Atlas / MCP servers / jonnoc / CodeRAG

CodeRAGBLOCK

mcp/jonnoc/coderag

Advanced graph-based code analysis for AI-assisted software development

Verdict
BLOCK
Grade
D
Trust score
69 /100
Exposed tools
51 42r · 6w · 3d
Transport
sse · stdio · streamable-http
License
MIT
Stars
28
01

Overview

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

Advanced graph-based code analysis for AI-assisted software development

CodeRAG is a professional code intelligence platform that transforms complex software projects into searchable knowledge graphs. By mapping code structures, dependencies, and relationships, it enables AI development tools to provide contextually accurate assistance for enterprise-scale codebases.

What CodeRAG Does

CodeRAG creates a comprehensive graph database representation of your codebase using Neo4J, enabling sophisticated analysis and AI-powered insights:

  • Automated Code Analysis - Scans and maps classes, methods, interfaces, dependencies, and architectural relationships across multiple programming languages
  • Remote Repository Analysis - Directly analyze any GitHub, GitLab, or Bitbucket repository without local cloning, supporting both public and private repositories with secure authentication
  • Intelligent Language Detection - Automatically identifies project languages, frameworks, and build configurations from metadata and build files
  • Quality Assessment - Calculates industry-standard software metrics (CK metrics, package coupling, architectural patterns) to identify technical debt and improvement opportunities
  • Semantic Code Search - Enables natural language queries to find code by functionality rather than syntax
  • Multi-Project Management - Supports enterprise environments with multiple codebases, providing unified analysis and cross-project insights

Who Should Use CodeRAG

Enterprise Development Teams

  • Large-scale projects with complex architectures requiring deep code understanding
  • Legacy system maintenance where comprehensive codebase mapping is essential
  • Code quality initiatives needing objective metrics and architectural analysis

AI-Assisted Development

  • Development teams using AI coding assistants (Claude Code, GitHub Copilot, Cursor, Windsurf) who need e
Read from source at commit e4e97b4ff7bcOBSERVED · 2026-10-08
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02

Connect

Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control. Replace the environment placeholders with a token scoped to the least it needs.

claude-code
claude mcp add coderag --env BITBUCKET_APP_PASSWORD=${BITBUCKET_APP_PASSWORD} --env EMBEDDING_MAX_TOKENS=${EMBEDDING_MAX_TOKENS} --env GH_TOKEN=${GH_TOKEN} --env GITHUB_TOKEN=${GITHUB_TOKEN} -- npx -y [email protected]
claude-desktop
{
  "mcpServers": {
    "coderag": {
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "env": {
        "BITBUCKET_APP_PASSWORD": "${BITBUCKET_APP_PASSWORD}",
        "EMBEDDING_MAX_TOKENS": "${EMBEDDING_MAX_TOKENS}",
        "GH_TOKEN": "${GH_TOKEN}",
        "GITHUB_TOKEN": "${GITHUB_TOKEN}"
      }
    }
  }
}
03

Exposed tools (51)

42 read · 6 write · 3 destructive. Blast radius: 3 tools can delete or overwrite — an agent that can be talked into calling a tool can be talked into calling this one.

ToolRiskDescription
add_edgewriteAdd a relationship edge between two nodes
add_filewriteParse a single source file and add its entities to the graph
add_nodewriteAdd a new code node (class, interface, method, etc.) to the graph
analyze_codebasereadGet guidance on analyzing a codebase using CodeRAG tools
analyze_inheritancereadGuide to analyze inheritance hierarchies and interface implementations
analyze_testing_annotationsreadAnalyze testing patterns and coverage based on test annotations/decorators
calculate_ck_metricsreadCalculate Chidamber & Kemerer metrics for a class (WMC, DIT, NOC, CBO, RFC, LCOM)
calculate_package_metricsreadCalculate package metrics (Afferent/Efferent Coupling, Instability, Abstractness, Distance)
class_or_interfacereadName of class or interface to analyze
clear_git_cachedestructiveClear all cached Git repositories to free up disk space.
com.example.TestClassreadUpdated description
com.example.TestClass.testMethodreadA test method
com.example.UserValidatorreadValidates user input data
delete_edgedestructiveDelete an edge by ID
delete_nodedestructiveDelete a code node by ID
find_architectural_issuesreadFind architectural issues (circular dependencies, god classes, high coupling)
find_classes_calling_methodreadFind all classes that call a specific method
find_classes_implementing_interfacereadFind all classes that implement a specific interface
find_dependenciesreadGuide to find class dependencies and method calls
find_deprecated_codereadFind all code elements marked as deprecated and optionally their dependencies
find_edges_by_sourcereadFind all edges originating from a source node
find_implementationsread
find_inheritance_hierarchyread
find_method_callersread
find_nodes_by_annotationreadFind code nodes (classes, methods, etc.) that have specific annotations/decorators
find_nodes_by_typereadFind nodes by their type
find_untestable_codereadFind code patterns that may be difficult to test (private methods, static methods, etc.)
find_usage_of_deprecated_codereadFind code that uses deprecated elements and assess migration impact
get_annotation_usagereadGet comprehensive statistics on annotation/decorator usage patterns across the codebase
get_edgereadGet an edge by ID
get_framework_usagereadGet statistics on framework usage based on annotations/decorators across the codebase
get_inheritance_hierarchyreadGet the inheritance hierarchy for a class
get_nodereadGet a code node by ID
get_project_summaryreadGet overall project metrics summary and quality assessment
get_similar_codereadFind code entities that are semantically similar to a specific node
git_cache_statsreadGet statistics about the Git repository cache, including number of cached repositories and total size.
initialize_semantic_searchreadInitialize semantic search infrastructure including vector indexes
languagereadProgramming language of the project
list_projectsreadList all projects in the CodeRAG graph database with optional statistics
project_typereadType of project (java, typescript, python, etc.)
scan_dirreadScan a directory for source files and populate the graph
scan_remote_reporeadScan a remote Git repository and populate the graph database. Supports GitHub, GitLab, Bitbucket, and custom Git servers.
search_nodesreadSearch nodes by name, qualified name, or description
semantic_searchreadSearch for code using natural language queries to find functionality by meaning rather than syntax
setup_code_graphwriteStep-by-step guide to set up a code graph for a new project
target_classreadThe class to analyze dependencies for
update_embeddingswriteGenerate or update semantic embeddings for code entities to enable semantic search
update_nodewriteUpdate an existing code node
utils.testFunctionreadA test function
utils.validateEmailreadValidates email addresses
validate_remote_reporeadValidate that a remote Git repository is accessible and can be scanned.
04

Trust audit

BLOCKgrade D · trust 69/100 Do not install this without reading the findings. The audit found something that could harm you or your machine.

LayerWhat it checksResult
L0Provenance & inventoryPASS
L1Static analysis of the codeFAIL
L2Instruction surface (what it tells the agent)PASS
L3Class-specific surfaceWARN
L4Behavioural (sandbox)SKIPPED

What the source does

Filesystem
declared (10 observation(s))
Network
declared (1 observation(s))
Shell
none-observed
Dependencies
not all pinned
Secrets in source
found

Findings (12)

HIGHFilesystem / path · fs.credential_store · CWE-22, CWE-59
src/scanner/git/git-auth-manager.ts:35
const privateKeyPath = path.join(sshDir, 'id_rsa');
Why it matters. touches a credential store
MEDIUMHard-coded secrets · secret.generic · CWE-798, CWE-321
tests/git-auth-manager.test.ts:107
github: { token: 'ghp_valid_token_123456789012345678901234567890' }
MEDIUMHard-coded secrets · secret.github · CWE-798, CWE-321
tests/git-auth-manager.test.ts:107
github: { token: 'ghp_valid_token_123456789012345678901234567890' }
MEDIUMFilesystem / path · mcp.destructive_tools · CWE-22, CWE-59
clear_git_cache, delete_edge, delete_node
Why it matters. 3 tool(s) can delete or overwrite
Fix. prefer a read-only mode or scoped tokens; the page states the blast radius
LOWFilesystem / path · fs.traversal · CWE-22, CWE-59
src/mcp/tools/analyze-testing-annotations.ts:1
import { Neo4jClient } from '../../graph/neo4j-client.js';
LOWFilesystem / path · fs.traversal · CWE-22, CWE-59
src/mcp/tools/edge-management.ts:1
import { EdgeManager } from '../../graph/edge-manager.js';
LOWFilesystem / path · fs.traversal · CWE-22, CWE-59
src/mcp/tools/edge-management.ts:2
import { CodeEdge } from '../../types.js';
LOWFilesystem / path · fs.traversal · CWE-22, CWE-59
src/mcp/tools/find-deprecated-code.ts:1
import { Neo4jClient } from '../../graph/neo4j-client.js';
LOWFilesystem / path · fs.traversal · CWE-22, CWE-59
src/mcp/tools/find-nodes-by-annotation.ts:1
import { Neo4jClient } from '../../graph/neo4j-client.js';
LOWNetwork egress · net.raw_ip · CWE-200, CWE-319
docs/semantic-search/ollama-setup.md:100
OLLAMA_BASE_URL=http://192.168.1.100:11434
LOWSupply chain · supply.unpinned · CWE-829, CWE-1357
package.json
@modelcontextprotocol/sdk, @types/tmp, @typescript-eslint/parser, @typescript-eslint/types, commander, dotenv, express, glob
Why it matters. 22 dependency range(s) float
Fix. pin exact versions or ship a lockfile
INFOSupply chain · prompt.pipe_to_shell · CWE-829, CWE-1357
docs/semantic-search/ollama-setup.md:29
curl -fsSL https://ollama.ai/install.sh | sh

Gates applied: no_behavioural_pass.

Audited 2026-10-08 · audit v0.4.1 · source sha e4e97b4ff7bcfull audit observations/trust-audit/mcp-server/jonnoc__coderag.json · Report an issue / request a re-scan
05

Audit history

Every audit this server has had. A grade with a past is a grade somebody is still checking.

DateSourceVerdictGradeScoreChange
2026-10-08e4e97b4ff7bcBLOCKD69first audit
06

Questions

What is the CodeRAG MCP server?

Advanced graph-based code analysis for AI-assisted software development

What tools does CodeRAG expose?

51 in total: 42 read-only, 6 that write, and 3 that can delete or overwrite (clear_git_cache, delete_edge, delete_node). Every one is listed on this page with its risk.

Is CodeRAG safe to connect to an agent?

No — not without reading the findings first. The audit graded it D (69/100) and found 1 critical or high issue in the source. Each one is listed on this page with the file and line it is on. Separately from the audit: 3 of its tools can destroy data, so scope the token you give it to what you actually need.

What credentials does CodeRAG need?

It reads BITBUCKET_APP_PASSWORD, EMBEDDING_MAX_TOKENS, GH_TOKEN, GITHUB_TOKEN, GITLAB_TOKEN, GL_TOKEN, MCP_TOKEN_LIMIT, NEO4J_PASSWORD and OPENAI_API_KEY from the environment. Give it a token scoped to the least it needs — an agent that can be talked into calling a tool can be talked into calling it with your credentials.

How does CodeRAG run?

It speaks sse, stdio and streamable-http, so it runs as a local process your client starts. It is published on npm as coderag at 1.0.0.

How current is this page?

The grade is for one exact copy of the source (e4e97b4ff7bc), read on 2026-10-08. The repository is watched and re-audited when it changes.

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