Plugin Best Practices Advanced

Guidelines for building robust, secure, and maintainable Claude Code plugin configurations that work well for individuals and teams.

Plugin Architecture Decisions

Need Use This Not This
Auto-format after edits Hooks (postToolUse) Custom MCP server
Database access MCP server with read-only user Bash tool with raw SQL
Team workflows Custom commands (.claude/commands/) Shared shell scripts
Third-party API access MCP server with auth handling Bash with curl and hardcoded tokens
Editor integration Official VS Code extension Custom terminal wrapper

Security Considerations

🔑

Secrets Management

Never commit API keys, tokens, or credentials. Use environment variable references in configuration and set values in your shell profile or .env files excluded from git.

🛡

Least Privilege

MCP servers should have minimal permissions. Use read-only database users, scoped API tokens, and restricted file system access.

🔎

Input Validation

Custom tools must validate all inputs. Never pass user-provided strings directly to SQL queries, shell commands, or API calls without sanitization.

📋

Audit Trail

Log all tool invocations, especially for destructive operations. Include timestamps, parameters, and results in your logs.

Critical: Hooks run shell commands with your user permissions. A malicious or poorly written hook could delete files, leak credentials, or modify system settings. Always review hook configurations carefully, especially in shared projects.

Performance Impact

  • Hooks are synchronous - Claude Code waits for each hook to finish. Keep hook commands under 2 seconds. For slow operations, use & to run in the background.
  • MCP servers run as separate processes - Each server consumes memory. On resource-constrained machines, limit the number of active servers.
  • Tool definitions consume tokens - Every MCP tool's description is included in Claude's context. More tools = more overhead per request.
Optimization: Only configure MCP servers you actually need for the current project. Use project-level .mcp.json instead of user-level configuration to keep irrelevant servers from loading.

Team Plugin Sharing

Recommended Project Structure 
project-root/
  .claude/
    commands/              # Custom slash commands (git-tracked)
      deploy.md
      code-review.md
      test-all.md
    settings.json          # Project-level hooks (git-tracked)
  .mcp.json                # MCP server config (git-tracked, no secrets)
  .env                     # API keys and tokens (git-ignored!)
  .env.example             # Template for .env (git-tracked)
  CLAUDE.md                # Project context (git-tracked)

Debugging Plugins

  1. Use /doctor for diagnostics

    Claude Code's /doctor command checks your configuration and reports issues with MCP servers, permissions, and settings.

  2. Test hooks manually

    Run the hook command directly in your terminal with test values for environment variables to verify it works outside of Claude Code.

  3. Check MCP server logs

    MCP servers may log errors to stderr. Check ~/.claude/logs/ for server connection issues.

  4. Validate JSON configuration

    A single misplaced comma in settings.json or .mcp.json can break all plugins. Use a JSON validator.

Common Pitfalls

⚠

Committing Secrets

Accidentally committing .mcp.json with hardcoded API keys. Always use environment variable references and add .env to .gitignore.

⚠

Slow Hooks

Hooks that run linters on the entire project instead of just the changed file. Always scope hook commands to the specific file being changed.

⚠

Too Many MCP Servers

Loading 10+ MCP servers means 10+ processes and potentially hundreds of tool descriptions in context. Only configure what you need.

⚠

Not Testing After Updates

Claude Code updates may change hook behavior or MCP protocol versions. Re-test your plugins after major Claude Code updates.

Frequently Asked Questions

Can I disable a hook temporarily?

You can comment out hook entries in your settings.json (JSON does not support comments, so you would need to remove and re-add them) or rename the settings file temporarily. There is no built-in toggle mechanism.

Do MCP servers persist between Claude Code sessions?

No. MCP servers are started when Claude Code launches and stopped when it exits. They do not run in the background. Each new Claude Code session starts fresh MCP server instances.

Can I use MCP servers from Docker containers?

Yes. Set the command to docker run with the appropriate image. This is useful for MCP servers that require specific dependencies or isolation.

How do I share MCP server configurations across multiple projects?

Use user-level configuration (~/.claude/claude_desktop_config.json) for MCP servers you want available everywhere. Use project-level .mcp.json for project-specific servers.

Are there performance benchmarks for hooks?

As a guideline, hooks should complete in under 2 seconds. Formatting a single file with Prettier takes ~200ms, ESLint takes ~500ms. If your hook takes longer, consider running it in the background or scoping it more narrowly.

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