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Codebase Brain MCP

CI License: MIT Python 3.12+

An MCP server that gives AI assistants a cited, searchable memory of a codebase, including its history. Point it at a local folder or a public git URL. Claude, Cursor or any MCP client can then answer questions about the code with exact path:start-end citations.

Claude Code using Codebase Brain to explain the history, impact and docs of a function

Claude Code asks why TimestampSigner.unsign looks the way it does, what breaks if it changes, and whether its docs are current. Codebase Brain answers with commits, callers, tests and doc findings, all cited. (Waiting time sped up.)

The problem

AI coding assistants are good at writing new code but struggle to understand code that already exists:

  • They can't see the whole project. A real codebase has thousands of files. The assistant reads a few and guesses the rest, so it misses the function that matters or invents one that doesn't exist.

  • You can't check their answers. "Expiry is handled in the auth module" is no use if you can't see where. Without file and line references, you have to trust the answer or re-read the code yourself.

  • They don't know why code is the way it is. The code shows what it does. The reasons ("we added this check because it crashed on Windows") live in git history and pull requests, which assistants never read. So they "clean up" code that exists for a reason and bring old bugs back.

  • They don't know what a change will break, or whether the documentation still matches the code.

  • Many tools send your code to someone else's server to make it searchable.

Related MCP server: OmniDocs-RAG-CN

What Codebase Brain gives you

A plug-in for any AI assistant that turns a codebase into something it can actually look things up in:

  • Answers with proof. Every result points to the exact file and lines, and the assistant can open them.

  • Search that understands code. It finds code whether you type the exact name (calculate_invoice_total) or describe it in plain words ("how are invoices totalled?").

  • The story behind the code. For any function, it shows every change made to it, who made it, why (from the commit message and pull request), and what the change was.

  • What breaks if you change something. Everything that uses a function, directly or indirectly, and the tests that cover it.

  • Out-of-date docs, found automatically. Documentation that mentions functions, files or settings that no longer exist, or shows examples that would no longer work.

  • Private by design. Everything runs on your machine. No API keys, and your code never leaves your computer.

Why it's different (technical)

  • Code-aware chunking. Python (with ast) and JavaScript / TypeScript / JSX / TSX (with tree-sitter) are split by function, class, method, arrow function, interface, type and enum, with their doc comments. Markdown is split by heading. Each chunk knows its symbol (TimestampSigner.unsign, Ky.#retry) and exact lines, so citations point at real code. Other languages are indexed in overlapping line windows.

  • Hybrid retrieval. SQLite FTS5 BM25 (with camelCase / snake_case identifier splitting) plus local embeddings, merged with reciprocal-rank fusion. Exact names and fuzzy questions both work.

  • Local and free. Embeddings run on your machine (fastembed, ONNX). No API keys, and no code leaves your computer.

  • Incremental. Re-indexing only re-embeds files whose content changed. On a 42-file repo, a re-index with no changes takes about 2 seconds.

  • History-aware. explain_history follows a function's lines back through git (git log -L), shows who wrote the current lines, and links the pull requests behind each change. So agents can answer "why is it built this way?", not just "what does it do?".

  • Impact analysis. impact_of_change lists everything that uses a function, directly and transitively, plus the tests that exercise it, before an agent changes anything. It works across Python, JavaScript and TypeScript files, and follows a constructor to the code that builds its class.

  • Doc-drift detection. find_doc_drift checks Markdown and reStructuredText docs against the code. It finds files, functions, settings and flags that don't exist; examples passing parameters a function doesn't take; imports that would fail; and sections last edited long before the code they describe changed. Each finding cites the doc section and suggests a fix ("Was it renamed to checkout_total?").

  • Agent-friendly output. Structured tool results, read-only tool annotations, progress notifications while indexing, and clear error messages the model can act on.

Tools

Tool

What it does

index_repo(source, name?)

Index a local path or an https:// git URL (blobless clone with full history). Reports progress.

ask_codebase(question, repo?, k?)

The most relevant code and docs as cited sources, plus related commits, with instructions to answer only from them.

search(query, repo?, k?, path_prefix?, kinds?)

Raw hybrid search, filterable by path and chunk kind.

explain_history(symbol? | path, start_line?, end_line?, repo?)

Every commit that changed a function or line range, newest first, with the relevant diff, current authorship, and PR titles and descriptions (GitHub).

search_history(query, repo?, k?)

Find commits by what their messages say.

impact_of_change(symbol, path?, depth?, repo?)

Direct and indirect users of a function or class, and the tests involved.

find_doc_drift(path_prefix?, check_history?, repo?)

Documentation that no longer matches the code, by severity (high, medium, low).

read_lines(path, start, end, repo?)

Open the exact lines behind a citation. Refuses paths outside the repo.

list_repos()

What's indexed, at which commit, and in which languages.

Also included: the resource brain://repos, and the prompt answer_with_citations.

Install

Codebase Brain runs on your own machine, so there's no server or account, and it's free. It works with any MCP-compatible assistant. All you need is uv, and every client runs the same command: uvx codebase-brain-mcp.

Claude Code

claude mcp add codebase-brain -- uvx codebase-brain-mcp

Cursor: ~/.cursor/mcp.json (all projects) or .cursor/mcp.json (one project)

{
  "mcpServers": {
    "codebase-brain": { "command": "uvx", "args": ["codebase-brain-mcp"] }
  }
}

Claude Desktop: Settings → Developer → Edit Config (claude_desktop_config.json), then restart the app

{
  "mcpServers": {
    "codebase-brain": { "command": "uvx", "args": ["codebase-brain-mcp"] }
  }
}

VS Code (GitHub Copilot agent mode): .vscode/mcp.json

{
  "servers": {
    "codebase-brain": { "type": "stdio", "command": "uvx", "args": ["codebase-brain-mcp"] }
  }
}

Windsurf: ~/.codeium/windsurf/mcp_config.json. Gemini CLI: ~/.gemini/settings.json. Both use the same mcpServers block as Cursor.

OpenAI Codex CLI

codex mcp add codebase-brain -- uvx codebase-brain-mcp

Tool doesn't start? Desktop apps often don't see your shell's PATH. Run which uvx and put that full path in "command", for example "/Users/you/.local/bin/uvx".

Optional: install the skill. It tells the agent which tool fits which question, to cite every claim, to check history before removing odd code, and to run impact analysis before editing. For Claude Code, run the commands below. Other agents that read SKILL.md files take the same file in their own skills folder.

mkdir -p ~/.claude/skills/codebase-brain
curl -fsSL https://raw.githubusercontent.com/Nomannazir/codebase-brain-mcp/main/skills/codebase-brain/SKILL.md \
  -o ~/.claude/skills/codebase-brain/SKILL.md

Quick start

uv sync
uv run codebase-brain index https://github.com/pallets/itsdangerous
uv run codebase-brain search "how is the signature timestamp checked for expiry"
0.0313  src/itsdangerous/timed.py:72-158  method TimestampSigner.unsign
0.0311  docs/timed.rst:1-28  code
0.0301  src/itsdangerous/timed.py:170-228  class TimedSerializer

Ask why it looks like that. explain_history(symbol="TimestampSigner.unsign") returns its line-by-line history:

src/itsdangerous/timed.py:72-158
  3edfbbbc 2022-03-24 handle OverflowError in timed unsign on 32-bit systems
  177196d3 2022-03-09 catch OSError on Windows
  37f09970 2022-03-08 catching year overflow ValueError
  c30678d1 2019-05-31 don't allow timestamps from the future
  910a7a94 2020-04-17 datetimes are timezone-aware utc
  ...

Use a local checkout instead (for development)

claude mcp add codebase-brain -- uv run --directory /path/to/codebase-brain-mcp codebase-brain

Run it as a remote server (Streamable HTTP)

export CODEBASE_BRAIN_TOKEN="$(python -c 'import secrets; print(secrets.token_urlsafe(32))')"
uv run codebase-brain serve --transport streamable-http --host 0.0.0.0 --port 8765

Clients connect to http://<host>:8765/mcp with Authorization: Bearer <token>. GET /healthz is open for load balancers. Remote mode is locked down by default:

  • No token, no public port. The server refuses to listen beyond localhost without a token of at least 24 characters. Tokens are compared in constant time.

  • Remote clients can't read the server's disk. Only public https:// git URLs can be indexed, not local paths, unless you set CODEBASE_BRAIN_ALLOW_LOCAL_PATHS=1.

  • Big repos are refused above CODEBASE_BRAIN_MAX_FILES (default 20,000), and every git command has a timeout.

  • DNS-rebinding protection is on for localhost, and for any hosts listed in CODEBASE_BRAIN_ALLOWED_HOSTS.

Docker

docker build -t codebase-brain-mcp .
docker run -p 8765:8765 -e CODEBASE_BRAIN_TOKEN="$CODEBASE_BRAIN_TOKEN" -v brain-data:/data codebase-brain-mcp

The image runs as a non-root user and includes the embedding model, so it starts fast and needs no download at runtime. It has a health check, and keeps indexes in the /data volume. Indexing uses about 1.2 GB of memory, so give the container 2 GB.

Configuration

Variable

Default

CODEBASE_BRAIN_HOME

~/.codebase-brain

Indexes and clones

CODEBASE_BRAIN_EMBEDDER

fastembed

hash gives an offline, deterministic embedder (used in tests)

CODEBASE_BRAIN_EMBED_MODEL

BAAI/bge-small-en-v1.5

Any fastembed text model

CODEBASE_BRAIN_MAX_FILE_BYTES

512000

Larger files are skipped

GITHUB_TOKEN

unset

Optional. Raises GitHub's API rate limit for PR lookups

CODEBASE_BRAIN_FETCH_PRS

1

Set to 0 to never call the GitHub API

CODEBASE_BRAIN_TOKEN

unset

Bearer token for HTTP mode (required unless bound to localhost)

CODEBASE_BRAIN_ALLOWED_HOSTS

unset

Comma-separated Host values to accept (DNS-rebinding protection)

CODEBASE_BRAIN_ALLOW_LOCAL_PATHS

1 (stdio) / 0 (HTTP)

Whether index_repo may read local directories

CODEBASE_BRAIN_MAX_FILES

20000

Refuse repos with more indexable files

PORT

8765

HTTP port (platforms such as Cloud Run set this)

Doc drift, tested honestly

On a well-maintained project (itsdangerous), find_doc_drift reports no false alarms. It only reports three "worth a look" sections whose docs date from 2020 while the code they describe changed in 2024–2025. On docs with planted mistakes, it catches every one: a moved file, a renamed function (with the right suggestion), an unknown setting and flag, a keyword argument the function doesn't take, and an import that would fail. Changelogs are skipped, because they're supposed to mention removed things.

Evaluation

Does search actually put the right code in front of the model? codebase-brain eval answers that with a benchmark. There are two, each with 32 questions pinned to one commit, and each question lists the code or docs a good answer must come from. The questions were written by reading the code before any results were measured, and haven't been changed since.

Python: pallets/itsdangerous

32 questions about pallets/itsdangerous at commit 672971d, in evals/datasets/itsdangerous.toml.

Mode

Hit@1

Hit@3

Hit@5

Hit@10

MRR@10 (95% CI)

nDCG@10

p50 latency

hybrid (default)

56%

88%

88%

91%

0.697 (0.56–0.82)

0.735

5 ms

keyword only (BM25)

56%

75%

78%

84%

0.667 (0.52–0.80)

0.699

<1 ms

vector only (bge-small)

56%

72%

75%

94%

0.658 (0.51–0.80)

0.701

4 ms

Hit@5 by question type

describes behaviour (14)

about the docs (7)

names the code (11)

hybrid

71%

100%

100%

keyword only

64%

71%

100%

vector only

57%

71%

100%

What this shows:

  • Hybrid finds a right answer in the top 3 for 88% of questions, against 75% and 72% for either method alone. The gain comes from questions written in plain words and questions about the docs. When the question names the code, every mode finds it.

  • It's honest about uncertainty. With 32 questions, the confidence intervals for MRR overlap, so hybrid is better on this set but not yet proven in general. Per question, hybrid beats keyword-only on 8 questions and loses on 4.

  • It has known misses. Four questions describing behaviour in very different words from the code don't reach the top 5. They're listed in evals/results/itsdangerous.md and are the next thing to improve. A larger, held-out question set will come first, so any tuning isn't fitted to these 32.

TypeScript: sindresorhus/ky

32 questions about sindresorhus/ky at commit 3541888, in evals/datasets/ky.toml. The readme is one 2,000-line file, so docs questions must find the right section, not just the file.

Mode

Hit@1

Hit@3

Hit@5

Hit@10

MRR@10 (95% CI)

nDCG@10

p50 latency

hybrid (default)

47%

66%

69%

78%

0.563 (0.41–0.71)

0.576

6 ms

keyword only (BM25)

38%

44%

53%

62%

0.436 (0.29–0.59)

0.455

1 ms

vector only (bge-small)

47%

69%

75%

78%

0.594 (0.46–0.74)

0.604

5 ms

Hit@5 by question type

describes behaviour (14)

about the docs (7)

names the code (11)

hybrid

36%

100%

91%

keyword only

7%

86%

91%

vector only

43%

100%

100%

What this shows:

  • Naming the code or asking about the docs works well: 91–100% in the top 5.

  • Describing behaviour in plain words is the weak spot (36%). ky has about 25,000 lines of tests next to 5,000 lines of source, and the tests describe the same behaviour in plain words, so they outrank the source. Every miss is listed in evals/results/ky.md.

  • Hybrid is not better than vector-only here. The intervals overlap heavily (hybrid beats vector on 5 questions and loses on 9), so neither is proven better. Keyword-only is clearly worst: hybrid beats it on 12 questions and loses on none.

  • These results are published as measured. Tuning (for example, ranking source above tests) will be checked against a new held-out set, so it isn't fitted to these questions.

Reproduce either benchmark (the first run downloads the repo and the embedding model):

uv run codebase-brain eval evals/datasets/itsdangerous.toml --out evals/results
uv run codebase-brain eval evals/datasets/ky.toml --out evals/results

How it's measured:

  • Hit@k: a relevant result is in the top k.

  • MRR: 1 / rank of the first relevant result.

  • nDCG@10: each target is credited once, so duplicate chunks don't inflate the score.

  • Confidence intervals: 95% bootstrap over questions, seeded.

  • Relevance: a result is relevant if it's in the target file and, when the target names a symbol, is that symbol or one of its methods. A docs target can name a section (FAQ > How do I stop retrying early?), and then that section or one of its subsections counts.

  • Dataset rot: the harness fails if a target no longer exists at the pinned commit.

How it works

source ─► resolve (local dir / blobless https clone) ─► list files (.gitignore-aware, skips binaries and lockfiles)
       ─► chunk (ast / tree-sitter / headings / windows) ─► embed (fastembed) ─► SQLite: chunks + vectors + FTS5
query  ─► BM25 top 50 ┐
       ─► vector top 50 ┴─► reciprocal-rank fusion ─► filters ─► cited sources

Security

  • Clones are blobless (--filter=blob:none): full history, with file contents fetched only when needed.

  • Commit authors are shown by name only; email addresses are never stored or returned.

  • Only https:// clone URLs are accepted. Git runs with GIT_ALLOW_PROTOCOL=https:file and no terminal prompts.

  • read_lines resolves paths and refuses anything outside the indexed repository.

  • Repo names are validated, so they can't escape the index directory.

  • All query tools are marked read-only.

  • In HTTP mode: a required bearer token (constant-time check), git URLs only, repo size limits, DNS-rebinding protection, and a non-root container.

Development

uv run pytest           # 67 tests, offline (hash embedder, temporary git repos, in-process MCP client)
uv run ruff check .     # lint
uv run ruff format .    # format
uv run pyright          # types

Roadmap

  • Git history and PR discussions: explain_history, search_history

  • Symbol references and transitive dependents: impact_of_change

  • find_doc_drift: Markdown and reStructuredText, signatures, imports, settings, flags, staleness

  • JavaScript and TypeScript (tree-sitter): chunking, references, impact analysis

  • More languages (Go, Rust, Java) with tree-sitter

  • Retrieval evals with confidence intervals (codebase-brain eval)

  • Larger held-out eval set, then retrieval tuning (reranking, query expansion)

  • Streamable HTTP with bearer-token auth, Docker image

  • PyPI package, MCP Registry listing

  • Hosted demo

  • OpenTelemetry tracing

Available Tools

9 tools
ask_codebaseA
Read-only

Gather the code and docs most relevant to a question, plus related commits, as numbered, cited sources. Use this to answer "how does X work?" or "where is Y handled?" questions. Answer from these sources only and cite each claim as path:start-end; open a source in full with read_lines. For filters, use search.

NameRequiredDescriptionDefault
kNoHow many results to return, 1 to 25.
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
questionYesA question in plain words, e.g. "How are sessions expired?"

Output Schema

NameRequiredDescription
repoYes
sourcesYes
questionYes
instructionsYes
related_commitsYesCommits whose messages match the question.

TDQS

A4.3/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint true and openWorldHint false, and the description adds real behavioral content on top: results arrive as numbered cited sources including related commits, claims must be cited as path:start-end, and there is an answer-from-sources-only rule. Output format is partly covered by the output schema, so the remaining detail is appropriate rather than a gap.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is densely front-loaded, leading with what the tool does and following with usage rules and routing. It is compressed almost to note form, but every sentence carries an instruction and there is no filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Annotations cover safety and an output schema exists, so the description does not need to explain returned structure. It still covers purpose, triggering conditions, citation format, and the alternatives, which is complete for a retrieval tool of moderate complexity; only the sourcing or ranking behavior is left implicit.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so k, repo, and question are already documented, and the description adds no parameter-level detail. The baseline 3 is correct when the schema does all the work.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and output: gather the code and docs most relevant to a question, plus related commits, returned as numbered cited sources. It is clearly distinguishable from search (filters) and read_lines (full source), both of which are named.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives concrete triggering questions ("how does X work?", "where is Y handled?") and explicitly routes the agent elsewhere: use search for filters and read_lines to open a source in full. It also imposes an answering constraint (answer from these sources only), so the agent knows what the tool is for and what it is not.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

explain_historyA
Read-only

Why code looks the way it does. Use this before removing or rewriting code that looks odd, or to answer "why is it like this?". Give a symbol, or a path with an optional line range. Returns who wrote the current lines, every commit that changed them (with the relevant diff), and the title and description of the pull request behind each commit (GitHub only).

NameRequiredDescriptionDefault
pathNoA file in the repo. Narrow it with start_line and end_line.
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
symbolNoA function, class or method, e.g. "unsign" or "Signer.sign". Use this or path.
end_lineNoLast line of the range (with path).
start_lineNoFirst line of the range (with path).
max_commitsNoHow many commits to return, newest first.

Output Schema

NameRequiredDescription
repoYes
symbolYes
changesYesCommits that changed these lines, newest first.
citationYes
authorshipYes
instructionsYes
pull_requestsYes

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Beyond the readOnlyHint/openWorldHint annotations, the description discloses the concrete payload (author of current lines, every commit that changed them with relevant diffs, and PR title/description) and flags a real caveat — PR metadata is GitHub-only. It does not explain behavior when both symbol and path are supplied, or when neither is, which is the remaining operational ambiguity.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three dense sentences with the motivation front-loaded, then usage, then inputs, then outputs. No filler and no repetition of schema text verbatim.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With six optional parameters, an output schema present, and safety already covered by annotations, the description carries the right load: purpose, trigger, selector modes, and the GitHub caveat. Complete enough to call correctly; only the both-params/neither-param edge cases are unaddressed.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3, but the description adds meaning the schema only hints at: it frames symbol and path as mutually alternative selectors and makes the line range explicitly optional and subordinate to path. The GitHub-only qualifier is also the only place backend support is tied to the output content.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a concrete framing ('Why code looks the way it does') and states both input modes (a symbol, or a path with an optional line range) plus the shape of the answer. It is clearly a blast-radius / provenance tool, distinguishable in spirit from search_history, but it never names that sibling or draws an explicit boundary against it.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives an explicit trigger scenario: use it before removing or rewriting code that looks odd, or when answering 'why is it like this?'. That is genuine when-to-use guidance. It stops short of exclusions or naming alternatives such as search_history or impact_of_change, so the agent must infer which history tool to pick.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

find_doc_driftA
Read-only

Documentation that no longer matches the code. Use this to check a README or docs folder, or before a release. Finds files, functions, settings and flags that don't exist; code examples that pass parameters a function doesn't take; imports that would fail; and stale sections. Each finding has a severity, cites the doc section and suggests a fix. Changelogs are skipped.

NameRequiredDescriptionDefault
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
limitNoMost findings to return, 1 to 200, most severe first.
path_prefixNoOnly consider files under this path, e.g. "src/auth/" or "docs/".
check_historyNoAlso flag doc sections last edited long before the code they describe.

Output Schema

NameRequiredDescription
repoYes
summaryYes
findingsYes
sections_checkedYes
references_checkedYes

TDQS

A3.6/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true and openWorldHint=false, so the safety profile is covered. The description adds genuine behavioral context — findings carry a severity, cite the doc section, and include a suggested fix, and changelogs are excluded — but it does not say whether analysis is post-index only (requiring index_repo first), how expensive a full-repo scan is, or whether results are ordered deterministically. Those gaps keep it at solid-but-partial rather than rich.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Dense and front-loaded: the problem statement, then use cases, then the specific detection categories, then the changelog exclusion. The fragment style in the opening sentence and the semicolon-chained finding list are slightly unruly but every clause carries information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present, the description need not explain return shape, and annotations cover read-only safety; the remaining burden is telling the agent what the tool checks and when to reach for it, which it does. The only shortfall is that it does not state the prerequisite of an indexed repo, which is instead buried in the repo parameter's schema description.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so each of the four parameters is already documented, including repo lookup via list_repos and the 1-200 limit bound. The description adds nothing parameter-specific beyond a vague nod to checking a "docs folder" (path_prefix) and release timing; baseline 3 applies when the schema does all the work.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The opening line names the resource and the problem domain (docs that no longer match code), and the middle of the description enumerates exactly what it detects: missing files/functions/settings/flags, bad parameters, failing imports, stale sections. That is far more specific than a sibling like search or ask_codebase, though it never explicitly contrasts itself with those siblings, and the leading sentence is a noun phrase rather than a verb+resource statement.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

"Use this to check a README or docs folder, or before a release" gives concrete triggering situations, and "Changelogs are skipped" supplies an explicit exclusion. What's missing is naming the alternatives an agent should pick instead when it wants code search or history (search, explain_history) for a drift-adjacent question.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

impact_of_changeA
Read-only

What breaks if a symbol changes: code that uses it directly, code that uses that code, and the tests involved. Use this before editing a shared function, and run or update the tests it lists. Python, JavaScript and TypeScript are analysed structurally. Matches are by name, so check the same-name notes it returns.

NameRequiredDescriptionDefault
pathNoThe file that defines symbol, when several files define that name.
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
depthNo1 = direct users only; 2 or 3 also follows users of those users.
symbolYesThe function, class or method you plan to change, e.g. "discount" or "Cart.total".

Output Schema

NameRequiredDescription
notesYes
testsYesCitations of tests that exercise the target, directly or not.
directYes
symbolYes
targetYespath:start-end of the definition analysed.
summaryYes
indirectYes
same_name_definitionsYes

TDQS

A4.5/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Beyond the readOnlyHint/openWorldHint annotations, it discloses the analysis is structural and limited to Python, JavaScript and TypeScript, and critically that matches are name-based so results may include false positives flagged in 'same-name notes'. Those precision caveats are exactly the behavioral context an agent needs before trusting the output.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, front-loaded with the outcome the agent cares about, then the usage trigger, then the caveat. Every clause carries information: scope, languages, matching caveat, and the test follow-up.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With a full input schema and an output schema present, the description need not explain return shape; it instead spends its space on language coverage, matching limitations, and pre-edit workflow — the pieces not covered by structured fields. Nothing an agent needs to invoke it correctly appears to be missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% and each parameter (path, repo, depth, symbol) already carries its own description, so the schema does the heavy lifting. The description adds no extra syntax or format guidance for depth levels or repo scoping, which is the expected baseline when the schema is fully documented.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific question the tool answers ('What breaks if a symbol changes') and enumerates the exact result classes: direct users, transitive users, and involved tests. That verb-plus-resource framing makes it immediately distinguishable from siblings such as search, ask_codebase, or explain_history.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It gives a concrete trigger ('Use this before editing a shared function') and a follow-up action ('run or update the tests it lists'), which tells the agent when this tool is the right call. It stops short of naming an explicit alternative or exclusion (e.g. when to prefer search or explain_history instead).

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

index_repoA
Idempotent

Index a repository so the other tools can search it. Use this first, and again after the code changes: re-running only re-embeds files whose content changed. A URL is cloned with full history (blobless), so explain_history works. Reports progress while it runs, and returns file counts and the commit indexed.

NameRequiredDescriptionDefault
nameNoName to index it under. Defaults to the folder or repository name.
sourceYesA local directory, or an https git URL such as https://github.com/owner/repo.

Output Schema

NameRequiredDescription
repoYes
rootYes
commitYes
secondsYes
files_seenYes
chunks_totalYes
full_rebuildYes
commits_addedYes
commits_totalYes
files_indexedYesFiles embedded this run (new or changed).
files_removedYes
files_unchangedYes

TDQS

A4.7/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare the mutation/idempotent/open-world profile, but the description adds genuine context beyond them: re-runs only re-embed changed files, URLs are cloned blobless with full history so explain_history works, and progress is reported during the run. The only thing not covered is whether re-indexing can overwrite or drop an existing index under the same name.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Four short sentences, front-loaded with the purpose and the 'use first' rule, then incremental re-index behavior, then clone semantics, then return/progress info. No filler and nothing repeated from the schema.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For an indexing/setup tool with two parameters, an output schema and full annotations, the description covers everything an agent needs to decide to call it, when to re-call it, and what side effects to expect.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3; the description goes slightly beyond by explaining what a URL source actually does (blobless clone with full history), which is behavior an agent needs when choosing between a local path and a remote URL.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The first sentence states a specific verb and resource ('Index a repository') and ties the purpose to the sibling ecosystem ('so the other tools can search it'), immediately distinguishing it from search, ask_codebase, explain_history and the read-only siblings.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explicitly states when to call it ('Use this first') and when to call it again ('again after the code changes'), with the reason re-running is cheap. That ordering constraint is the critical usage fact no sibling name or schema field conveys.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

list_reposA
Read-only

Repositories indexed so far, with their size, languages and the commit they were indexed at. Use this first to see what's available and to get the repo names the other tools take.

NameRequiredDescriptionDefault

No parameters

Output Schema

NameRequiredDescription
resultYes

TDQS

A4.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and closed-world behavior, so the description only needs to add context beyond them. It does so by disclosing the result set is limited to repos already indexed and that entries are tied to a specific indexing commit. It says nothing about empty results or staleness of the index, which keeps it below the top band.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, no filler. The result content is front-loaded and the workflow instruction follows, so an agent can act on the first clause alone.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a no-argument tool with an output schema and read-only annotations, the description covers everything needed to decide to call it and to know what comes back. Return-field detail is legitimately delegated to the output schema.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The tool takes no parameters, so the baseline of 4 applies; there is no input semantics for the description to explain. The description correctly spends its space on output scope instead of inventing parameter detail.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Names a specific verb and resource (list repositories) and states what each entry carries: size, languages, and the commit it was indexed at. The scope phrase 'indexed so far' separates it from index_repo, which is the tool that adds them.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives explicit ordering guidance ('Use this first') and a concrete reason: to obtain the repo names that the other tools require. It does not name a competing alternative or state when-not to call it, but for a zero-argument entry-point tool that guidance is sufficient.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

read_linesA
Read-only

Exact, numbered lines from a file in an indexed repo. Use this to open a citation in full before quoting or editing it, since search results are trimmed snippets. Refuses paths outside the repo.

NameRequiredDescriptionDefault
endYesLast line to return (inclusive).
pathYesThe file, relative to the repo root, as a citation shows it.
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
startYesFirst line to return (1-based).

Output Schema

NameRequiredDescription
resultYes

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true and openWorldHint=false, so the description only needs to add constraints. It does so usefully by stating the tool 'Refuses paths outside the repo', which tells the agent a sandbox boundary exists and invalid paths will error rather than silently resolve. Return-format detail is delegated to the output schema, which is appropriate.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, purpose front-loaded, followed by the use condition and then the safety constraint. No filler and nothing repeated from structured fields.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With annotations and an output schema present, the description covers purpose, trigger, and the repo-boundary constraint, which is enough to call the tool correctly. It leaves unaddressed edge behavior such as out-of-range start/end values or any cap on range size, a minor gap for a read tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so path, start, end, and repo are all already documented in the schema, including 1-based indexing and the inclusive end. The description adds no extra syntax or range semantics beyond that, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Exact, numbered lines from a file in an indexed repo') and scopes it to a repo. It also distinguishes itself from the snippet-based search sibling by noting that 'search results are trimmed snippets'.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives a concrete trigger for use: open a citation in full before quoting or editing it. The alternative (search snippets) is implied clearly, but there is no explicit when-not-to-use guidance, such as preferring search for discovery.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

search_historyA
Read-only

Find commits by what their messages say. Use this to answer "when did we change X?" or "which commit fixed Y?". For the history of one function or file, use explain_history instead.

NameRequiredDescriptionDefault
kNoHow many results to return, 1 to 25.
repoNoName of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed.
queryYesWords from commit messages, e.g. "fix timezone" or "drop python 3.8".

Output Schema

NameRequiredDescription
resultYes

TDQS

A4.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true and openWorldHint=false, so safety is covered. The description adds meaningful behavioral context by scoping the match to commit message text rather than diffs or code, which prevents a likely misuse; it does not discuss ranking or result ordering, but the output schema covers the return shape.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, each earning its place: scope, use cases, and the redirect to an alternative. The key disambiguation is placed after the core purpose but nothing is buried or padded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple three-parameter read-only search with a fully documented schema and an output schema, the description covers purpose, usage, and the nearest competing tool. An agent has everything needed to call it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with k, repo, and query all documented including defaults and the single-repo case, so the schema carries the parameter burden. The description reinforces the query semantics ('words from commit messages') with an example but adds no syntax or format detail beyond what the schema already states.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb and resource -- 'Find commits by what their messages say' -- which immediately separates it from code-content search. It also explicitly names the sibling tool explain_history as the one to use for a different scope, so the agent can discriminate without opening schemas.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It supplies two concrete natural-language questions this tool answers ('when did we change X?', 'which commit fixed Y?') and an explicit when-not rule routing function/file history to explain_history. Both the use case and the alternative are stated, leaving nothing to inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 8 tool updatesv0.2.1
    • Changedask_codebase3 fields changed
      • addedInput schema / properties / k / description
        Added value: +"How many results to return, 1 to 25."
      • addedInput schema / properties / question / description
        Added value: +"A question in plain words, e.g. \"How are sessions expired?\""
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
    • Changedexplain_history6 fields changed
      • addedInput schema / properties / end_line / description
        Added value: +"Last line of the range (with path)."
      • addedInput schema / properties / max_commits / description
        Added value: +"How many commits to return, newest first."
      • addedInput schema / properties / path / description
        Added value: +"A file in the repo. Narrow it with start_line and end_line."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
      • addedInput schema / properties / start_line / description
        Added value: +"First line of the range (with path)."
      • addedInput schema / properties / symbol / description
        Added value: +"A function, class or method, e.g. \"unsign\" or \"Signer.sign\". Use this or path."
    • Changedfind_doc_drift4 fields changed
      • addedInput schema / properties / check_history / description
        Added value: +"Also flag doc sections last edited long before the code they describe."
      • addedInput schema / properties / limit / description
        Added value: +"Most findings to return, 1 to 200, most severe first."
      • addedInput schema / properties / path_prefix / description
        Added value: +"Only consider files under this path, e.g. \"src/auth/\" or \"docs/\"."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
    • Changedimpact_of_change4 fields changed
      • addedInput schema / properties / depth / description
        Added value: +"1 = direct users only; 2 or 3 also follows users of those users."
      • addedInput schema / properties / path / description
        Added value: +"The file that defines symbol, when several files define that name."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
      • addedInput schema / properties / symbol / description
        Added value: +"The function, class or method you plan to change, e.g. \"discount\" or \"Cart.total\"."
    • Changedindex_repo2 fields changed
      • addedInput schema / properties / name / description
        Added value: +"Name to index it under. Defaults to the folder or repository name."
      • addedInput schema / properties / source / description
        Added value: +"A local directory, or an https git URL such as https://github.com/owner/repo."
    • Changedread_lines4 fields changed
      • addedInput schema / properties / end / description
        Added value: +"Last line to return (inclusive)."
      • addedInput schema / properties / path / description
        Added value: +"The file, relative to the repo root, as a citation shows it."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
      • addedInput schema / properties / start / description
        Added value: +"First line to return (1-based)."
    • Changedsearch5 fields changed
      • addedInput schema / properties / k / description
        Added value: +"How many results to return, 1 to 25."
      • addedInput schema / properties / kinds / description
        Added value: +"Only these chunk kinds: function, class, method, interface, type, enum, module, section (docs) or code (other files)."
      • addedInput schema / properties / path_prefix / description
        Added value: +"Only consider files under this path, e.g. \"src/auth/\" or \"docs/\"."
      • addedInput schema / properties / query / description
        Added value: +"An identifier (normalizeRetryOptions) or plain words."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
    • Changedsearch_history3 fields changed
      • addedInput schema / properties / k / description
        Added value: +"How many results to return, 1 to 25."
      • addedInput schema / properties / query / description
        Added value: +"Words from commit messages, e.g. \"fix timezone\" or \"drop python 3.8\"."
      • addedInput schema / properties / repo / description
        Added value: +"Name of an indexed repo, as list_repos shows it. Leave out when only one repo is indexed."
  2. 9 tool updatesv0.2.0
    • First observedask_codebase
    • First observedexplain_history
    • First observedfind_doc_drift
    • First observedimpact_of_change
    • First observedindex_repo
    • First observedlist_repos
    • First observedread_lines
    • First observedsearch
    • First observedsearch_history

TDQS

A4.1/5.0

Scored across 9 tools

Disambiguation5/5

Each tool has a clearly distinct role: indexing, targeted search, prose Q&A, history explanation, impact analysis, doc drift, commit-message search, line reading, and repo listing. The descriptions explicitly route agents between overlapping-sounding tools, such as search vs. ask_codebase and explain_history vs. search_history.

Naming Consistency4/5

Most tools follow a clear verb_noun pattern: index_repo, ask_codebase, explain_history, find_doc_drift, search_history, read_lines, list_repos. Minor deviations are the bare search and noun-phrase impact_of_change, but the set remains predictable and readable.

Tool Count5/5

Nine tools is well-scoped for a codebase indexing and intelligence server. Each tool covers a meaningful operation without obvious redundancy or bloat.

Completeness4/5

The surface covers indexing, discovery, search, Q&A, history, impact analysis, doc drift, and exact file reading, which supports the core workflows. Minor lifecycle gaps remain, such as no explicit repo removal or unindex operation, but agents can work around them.

Maintenance

ActivityMaintained
ResponsivenessNo recent community issues

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