MCP Server Management

Expert knowledge for managing Model Context Protocol (MCP) servers on a project-by-project basis, with support for runtime management, OAuth remote servers, and dynamic server discovery.

For server config examples, the OAuth deep-dive, dynamic-discovery detail, troubleshooting scripts, and full configuration-pattern examples, see REFERENCE.md.

When to Use This Skill

Use this skill when...	Use configure-mcp instead when...
Understanding MCP architecture and concepts	Setting up .mcp.json for a new project
Managing servers at runtime (enable/disable)	Installing new servers interactively
Setting up OAuth remote MCP servers	Running compliance checks on MCP configuration
Troubleshooting connection failures	Adding specific servers from the registry
Implementing list_changed dynamic discovery	Generating project standards reports

MCP Architecture Overview

MCP connects Claude Code to external tools and data sources via two transport types:

Transport	Usage	Auth	Configuration
Stdio (local)	Command-based servers via npx, bunx, uvx, go run	None needed	.mcp.json
HTTP+SSE (remote)	URL-based servers hosted externally	OAuth 2.1	.mcp.json with url field

Local servers declare a command + args; remote servers declare a url + headers (with ${VAR_NAME} token references, never hardcoded). See REFERENCE.md → Server configuration examples.

Runtime Server Management

/mcp Commands (Claude Code 2.1.50+)

Manage servers without editing configuration files:

Command	Description
/mcp	List all configured MCP servers and their connection status
/mcp enable <server>	Enable a server for the current session
/mcp disable <server>	Disable a server for the current session (session-scoped only)

Note: Enable/disable are session-scoped. Edit .mcp.json for permanent changes.

Check Server Status

jq -r '.mcpServers | keys[]' .mcp.json   # List configured servers
jq '.mcpServers.context7' .mcp.json      # Verify a server's config

OAuth Remote Servers (2.1.50+)

Remote HTTP+SSE servers use OAuth 2.1: Claude Code discovers metadata from /.well-known/oauth-authorization-server (cached per URL), the user authorizes in-browser once, and step-up auth re-prompts when a tool needs elevated scope. To refresh stale OAuth config, /mcp disable then /mcp enable the server. Full flow, step-up detail, and caching behavior in REFERENCE.md → OAuth support.

Dynamic Tool Discovery (list_changed)

Servers declaring {"tools": {"listChanged": true}} push notifications/tools/list_changed when their tool set changes, and Claude Code refreshes that server's tools without a session restart — useful for servers exposing project-context-specific tools. Same pattern for resources and prompts. Subscription is automatic; no client config needed. See REFERENCE.md → Dynamic tool discovery.

Troubleshooting

Common failure modes and the diagnostic scripts for each (server won't connect, missing env vars, OAuth issues, the SDK MCP race condition) are in REFERENCE.md → Troubleshooting scripts. Quick OAuth triage:

Symptom	Likely Cause	Action
Authorization prompt repeats	Token not persisted	Check token storage permissions
Step-up auth loop	Scope mismatch	Revoke and re-authorize
Discovery fails	Server down or URL wrong	Verify server URL and connectivity
Cache stale	Server changed OAuth config	Disable/enable server to refresh

Configuration Patterns

Three scopes, each with a worked .mcp.json / settings.json / plugin.json example in REFERENCE.md → Configuration patterns:

• Project-scoped (recommended) — .mcp.json at project root; .gitignore it for personal configs or track for team configs.
• User-scoped (personal) — ~/.claude/settings.json for servers available everywhere.
• Plugin-scoped — declared in plugin.json (or referenced via "mcpServers": "./.mcp.json").

Agentic Optimizations

Context	Command
Quick status check	jq -c '.mcpServers | keys' .mcp.json 2>/dev/null
Validate JSON	jq empty .mcp.json 2>&1
List env vars needed	jq -r '.mcpServers[] | .env // {} | keys[]' .mcp.json 2>/dev/null | sort -u
Check specific server	jq -e '.mcpServers.context7' .mcp.json >/dev/null 2>&1 && echo "installed"
Find servers in plugin	find . -name '.mcp.json' -maxdepth 2

Quick Reference

Server Types by Transport

Type	When to Use	Example
command (stdio)	Local tools, no auth needed	bunx, npx, uvx, go run
url (HTTP+SSE)	Remote hosted servers, OAuth needed	https://...

Key Files

File	Purpose
.mcp.json	Project-level MCP server config (team-shareable)
~/.claude/settings.json	User-level MCP server config (personal)
plugin.json	Plugin-level MCP server declarations