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How to Document MCP Repositories Effectively: A Practical Playbook

#MCP #documentation #developer docs #technical writing #open source #repo structure #API design #tooling
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How to Document MCP Repositories Effectively: A Practical Playbook

Stop losing contributors to vague READMEs. Here’s a practical recipe to document MCP repos the right way.

Why MCP documentation is different

Documenting a Model Context Protocol (MCP) repository isn’t the same as describing a typical API or CLI. You’re explaining a contract between a client (often an LLM-aware runtime or IDE) and a server capable of exposing tools, resources, prompts, and models via a consistent protocol. The audience is a mix: developers integrating your server into clients, maintainers extending it, and security reviewers verifying data flows and permissions. Great docs must cover three layers:

  • What it does: capabilities and example use
  • How it works: protocol versions, transports, schemas
  • How to trust it: security, limits, and failure modes

The single source of truth: a top-tier README

Your README is the front door. Use a predictable structure so people find answers fast. A proven scaffold:

  1. Name and purpose
  2. Badge row (license, CI, latest release)
  3. Compatibility overview (MCP version, client matrix)
  4. Quickstart (install, run, verify)
  5. Configuration (env vars, files, auth)
  6. Capabilities (tools/resources/prompts/models)
  7. Examples (requests and responses)
  8. Development (run tests, lint, format)
  9. Security (permissions, data egress, secrets)
  10. Troubleshooting (common errors)
  11. Versioning and changelog
  12. Contributing and code of conduct
  13. License

A short mission statement belongs at the top. Avoid vague claims. Make it clear what your MCP server or client unlocks and who should use it.

State the contract: protocol and compatibility

Every MCP repository should declare:

  • Protocol version supported (e.g., MCP 1.2)
  • Feature support: tools, resources, prompts, models, streaming, cancellation
  • Transport(s): stdio, WebSocket, HTTP
  • Client compatibility: which clients and versions you test against
  • Platform support: Linux, macOS, Windows; CPU/ARM; container support

Spell out breaking changes and deprecations. If you maintain multiple branches for protocol versions, document which branch fits which client versions and how long you’ll support each line.

Be explicit about transports and runtime expectations

MCP tolerates different transports; your docs must pin down what you actually implement:

  • Stdio: how the process is launched, I/O framing, expected cwd
  • WebSocket: URL path, subprotocols, auth headers, TLS guidance
  • HTTP: endpoints, content type, streaming, CORS rules

Document resource limits and defaults:

  • Max request size
  • Streaming chunk size and cadence
  • Timeouts and keepalive settings
  • Recommended memory/CPU for production

Include one “hello world” handshake transcript per transport so readers can see the opening messages.

Capabilities: document tools, resources, prompts, and models

Treat each capability like a mini-API with examples and guarantees.

  • Tools: name, description, JSON Schema for input, output format, side-effects, idempotency, latency profile, rate limits, permissions required
  • Resources: discovery rules, path patterns, supported read/write ops, paging or streaming
  • Prompts: placeholders, variables, default values, constraints
  • Models: selection rules, sampling options, token limits, known quirks

For tools, favor JSON Schema examples with both minimal and complete payloads. Include at least one error example per tool, with guidance on retries or fallbacks.

Write JSON Schema like you mean it

Schemas are executable documentation. Make them clear and enforceable:

  • Give every schema an $id and version in a dedicated schemas/ directory
  • Use $defs for shared types (e.g., Pagination, FilePath, URL)
  • Provide examples and defaults
  • Use format (uri, email, date-time) and pattern responsibly
  • Constrain with minimum, maximum, minLength, maxLength
  • Explain enum choices in descriptions
  • Document nullability and backward-compatible additions

Example:

{
	"$id": "https://example.org/schemas/tools/summarize.v1.json",
	"$schema": "https://json-schema.org/draft/2020-12/schema",
	"title": "summarize",
	"type": "object",
	"additionalProperties": false,
	"properties": {
		"text": {
			"type": "string",
			"minLength": 1,
			"description": "Plaintext to summarize."
		},
		"max_sentences": {
			"type": "integer",
			"minimum": 1,
			"maximum": 10,
			"default": 3,
			"description": "Cap the summary length."
		}
	},
	"required": ["text"],
	"examples": [{ "text": "Long article...", "max_sentences": 2 }]
}

Explain how you version schemas and how the server chooses the right version.

Configuration: names, formats, and safe defaults

Reduce guesswork with explicit configuration docs:

  • Environment variables: names, default values, examples
  • Config files: path, format (JSON/YAML/TOML), precedence rules
  • Secrets: how to provide (env vars, secret managers), never commit, local dev tips
  • Profiles: dev vs prod settings, toggles for verbose logs, mock modes

Template:

# .env
MCP_SERVER_PORT=8080
MCP_TRANSPORT=ws
MCP_ALLOWED_ORIGINS=https://localhost:3000
THIRD_PARTY_API_KEY=...
LOG_LEVEL=info

Document how configuration is validated at startup and what happens when it’s invalid.

Authentication, authorization, and sensitive scopes

Security reviewers need crisp answers:

  • What secrets are required (API keys, OAuth tokens)
  • Where tokens are stored in memory and at rest
  • Which scopes are requested and why
  • How consent is surfaced to users in clients
  • Data egress destinations (domains, ports)
  • Least-privilege recommendations
  • Rotation and revocation steps

If your server can perform file operations or network calls on behalf of the user, say so loudly. Provide a permission map: capability → required privileges → user prompts.

Usage examples that actually run

Show concrete invocations with common clients or curl-esque requests for HTTP:

// tools/list response (excerpt)
{
	"tools": [
		{
			"name": "summarize",
			"description": "Create a short summary from longer text.",
			"input_schema": "https://example.org/schemas/tools/summarize.v1.json"
		}
	]
}
// tools/call request (excerpt)
{
	"name": "summarize",
	"arguments": { "text": "Article text...", "max_sentences": 2 }
}

Then show the matching response. Include one error pathway with an actionable fix.

Observability: logs, metrics, and tracing

Docs should teach users to see what the server is doing:

  • Log format (structured JSON vs text), levels, redact rules
  • Request IDs and correlation IDs propagated across messages
  • Metrics (latency per tool, error rates, queue depth)
  • Optional tracing (OpenTelemetry setup, context propagation)
  • Where logs go by default and how to redirect them

Provide a one-liner to toggle verbose diagnostic output for bug reports.

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Performance and limits

Make performance expectations predictable:

  • Cold start and warm latency targets
  • Concurrency model and default worker counts
  • Rate limits per tool and per user
  • Timeouts and retry policies, both inbound and outbound
  • Max payload sizes and streaming back-pressure behavior
  • Memory spikes and known hotspots

Add a “Sizing” section with simple rules of thumb for small, medium, and large deployments.

Error model and failure semantics

Ambiguous errors erode trust. Standardize:

  • Error types with stable codes and human messages
  • Which errors are retryable and suggested backoff
  • Partial successes and how they’re signaled
  • Cancellation semantics and what cleanup occurs
  • Idempotency guarantees and request deduplication

Map internal failures to protocol-level errors clearly and consistently.

File layout and documentation assets

A clean repo teaches by structure. Consider:

  • README.md as the entry point
  • docs/ for guides (capabilities.md, security.md, transports.md)
  • schemas/ with versioned JSON Schemas and a README of the release policy
  • examples/ containing runnable demos and fixtures
  • tests/ contract tests targeting protocol behavior
  • .github/ with PR templates, issue templates, workflows
  • CHANGELOG.md for human-readable changes
  • CONTRIBUTING.md, CODE_OF_CONDUCT.md, SECURITY.md

Link these from the main README so nothing is buried.

Development, testing, and contract checks

Reduce maintenance friction with documented test strategies:

  • Unit tests for handlers and schema validation
  • Contract tests that exercise the MCP handshake and capability discovery
  • Golden files for stable responses (when appropriate)
  • Integration tests against the most-used clients
  • Fuzz tests for schema-driven inputs
  • CI matrix: OS, language versions, protocol versions

Include commands to run the full test suite locally and a description of CI gates.

Versioning, releases, and migrations

Use SemVer and make it visible:

  • How you bump versions for protocol-level changes vs internal fixes
  • Release cadence and how releases are tagged
  • Release notes highlighting deprecations, new capabilities, migration steps
  • Deprecation policy with dates and code paths
  • Checklist for releasing (tests, docs updated, schema IDs bumped)

Pin dependency ranges to avoid surprise breaks and document any known incompatible versions upstream.

Security policy and disclosures

Add a SECURITY.md and reference it in the README:

  • Supported versions for security fixes
  • How to report vulnerabilities (private channels, response window)
  • Safe harbor language for good-faith research
  • Dependency scanning instructions for contributors
  • Hardening guidance (sandboxing, file system isolation, outbound allowlists)

If your server accesses local files or systems, document sandbox defaults and how to confine them.

Troubleshooting that solves real problems

A good troubleshooting section is more than a few tips. For each common error, document:

  • The exact error message or symptom
  • Why it happens
  • How to diagnose (command, log filter)
  • How to fix it
  • How to prevent it in the future

Examples:

  • “Client cannot discover tools” → schema URL not reachable; fix by vendoring schemas or enabling CORS
  • “Schema mismatch error” → client cached old schema; clear cache or bump schema $id
  • “WebSocket disconnects” → proxy idle timeout; increase keepalive

Practical templates you can copy

Offer templates in the repo that people can reuse and adapt.

README boilerplate snippet:

# Project Name

Short purpose statement.

## Compatibility

- MCP version: 1.2
- Transports: stdio, ws
- Tested clients: ClientA vX, ClientB vY

## Quickstart

1. Install...
2. Run...
3. Verify with tools/list...

Issue templates for bug reports should prompt for protocol version, transport, logs, and minimal reproduction steps.

Document the human workflow, not just the code

People maintain your MCP repo. Explain:

  • How to set up a dev environment from scratch
  • How to run a single capability in isolation
  • How to stage a schema change and cut a pre-release
  • Who reviews what and in what order
  • How to get a test account for third-party services

A small “Maintainer’s Guide” in docs/ pays for itself quickly.

Keep docs in sync with automation

Stale docs are worse than no docs. Add automation:

  • CI check that fails if schemas change without updating docs
  • Script that generates a tools catalog from schemas
  • Doc coverage checklist in PR template
  • Link checkers and schema validators wired into CI
  • Periodic job that runs client compatibility smoke tests

Small bots can rebuild examples/ when schemas or handlers evolve.

Accessibility and clarity for mixed audiences

Because MCP sits at the boundary between LLM tooling and classic software stacks, don’t assume prior knowledge. Explain jargon once. Add diagrams showing:

  • Client ↔ transport ↔ server flow
  • Permission prompts and data paths
  • Lifecycle from handshake to teardown

Use clear headings, short paragraphs, and numbered steps. Where choices exist, say which one you recommend and why.

A release-ready checklist

Before you tag a release, confirm the docs are truly shippable:

  • README updated with version and compatibility
  • New or changed schemas carry new $id values
  • Examples verified against the release build
  • Security changes recorded in SECURITY.md
  • CHANGELOG entries include migration notes
  • CI badges are green and links work
  • Issue and PR templates reflect current workflow

When in doubt, add a one-paragraph migration guide per release that touches protocol changes, schema bumps, and behavior changes.

Put it all together

An MCP repository is a living contract. Document the contract first, then the code. Make every capability discoverable, every schema enforceable, and every failure diagnosable. If a new contributor can clone, run, and verify your server in 10 minutes without asking a question, your docs are doing their job. Now go implement the checklist, wire automation to keep it honest, and ship documentation that earns trust.

How to Write Effective Documentation for Your MCP Server Projects How to use MCP servers to generate docs - Mintlify read-docs-mcp | MCP Servers - LobeHub GitMCP - an instant MCP server for any GitHub repo documentation MCP Integration: Streamlining Multi-Repo Development