codebase-memory-mcp vs EKOS: Code Knowledge Graph MCP Servers
codebase-memory-mcp and EKOS both give AI coding agents a persistent knowledge graph over MCP. What each one indexes, where each is stronger, and when to use one, the other or both.
codebase-memory-mcp and EKOS solve the same first problem: an AI coding agent that rediscovers a repository from scratch in every session. Both index the code once into a knowledge graph, keep it on your machine, and serve it to agents over the Model Context Protocol. Both are open source under the MIT license. They differ in what else they cover and how much each fact can be checked.
This comparison describes codebase-memory-mcp from its own README as read on 2026-10-21. It moves quickly, so check there for the current state.
At a glance
| codebase-memory-mcp | EKOS | |
|---|---|---|
| Languages | 162 with vendored tree-sitter grammars; LSP type resolution for 11, including Python, TypeScript, Go, Java and Rust | Rust, Python, JavaScript/TypeScript, Elixir, Perl (real parsers); compiled .NET and JVM binaries through a separately licensed extension |
| Infrastructure files | Dockerfiles, Compose, Kubernetes, Helm, Terraform, Ansible, CI configuration | GitHub Actions workflows and Cargo manifests |
| Databases | not a focus | tables, columns, keys, views, stored procedures and triggers from six SQL dialects plus PL/pgSQL; which code and procedures read and write which table; column-level lineage |
| ETL | not a focus | dbt projects and Pentaho jobs, into a shared transformation IR |
| Documents | Markdown, reStructuredText, AsciiDoc, PDF text | Markdown, PDF, DOCX, HTML, email, Confluence; links from documents to the code and columns they describe |
| Git | watches and re-indexes changed files | history, authorship and co-change as knowledge, plus GitHub issues and pull requests |
| Evidence | some edges carry line, method and confidence | every fact cites file, line and fragment; an append-only ledger with point-in-time queries and an audit trail of which run wrote it |
| Uncertain matches | confidence scores | recorded as unconfirmed claims for a person to confirm or reject; never merged silently |
| Runtime | a single static C binary, SQLite | a Rust binary, a fact-segment ledger; optional web console |
When to use which
Use codebase-memory-mcp when the job is code navigation across many languages or a large polyglot monorepo, and you want the lightest possible install. Its language coverage is far wider than EKOS's.
Use EKOS when the questions cross the boundary between code and data: which procedure writes this table, what breaks if this column is renamed, what this Pentaho job or SQL view does, what a status code means. Use it too when an answer has to cite the exact source line to be trusted. EKOS was built for old enterprise systems where much of the logic lives in the database. On LedgerSMB, a twenty-year-old PostgreSQL and Perl application, it recovered all 212 stored routines from source and linked each to the tables it reads and writes.
Use both when you need the two kinds of coverage. MCP clients can connect to several servers, and an agent will call whichever tool fits the question.
Try EKOS on the same repository
curl -fsSL https://raw.githubusercontent.com/alexeyban/EKOS/main/install.sh | sh
cd /path/to/repo && ekos init --detect
ekos build && ekos recover && ekos resolve && ekos compile && ekos commit
claude mcp add ekos -- ekos --config "$PWD/ekos.toml" mcp serve --workspace "$PWD"
How many tokens this saves on a real repository, including the case where a plain grep wins: benchmarks.
Frequently asked questions
Is EKOS an alternative to codebase-memory-mcp?
For code navigation they overlap: both build a persistent graph of a repository and serve it to agents over MCP. EKOS covers fewer programming languages. It goes further into databases, ETL, documentation and Git history, and it attaches source evidence to every fact.
Can I use both MCP servers at once?
Yes. MCP clients such as Claude Code can register several servers, and the agent calls whichever tool fits the question.
Does EKOS index SQL databases and stored procedures?
Yes. EKOS recovers tables, columns, keys, views, stored procedures and triggers from SQL files in six dialects plus PL/pgSQL, and links them to the code and procedures that read and write them.