Three-Tier Architecture
Tier 1: Built-in MCPs
Source:
Type: Remote HTTP
Servers: websearch, context7, grep_app
Management: Plugin-managed, always available
src/mcp/Type: Remote HTTP
Servers: websearch, context7, grep_app
Management: Plugin-managed, always available
Tier 2: Claude Code MCPs
Source:
Type: stdio or HTTP
Management: Environment variable expansion (
Loader:
.mcp.jsonType: stdio or HTTP
Management: Environment variable expansion (
${VAR})Loader:
claude-code-mcp-loaderBuilt-in MCPs
websearch
URL:https://mcp.exa.ai/mcp (default) or https://mcp.tavily.com/mcp/Provider: Exa (default) or Tavily
Auth: Optional (
EXA_API_KEY or TAVILY_API_KEY)
Configuration
Configuration
Default (Exa):With API Key (Exa):Tavily Provider:Source:
src/mcp/websearch.ts:11websearch_web_search_exa- Web search with Exa/Tavily
- Documentation discovery
- Latest information retrieval
- Site verification
- Release notes lookup
context7
URL:https://mcp.context7.com/mcpAuth: Optional (
CONTEXT7_API_KEY)Purpose: Library documentation lookup
Configuration
Configuration
No Authentication (Public docs):With Authentication:Source:
src/mcp/context7.ts:1context7_resolve-library-id- Resolve library name to IDcontext7_query-docs- Query library documentationcontext7_get-library-docs- Get full library docs
grep_app
URL:https://mcp.grep.appAuth: None required
Purpose: GitHub code search
Configuration
Configuration
No Configuration Needed:Source:
src/mcp/grep-app.ts:1grep_app_searchGitHub- Search GitHub repositories for code patterns
Disabling Built-in MCPs
Claude Code MCPs (.mcp.json)
Configuration Format
Environment Variable Expansion
Supported patterns:${VAR}- Required variable (throws if missing)${VAR:-default}- Optional with default value
src/features/claude-code-mcp-loader/env-expander.ts
Loader Implementation
Source:src/features/claude-code-mcp-loader/ (5 files)
Loader Files
Loader Files
loader.ts- Main loader logictransformer.ts- Config transformationenv-expander.ts-${VAR}expansiontypes.ts- Type definitionsindex.ts- Barrel exports
Skill-embedded MCPs
SKILL.md Configuration
SkillMcpManager
Source:src/features/skill-mcp-manager/manager.ts:9
Manages per-session MCP client lifecycle.
Connection Types
Connection Files
Source:src/features/skill-mcp-manager/
Connection Implementation (10 files)
Connection Implementation (10 files)
connection.ts- Client factorystdio-client.ts- stdio connectionhttp-client.ts- HTTP connectionoauth-handler.ts- OAuth 2.0 + PKCE flowcleanup.ts- Session cleanupconnection-type.ts- Connection type detectionenv-cleaner.ts- Environment variable sanitizationtypes.ts- Type definitionsmanager.ts- SkillMcpManager classindex.ts- Barrel exports
MCP OAuth Support
Source:src/features/mcp-oauth/ (10 files, HIGH complexity)
Supports OAuth 2.0 with PKCE and Dynamic Client Registration (RFC 7591).
OAuth Flow
Configuration
MCP Tool Permissions
Restrict MCP tools per agent:Doctor Check
Verify MCP configuration:- Built-in MCPs connectivity
- Claude Code
.mcp.jsonvalidity - Environment variable availability
- Skill-embedded MCP configurations
src/cli/doctor/checks/tools-mcp.ts
Source Files
Built-in MCPs (6 files)
Built-in MCPs (6 files)
src/mcp/index.ts- createBuiltinMcps factorysrc/mcp/websearch.ts- Exa/Tavily configurationsrc/mcp/context7.ts- Context7 configurationsrc/mcp/grep-app.ts- Grep.app configurationsrc/mcp/types.ts- McpNameSchemasrc/config/schema/websearch.ts- Websearch config schema
Claude Code MCP Loader (5 files)
Claude Code MCP Loader (5 files)
src/features/claude-code-mcp-loader/loader.tssrc/features/claude-code-mcp-loader/transformer.tssrc/features/claude-code-mcp-loader/env-expander.tssrc/features/claude-code-mcp-loader/types.tssrc/features/claude-code-mcp-loader/index.ts
Skill MCP Manager (10 files)
Skill MCP Manager (10 files)
src/features/skill-mcp-manager/manager.tssrc/features/skill-mcp-manager/connection.tssrc/features/skill-mcp-manager/stdio-client.tssrc/features/skill-mcp-manager/http-client.tssrc/features/skill-mcp-manager/oauth-handler.tssrc/features/skill-mcp-manager/cleanup.tssrc/features/skill-mcp-manager/connection-type.tssrc/features/skill-mcp-manager/env-cleaner.tssrc/features/skill-mcp-manager/types.tssrc/features/skill-mcp-manager/index.ts
MCP OAuth (10 files)
MCP OAuth (10 files)
src/features/mcp-oauth/- OAuth 2.0 + PKCE + DCR (RFC 7591)
Related
Skills
Skill system with embedded MCPs
Tools
26 tools including MCP tool wrappers