docs: Added example MCP server allowlisting to the example configuration files

config.agent.example.yaml

@@ -14,7 +14,8 @@
 model: openai:gpt-4o # Specify the LLM to use
 temperature: null # Set default temperature parameter, range (0, 1)
 top_p: null # Set default top-p parameter, with a range of (0, 1) or (0, 2) depending on the model
-reasoning_effort: null           # Reasoning effort level for models that support it (e.g. low, medium, high).
+reasoning_effort:
+  null # Reasoning effort level for models that support it (e.g. low, medium, high).
   # Only valid when the agent's model declares reasoning_levels.
 agent_session: null # Set a session to use when starting the agent. (e.g. temp, default); defaults to globally set agent_session
 name: <agent-name> # Name of the agent, used in the UI and logs
@@ -41,7 +42,8 @@ can_spawn_agents: false          # Enable the agent to spawn child agents
 # Graph agents (graph.yaml) ignore this; they declare spawn targets in agent nodes.
 max_concurrent_agents: 4 # Maximum number of agents that can run simultaneously
 max_agent_depth: 3 # Maximum nesting depth for sub-agents (prevents runaway spawning)
-max_concurrent_jobs: 5           # Max background jobs (`job__*` tools) running at once for this agent
+max_concurrent_jobs:
+  5 # Max background jobs (`job__*` tools) running at once for this agent
   # (overrides the global setting; 0 disables background jobs for this agent)
 inject_spawn_instructions: true # Inject the default agent spawning instructions into the agent's system prompt
 summarization_model: null # Model to use for summarizing sub-agent output (e.g. 'openai:gpt-4o-mini'); defaults to current model
@@ -49,26 +51,34 @@ summarization_threshold: 4000    # Character threshold above which sub-agent out
 escalation_timeout: 300 # Seconds a sub-agent waits for a user interaction response before timing out (default: 5 minutes)
 mcp_servers: # Optional list of MCP servers that the agent utilizes
   - github # Corresponds to the name of an MCP server in the `<coyote-config-dir>/mcp.json` file
+mcp_tools: # Optional per-server tool allowlist for the agent's MCP servers
+  github: # (glob patterns: * and ?). Intersects with the global config,
+    - get_* # mcp.json `allowedTools`, and every other configured layer. It
+    - search_* # can only narrow access, never widen it.
 global_tools: # Optional list of additional global tools to enable for the agent; i.e. not tools specific to the agent
   - web_search
   - fs
   - python
-skills_enabled: true             # Master switch for skills in this agent (default: inherit from global).
+skills_enabled:
+  true # Master switch for skills in this agent (default: inherit from global).
   # Skills also require `function_calling_support: true` in the global config.
 enabled_skills: # Optional list of skills available when this agent runs.
   # Must be a subset of global `visible_skills`. Omit to inherit the global default.
   - git-master
   - ai-slop-remover
-inject_skill_instructions: true  # Inject a short hint pointing the model at `skill__list` when skills are enabled
+inject_skill_instructions:
+  true # Inject a short hint pointing the model at `skill__list` when skills are enabled
   # (default: true). Suppressed automatically when no skills are available.
 skill_instructions: null # Custom text for the skill hint (optional; uses built-in default if null)
 enabled_macros: # Optional list of macros invocable when this agent is active in the REPL.
   - generate-commit-message # An empty list disables all macros. Omit to inherit the role/global default.
-memory: null                     # Per-agent memory override (default: inherit). Set to `false` to disable memory
+memory:
+  null # Per-agent memory override (default: inherit). Set to `false` to disable memory
   # for this agent regardless of workspace/global presence. See the Memory wiki page.
 
 dynamic_instructions: false # Whether to use dynamic instructions for the agent; if false, static instructions are used
-instructions: |                  # Static instructions for the agent; ignored if dynamic instructions are used
+instructions:
+  | # Static instructions for the agent; ignored if dynamic instructions are used
   You are a AI agent designed to demonstrate agent capabilities.
 
   <tools>

config.example.yaml

@@ -2,7 +2,8 @@
 model: openai:gpt-4o # Specify the LLM to use
 temperature: null # Set default temperature parameter (0, 1)
 top_p: null # Set default top-p parameter, with a range of (0, 1) or (0, 2) depending on the model
-reasoning_effort: null           # Reasoning effort level for models that support it (e.g. low, medium, high).
+reasoning_effort:
+  null # Reasoning effort level for models that support it (e.g. low, medium, high).
   # Only valid when the active model declares reasoning_levels. See the Clients docs.
 
 # ---- Behavior ----
@@ -31,10 +32,8 @@ sync_models_url: >               # URL to sync model changes from
 
 # ---- REPL Prompt ----
 # Custom REPL left/right prompts; see the [REPL Prompt Documentation](https://github.com/Dark-Alex-17/coyote/wiki/REPL-Prompt) for more information
-left_prompt:
+left_prompt: '{color.red}{model}){color.green}{?session {?agent {agent}>}{session}{?role /}}{!session {?agent {agent}>}}{role}{?rag @{rag}}{color.cyan}{?session )}{!session >}{color.reset} '
-  '{color.red}{model}){color.green}{?session {?agent {agent}>}{session}{?role /}}{!session {?agent {agent}>}}{role}{?rag @{rag}}{color.cyan}{?session )}{!session >}{color.reset} '
+right_prompt: '{color.cyan}{?reasoning_effort [{reasoning_effort}] }{color.purple}{?session {?consume_tokens {consume_tokens}({consume_percent}%)}{!consume_tokens {consume_tokens}}}{color.reset}'
-right_prompt:
-  '{color.cyan}{?reasoning_effort [{reasoning_effort}] }{color.purple}{?session {?consume_tokens {consume_tokens}({consume_percent}%)}{!consume_tokens {consume_tokens}}}{color.reset}'
 
 # ---- Vault ----
 # See the [Vault documentation](https://github.com/Dark-Alex-17/coyote/wiki/Vault) for more information on the Coyote vault.
@@ -85,7 +84,8 @@ vault_password_file: null        # Path to a file containing the password for th
 function_calling_support: true # Enables or disables function calling (Globally).
 mapping_tools: # Alias for a tool or toolset
   fs: 'fs_cat,fs_ls,fs_mkdir,fs_rm,fs_write,fs_read,fs_glob,fs_grep'
-enabled_tools: null              # Which tools to enable by default.
+enabled_tools:
+  null # Which tools to enable by default.
   # Accepts either a YAML list or a comma-separated string. Use 'all' to enable everything.
   # Example (list form):
   #   enabled_tools:
@@ -129,7 +129,8 @@ visible_tools:                   # Which tools are visible to be compiled (and a
 mcp_server_support: true # Enables or disables MCP servers (globally).
 mapping_mcp_servers: # Alias for an MCP server or set of servers
   git: github,gitmcp
-enabled_mcp_servers: null        # Which MCP servers to enable by default.
+enabled_mcp_servers:
+  null # Which MCP servers to enable by default.
   # Accepts either a YAML list or a comma-separated string. Use 'all' to enable everything.
   # Example (list form):
   #   enabled_mcp_servers:
@@ -137,7 +138,21 @@ enabled_mcp_servers: null        # Which MCP servers to enable by default.
   #     - slack
   # Example (comma-separated form):
   #   enabled_mcp_servers: github,slack,ddg-search
-no_workspace_mcp: false          # Disable loading workspace-local MCP servers (default: false).
+mcp_tools:
+  null # Per-server MCP tool allowlists (glob patterns: * and ? supported).
+  # Tools that match no pattern are hidden from the model as if they
+  # don't exist. Stacks with the other allowlist layers (mcp.json
+  # `allowedTools`, role, agent, session, skill, graph node). Every
+  # configured layer must allow a tool, so layers only ever narrow.
+  # An empty list blocks all of a server's tools.
+  # Example:
+  #   mcp_tools:
+  #     github:
+  #       - get_*
+  #       - list_*
+  #     slack: []
+no_workspace_mcp:
+  false # Disable loading workspace-local MCP servers (default: false).
   # When false (the default), Coyote merges the first workspace MCP config it finds
   # into the global MCP registry at startup, checking in order:
   #   1. .coyote/mcp.json
@@ -149,14 +164,16 @@ no_workspace_mcp: false          # Disable loading workspace-local MCP servers (
 # ---- Skills ----
 # Skills are modular knowledge or capability packs the LLM can load and unload mid-conversation.
 # See the [Skills documentation](https://github.com/Dark-Alex-17/coyote/wiki/Skills) for more details.
-skills_enabled: true              # Master switch. Set to false to hide all skill management tools from the model.
+skills_enabled:
+  true # Master switch. Set to false to hide all skill management tools from the model.
   # Skills also require `function_calling_support: true` above to work at all.
 visible_skills: # The universe of skills allowed to be enabled in any context. Omit (null) for "all installed".
   - ai-slop-remover
   - code-review
   - frontend-ui-ux
   - git-master
-enabled_skills: null              # Which skills are available by default (no role/agent/session active). null = all visible.
+enabled_skills:
+  null # Which skills are available by default (no role/agent/session active). null = all visible.
   # Accepts either a YAML list or a comma-separated string.
   # Example (list form):
   #   enabled_skills:
@@ -164,7 +181,8 @@ enabled_skills: null              # Which skills are available by default (no ro
   #     - ai-slop-remover
   # Example (comma-separated form):
   #   enabled_skills: git-master,ai-slop-remover
-inject_skill_instructions: true   # Inject a short hint pointing the model at `skill__list` when skills are enabled in
+inject_skill_instructions:
+  true # Inject a short hint pointing the model at `skill__list` when skills are enabled in
   # this context. Only injected if `function_calling_support`, `skills_enabled`, and the
   # effective enabled skill set is non-empty (default: true).
 skill_instructions: null # Custom text used for the skill hint when injected. If null, uses built-in default.
@@ -174,7 +192,8 @@ skill_instructions: null          # Custom text used for the skill hint when inj
 # (a macro file named `review.yaml` runs as `.review [args]`; built-in commands always win a name collision).
 # Workspace-local macros in `.coyote/macros/` shadow same-named global macros (skip them with --no-workspace-macros).
 # See the [Macros documentation](https://github.com/Dark-Alex-17/coyote/wiki/Macros) for more details.
-enabled_macros: null              # Which macros are invocable by default (no role/agent/session active). null = all visible.
+enabled_macros:
+  null # Which macros are invocable by default (no role/agent/session active). null = all visible.
   # An empty list means NO macros are invocable. Accepts either a YAML list or a
   # comma-separated string. Roles, agents, and sessions may define their own
   # `enabled_macros`; the most specific active one wins (session > agent > role > global).
@@ -198,9 +217,11 @@ continuation_prompt: null         # Custom prompt used when auto-continuing. If
 # See the [Session documentation](https://github.com/Dark-Alex-17/coyote/wiki/Sessions) for more information
 save_session: null # Controls the persistence of the session. If true, auto save; if false, don't auto-save save; if null, ask the user what to do
 compression_threshold: 4000 # Compress the session when the token count reaches or exceeds this threshold
-summarization_prompt: >          # The text prompt used for creating a concise summary of session message
+summarization_prompt:
+  > # The text prompt used for creating a concise summary of session message
   'Summarize the discussion briefly in 200 words or less to use as a prompt for future context.'
-summary_context_prompt: >        # The text prompt used for including the summary of the entire session as context to the model
+summary_context_prompt:
+  > # The text prompt used for including the summary of the entire session as context to the model
   'This is a summary of the chat history as a recap: '
 compression_keep_last: 0 # Number of most-recent messages to keep visible after compression (0 = compress all messages)
 max_tool_result_chars: null # Cap on tool result characters forwarded to the model per call (null = no cap)
@@ -214,9 +235,11 @@ max_concurrent_jobs: 5           # Max background jobs (`job__*` tools) running
 # Bootstrap with `coyote --init-memory [global|workspace]` to create the marker file
 # the LLM needs before it will write any memory.
 memory: null # null = enabled when memory exists on disk; true = force on; false = force off
-memory_cap_with_tools: null      # Char cap for injected memory when function calling is available (default: 6000).
+memory_cap_with_tools:
+  null # Char cap for injected memory when function calling is available (default: 6000).
   # Only MEMORY.md indexes are injected; the LLM uses memory__read to fetch drill files.
-memory_cap_without_tools: null   # Char cap when function calling is unavailable (default: 12000).
+memory_cap_without_tools:
+  null # Char cap when function calling is unavailable (default: 12000).
   # Indexes plus drill file bodies are injected up to this cap.
 
 # ---- Workspace Instructions ----
@@ -226,7 +249,8 @@ memory_cap_without_tools: null   # Char cap when function calling is unavailable
 # Disable per-invocation with --no-workspace-instructions, or override the chain with
 # repeatable --workspace-instructions-file flags.
 workspace_instructions: null # null/true = inject when an instructions file exists; false = never inject
-workspace_instructions_files: null # File name chain to search, in priority order.
+workspace_instructions_files:
+  null # File name chain to search, in priority order.
   # Default: [COYOTE.md, AGENTS.md, CLAUDE.md, GEMINI.md]
   # Set to a custom list to reorder or drop fallbacks, e.g.:
   #   workspace_instructions_files: [COYOTE.md]
@@ -277,7 +301,8 @@ document_loaders:
   # (see https://pandoc.org for details on how to install pandoc)
   jina: 'curl -fsSL https://r.jina.ai/$1 -H "Authorization: Bearer {{JINA_API_KEY}}' # Use Jina to translate a website into text;
   # Requires a Jina API key to be added to the Coyote vault
-  git: >                                                                                # Use yek to load a git repository into the knowledgebase (https://github.com/bodo-run/yek)
+  git:
+    > # Use yek to load a git repository into the knowledgebase (https://github.com/bodo-run/yek)
     sh -c "yek $1 --json | jq 'map({ path: .filename, contents: .content })'"
 
 # ---- Clients ----
@@ -339,7 +364,8 @@ clients:
   - type: gemini
     api_base: https://generativelanguage.googleapis.com/v1beta
     api_key: '{{GEMINI_API_KEY}}' # You can either hard-code or inject secrets from the Coyote vault
-    auth: null                                          # When set to 'oauth', Coyote will use OAuth instead of an API key
+    auth:
+      null # When set to 'oauth', Coyote will use OAuth instead of an API key
       # Authenticate with `coyote --authenticate` or `.authenticate` in the REPL
     patch:
       chat_completions:
@@ -359,7 +385,8 @@ clients:
   - type: claude
     api_base: https://api.anthropic.com/v1 # Optional
     api_key: '{{ANTHROPIC_API_KEY}}' # You can either hard-code or inject secrets from the Coyote vault
-    auth: null                                          # When set to 'oauth', Coyote will use OAuth instead of an API key
+    auth:
+      null # When set to 'oauth', Coyote will use OAuth instead of an API key
       # Authenticate with `coyote --authenticate` or `.authenticate` in the REPL
 
   # See https://docs.mistral.ai/
@@ -373,7 +400,8 @@ clients:
     name: xai
     api_base: https://api.x.ai/v1
     api_key: '{{XAI_API_KEY}}' # You can either hard-code or inject secrets from the Coyote vault
-    auth: null                                          # When set to 'oauth', Coyote will use OAuth instead of an API key
+    auth:
+      null # When set to 'oauth', Coyote will use OAuth instead of an API key
       # Authenticate with `coyote --authenticate` or `.authenticate` in the REPL
       # Note: Oauth requires SuperGrok/X Premium+ subscription
 
@@ -529,7 +557,6 @@ clients:
     api_base: https://api.deepinfra.com/v1/openai
     api_key: '{{DEEPINFRA_API_KEY}}' # You can either hard-code or inject secrets from the Coyote vault
 
-
   # ----- RAG dedicated -----
 
   # See https://jina.ai

config.role.example.md

@@ -16,6 +16,10 @@ enabled_tools:                        # Tools to enable for this role. Accepts a
 enabled_mcp_servers:                  # MCP servers to enable for this role. Accepts a YAML list (preferred)
   - github                            # or a comma-separated string (e.g. `enabled_mcp_servers: github,gitmcp`).
   - gitmcp                            # Use `all` to enable every configured MCP server.
+mcp_tools:                            # Per-server MCP tool allowlists for this role (globs: * and ?).
+  github:                             # Intersects with the global config / mcp.json `allowedTools`.
+    - get_*                           # Layers only narrow. Tools matching no pattern are hidden from
+    - search_*                        # the model as if they don't exist.
 skills_enabled: true                  # Master switch for skills in this role (default: inherit from global).
                                       # Skills also require `function_calling_support: true` in the global config.
 enabled_skills:                       # Skills available when this role is active. Accepts a YAML list (preferred)

graph.example.yaml

@@ -51,6 +51,10 @@ global_tools:                      # Tool universe an `llm` node's `tools:` whit
 mcp_servers:                       # MCP servers an `llm` node may reference via `mcp:<server>`
   - ddg-search
 
+mcp_tools:                         # Optional per-server tool allowlists (globs: * and ?) applied to
+  ddg-search:                      # every node that uses `mcp:<server>`; intersects with the other
+    - search                       # allowlist layers (global config, agent, mcp.json `allowedTools`).
+
 # ---------------------------------------------------------------------------
 # Skills policy (optional)
 # Skills only attach to `llm` nodes inside a graph. Both fields are optional.
@@ -402,6 +406,9 @@ nodes:
     tools:                     # Narrow whitelist: exactly these entries, nothing else
       - web_search_coyote        #   an exact global-tool / custom-tool name
       - mcp:ddg-search         #   `mcp:<server>` includes that server's functions
+    mcp_tools:                 # Optional per-node narrowing of MCP tools (globs: * and ?)
+      ddg-search:              #   keys must be servers this graph enables; intersects with
+        - search               #   the graph-level mcp_tools above and every other layer
     model: claude:claude-haiku-4-5  # Optional per-node model override
     temperature: 0.3           # Optional per-node sampling override
     reasoning_effort: null     # Optional per-node reasoning effort override (e.g. low, medium, high)