Most IDE MCP clients should use codespine mcp instead and manage the process themselves.
• codespine watch updates the dirty overlay first; it does not rewrite the committed base index on every save.
• codespine clear-index rebuilds the local index database from scratch. This also removes the read replica; run analyse again to republish it.
• codespine force-reset is the nuclear option — it deletes all data files without going through the DB engine. Use it when clear-index fails due to DB corruption.
• For large Spring or JPA-heavy repos, dead-code results should still be reviewed before deletion. The tool is conservative, not authoritative.

Project Docs

• Contributing
• Security
• Code of Conduct