Codebase Memory MCP vs Proof Layer
A side-by-side look at the Codebase Memory MCP and Proof Layer MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Codebase Memory MCP for knowledge & memory work as a local process; choose Proof Layer for cryptography as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Codebase Memory MCP when
- You need dedicated capabilities in the Knowledge & Memory domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You want tools like
index_repository, search_graph, query_graph.
Choose Proof Layer when
- You need dedicated capabilities in the Cryptography domain.
- You prefer a local stdio subprocess transport.
- You have the keys it needs:
PROOF_LAYER_API_KEY, PROOF_LAYER_API_URL. - You want tools like
pl_evaluate, pl_get_receipt, pl_verify_receipt.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Knowledge & Memory | Cryptography |
| Quality signal | 73/100 · Great | 55/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | None listed | PROOF_LAYER_API_KEYPROOF_LAYER_API_URL |
| Verified owner | Community listing | Community listing |
| GitHub stars | 47,004 | 0 |
| Directory activity | 8 views 1 installs 1 upvotes | 2 views 0 installs 0 upvotes |
| Tools | 17 | 8 |
| Full listing | View Codebase Memory MCP | View Proof Layer |
Tools & capabilities
Codebase Memory MCP tools 17
index_repositoryIndex a repository. full/moderate add semantics; fast omits them; cross-repo-intelligence links services. Reports coverage gaps.search_graphFind symbols via BM25 query, regex name/qn filters, or semantic_query. Rows keep qn/file/lines and in/out over CALLS/USAGE/CALL_REFERENCE/INHERITS/IMPLEMENTS.query_graphRead-only Cypher for multi-hop, aggregation, complexity, or cross-service analysis. Default: 200 visible rows with exact/lower-bound totals and truncation; continue safely with next_cursor. graph=missed is a file tree of flagged coverage gaps; absence is not proof of completeness. Use get_graph_schema(diagnostics=full) for properties.trace_pathTrace callers/callees, data flow, or cross-service paths. Defaults exclude tests and resolver evidence. Rows keep qn/hop with explicit totals, relations, and continuations.get_code_snippetRead a search_graph symbol. auto bounds source and outlines large containers; full restores up to 500 lines. Source/outline pages continue; coverage_note marks gaps.get_file_outlineDeclaration outline of one exact repository-relative file: optional exact label filter, source order, exact total/offset/limit paging; file/folder/container nodes excluded.get_graph_schemaGet node-label and edge-type counts. diagnostics=full also lists queryable properties.compare_graphsCompare two indexed snapshots: deterministic target-only additions and base-only removals of stable node/edge identities; each set capped by limit and a 512 KiB budget with exact totals and truncation reasons.get_architectureCompact counts, languages, packages, entry points. Request structure, dependencies, routes, hotspots, boundaries, layers, clusters, cycles, or file_tree; path scopes a directory.search_codeGraph-ranked text search: compact symbols, full bounded source, or file paths.list_projectsList projects with stable paging. Identity is lean; stats adds graph sizes.delete_projectDelete a project from the index- +5 more on the listing page
Proof Layer tools 8
pl_evaluateSubmit an AI agent action proposal to Proof Layer for governance evaluation. Returns a cryptographically-signed receipt with a verdict of EXECUTE, BLOCK, REVIEW, or SHADOW. Use this before any consequential agent action (sending emails, modifying data, making payments, etc.).pl_get_receiptRetrieve a Proof Layer audit receipt by its UUID. Returns the full receipt including verdict, signature, and policy pack hash.pl_verify_receiptCryptographically verify a Proof Layer receipt. Checks the Ed25519 signature and confirms the signing key is ACTIVE. Returns valid: true/false with a reason.pl_list_receiptsList recent Proof Layer audit receipts for the authenticated tenant. Supports filtering by agent and verdict.pl_usageGet current Proof Layer quota usage — receipts used, receipts remaining, credit balance, billing cycle dates, and plan tier.pl_list_policy_packsList all governance policy packs for the authenticated tenant, including which one is currently active.pl_create_planA human approves a governed plan — a scoped, time-bounded set of future actions across named agents. Returns a plan_id and JTI that agents use to request delegation receipts via pl_delegate. Scope patterns support wildcards: 'build:*' authorizes any action starting with 'build:'.pl_delegateAn agent requests authorization to perform a specific action under a parent plan. Returns 'ok' with a signed receipt (proceed with the action), 'checkpoint_required' (human must re-approve this specific action), or 'denied' (agent or action not authorized under the plan).
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Codebase Memory MCP
{
"mcpServers": {
"deusdata-codebase-memory-mcp": {
"command": "npx",
"args": [
"-y",
"codebase-memory-mcp"
]
}
}
}
Proof Layer
{
"mcpServers": {
"proof-layer": {
"command": "npx",
"args": [
"-y",
"@proof-layer/mcp@latest"
],
"env": {
"PROOF_LAYER_API_KEY": "YOUR_PROOF_LAYER_API_KEY_HERE",
"PROOF_LAYER_API_URL": "YOUR_PROOF_LAYER_API_URL_HERE"
}
}
}
}
Frequently asked questions
Codebase Memory MCP is categorized under Knowledge & Memory and uses a local stdio subprocess. Proof Layer belongs to Cryptography and uses a local stdio subprocess. Pick Codebase Memory MCP for knowledge & memory work and Proof Layer for cryptography.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Codebase Memory MCP is listed as free. Auth: no auth required. Proof Layer has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add deusdata-codebase-memory-mcp and proof-layer as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Codebase Memory MCP has a quality signal of 73/100 (Great) with 8 views, 1 installs and 47,004 GitHub stars. Proof Layer has 55/100 (Good) with 2 views, 0 installs and 0 GitHub stars.