hermes-agent/website/docs/reference/mcp-config-reference.md

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8	MCP Config Reference	Reference for Hermes Agent MCP configuration keys, filtering semantics, and utility-tool policy

MCP Config Reference

This page is the compact reference companion to the main MCP docs.

For conceptual guidance, see:

• MCP (Model Context Protocol)
• Use MCP with Hermes

Root config shape

mcp_servers:
  <server_name>:
    command: "..."      # stdio servers
    args: []
    env: {}

    # OR
    url: "..."          # HTTP servers
    headers: {}

    # Optional HTTP/SSE TLS settings:
    ssl_verify: true                # bool or path to a CA bundle (PEM)
    client_cert: "/path/to/cert.pem"  # mTLS client certificate (see below)
    # client_key: "/path/to/key.pem"  # optional, when key lives in a separate file

    enabled: true
    timeout: 120
    connect_timeout: 60
    supports_parallel_tool_calls: false
    tools:
      include: []
      exclude: []
      resources: true
      prompts: true

Server keys

Key	Type	Applies to	Meaning
command	string	stdio	Executable to launch
args	list	stdio	Arguments for the subprocess
env	mapping	stdio	Environment passed to the subprocess
url	string	HTTP	Remote MCP endpoint
headers	mapping	HTTP	Headers for remote server requests
ssl_verify	bool or string	HTTP	TLS verification. true (default) uses system CAs, false disables verification (insecure), or a string path to a custom CA bundle (PEM)
client_cert	string or list	HTTP	mTLS client certificate. String = path to a PEM file containing cert + key. List [cert, key] = separate files. List [cert, key, password] = encrypted key
client_key	string	HTTP	Path to the client private key, when client_cert is a string and the key is in a separate file
enabled	bool	both	Skip the server entirely when false
timeout	number	both	Tool call timeout
connect_timeout	number	both	Initial connection timeout
supports_parallel_tool_calls	bool	both	Allow tools from this server to run concurrently
tools	mapping	both	Filtering and utility-tool policy
auth	string	HTTP	Authentication method. Set to oauth to enable OAuth 2.1 with PKCE
sampling	mapping	both	Server-initiated LLM request policy (see MCP guide)

tools policy keys

Key	Type	Meaning
include	string or list	Whitelist server-native MCP tools
exclude	string or list	Blacklist server-native MCP tools
resources	bool-like	Enable/disable list_resources + read_resource
prompts	bool-like	Enable/disable list_prompts + get_prompt

Filtering semantics

include

If include is set, only those server-native MCP tools are registered.

tools:
  include: [create_issue, list_issues]

exclude

If exclude is set and include is not, every server-native MCP tool except those names is registered.

tools:
  exclude: [delete_customer]

Precedence

If both are set, include wins.

tools:
  include: [create_issue]
  exclude: [create_issue, delete_issue]

Result:

• create_issue is still allowed
• delete_issue is ignored because include takes precedence

Utility-tool policy

Hermes may register these utility wrappers per MCP server:

Resources:

• list_resources
• read_resource

Prompts:

• list_prompts
• get_prompt

Disable resources

tools:
  resources: false

Disable prompts

tools:
  prompts: false

Capability-aware registration

Even when resources: true or prompts: true, Hermes only registers those utility tools if the MCP session actually exposes the corresponding capability.

So this is normal:

• you enable prompts
• but no prompt utilities appear
• because the server does not support prompts

enabled: false

mcp_servers:
  legacy:
    url: "https://mcp.legacy.internal"
    enabled: false

Behavior:

• no connection attempt
• no discovery
• no tool registration
• config remains in place for later reuse

Empty result behavior

If filtering removes all server-native tools and no utility tools are registered, Hermes does not create an empty MCP runtime toolset for that server.

Example configs

Safe GitHub allowlist

mcp_servers:
  github:
    command: "npx"
    args: ["-y", "@modelcontextprotocol/server-github"]
    env:
      GITHUB_PERSONAL_ACCESS_TOKEN: "***"
    tools:
      include: [list_issues, create_issue, update_issue, search_code]
      resources: false
      prompts: false

Stripe blacklist

mcp_servers:
  stripe:
    url: "https://mcp.stripe.com"
    headers:
      Authorization: "Bearer ***"
    tools:
      exclude: [delete_customer, refund_payment]

Resource-only docs server

mcp_servers:
  docs:
    url: "https://mcp.docs.example.com"
    tools:
      include: []
      resources: true
      prompts: false

TLS client certificate (mTLS)

For HTTP/SSE servers that require a client certificate, set client_cert (and optionally client_key):

mcp_servers:
  # Combined cert + key in a single PEM file
  internal_api:
    url: "https://mcp.internal.example.com/mcp"
    client_cert: "~/secrets/mcp-client.pem"

  # Separate cert and key files
  partner_api:
    url: "https://mcp.partner.example.com/mcp"
    client_cert: "~/secrets/client.crt"
    client_key: "~/secrets/client.key"

  # Encrypted key with a passphrase (3-element list form)
  bank_api:
    url: "https://mcp.bank.example.com/mcp"
    client_cert: ["~/secrets/client.crt", "~/secrets/client.key", "my-passphrase"]

  # Custom CA bundle (private CA / self-signed server)
  lab_api:
    url: "https://mcp.lab.local/mcp"
    ssl_verify: "~/secrets/lab-ca.pem"
    client_cert: "~/secrets/lab-client.pem"

Notes:

• Paths support ~ expansion. Missing files fail fast at connect time with a server-scoped error message.
• ssl_verify: false disables server certificate verification entirely. Don't use this with real services.
• Works on both Streamable HTTP and SSE transports.

Reloading config

After changing MCP config, reload servers with:

/reload-mcp

Tool naming

Server-native MCP tools become:

mcp_<server>_<tool>

Examples:

• mcp_github_create_issue
• mcp_filesystem_read_file
• mcp_my_api_query_data

Utility tools follow the same prefixing pattern:

• mcp_<server>_list_resources
• mcp_<server>_read_resource
• mcp_<server>_list_prompts
• mcp_<server>_get_prompt

Name sanitization

Hyphens (-) and dots (.) in both server names and tool names are replaced with underscores before registration. This ensures tool names are valid identifiers for LLM function-calling APIs.

For example, a server named my-api exposing a tool called list-items.v2 becomes:

mcp_my_api_list_items_v2

Keep this in mind when writing include / exclude filters — use the original MCP tool name (with hyphens/dots), not the sanitized version.

OAuth 2.1 authentication

For HTTP servers that require OAuth, set auth: oauth on the server entry:

mcp_servers:
  protected_api:
    url: "https://mcp.example.com/mcp"
    auth: oauth

Behavior:

• Hermes uses the MCP SDK's OAuth 2.1 PKCE flow (metadata discovery, dynamic client registration, token exchange, and refresh)
• On first connect, a browser window opens for authorization
• Tokens are persisted to ~/.hermes/mcp-tokens/<server>.json and reused across sessions
• Token refresh is automatic; re-authorization only happens when refresh fails
• Only applies to HTTP/StreamableHTTP transport (url-based servers)