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docs: updated the docs to reflect the new and preferred mcp.json file location

Dark-Alex-17
2026-08-25 14:59:15 -06:00
parent 4d0b0839e3
commit 13ef6b4739
4 changed files with 22 additions and 15 deletions
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Agents.md
+1 -1
@@ -67,7 +67,7 @@ description: <description> # Description of the agent, used in the UI
version: 1 # Version of the agent version: 1 # Version of the agent
# Function Calling Configuration # Function Calling Configuration
mcp_servers: # Optional list of MCP servers that the agent utilizes 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>/functions/mcp.json` file - github # Corresponds to the name of an MCP server in the `<coyote-config-dir>/mcp.json` file
global_tools: # Optional list of additional global tools to enable for the agent; i.e. not tools specific to the agent global_tools: # Optional list of additional global tools to enable for the agent; i.e. not tools specific to the agent
- web_search - web_search
- fs - fs
MCP-Servers.md
+19 -12
@@ -17,18 +17,25 @@ number of configured MCP servers, enabling too many MCP servers may overwhelm th
and quickly exceed token limits. and quickly exceed token limits.
# MCP Server Configuration # MCP Server Configuration
Coyote stores the MCP server configuration file, `functions/mcp.json`, in the `functions` directory. You can find Coyote stores the user-scope MCP server configuration file, `mcp.json`, directly in the Coyote configuration
this directory using the following command: directory (e.g. `~/.config/coyote/mcp.json` on Linux). You can find the resolved location of the file Coyote is
actually using with the following command:
```shell ```shell
coyote --info | grep functions_dir | awk '{print $2}' coyote --info | grep mcp_config_file | awk '{print $2}'
``` ```
The syntax for the `functions/mcp.json` file matches [Claude Code's `.mcp.json` configuration format](https://docs.claude.com/en/docs/claude-code/mcp), > [!NOTE]
> **Historical location:** older Coyote versions stored this file at `functions/mcp.json` inside the `functions`
> directory. That location is still fully supported: if `<config-dir>/mcp.json` does not exist but
> `<config-dir>/functions/mcp.json` does, Coyote keeps using the historical file. Existing installs continue to
> work unchanged, and there is no need to move the file. If both files exist, `<config-dir>/mcp.json` wins.
The syntax for the `mcp.json` file matches [Claude Code's `.mcp.json` configuration format](https://docs.claude.com/en/docs/claude-code/mcp),
with one small difference: the `type` field is **always required** in Coyote, even for stdio servers (Claude Code with one small difference: the `type` field is **always required** in Coyote, even for stdio servers (Claude Code
allows it to be omitted and infers `stdio` from the presence of a `command`). So any time you're looking to add allows it to be omitted and infers `stdio` from the presence of a `command`). So any time you're looking to add
a new server, look at its docs and find the Claude Code configuration example. You should be able to use the a new server, look at its docs and find the Claude Code configuration example. You should be able to use the
exact same configuration in your `functions/mcp.json` file. Just make sure every entry has an explicit `type`. exact same configuration in your `mcp.json` file. Just make sure every entry has an explicit `type`.
**Note:** Coyote does not support Claude Code's `"streamable-http"` alias (use `"http"` instead) or `envFile`. **Note:** Coyote does not support Claude Code's `"streamable-http"` alias (use `"http"` instead) or `envFile`.
For secrets, use [Coyote Vault](Vault) interpolation rather than Claude Code's `${VAR}` shell-style expansion. For secrets, use [Coyote Vault](Vault) interpolation rather than Claude Code's `${VAR}` shell-style expansion.
@@ -45,7 +52,7 @@ Every server entry **must** include a `"type"` field set to one of: `"stdio"`, `
## Workspace-Local MCP Servers ## Workspace-Local MCP Servers
In addition to the global `functions/mcp.json`, Coyote automatically loads a workspace-local MCP config at startup. In addition to the global `mcp.json`, Coyote automatically loads a workspace-local MCP config at startup.
This lets you ship project-specific MCP servers alongside your code without touching your global configuration. This lets you ship project-specific MCP servers alongside your code without touching your global configuration.
Coyote checks the following locations in order and loads the **first** file it finds: Coyote checks the following locations in order and loads the **first** file it finds:
@@ -57,7 +64,7 @@ Coyote checks the following locations in order and loads the **first** file it f
``` ```
<project-root>/ <project-root>/
├── .coyote/ ├── .coyote/
│ └── mcp.json # same format as functions/mcp.json (preferred) │ └── mcp.json # same format as the global mcp.json (preferred)
└── .mcp.json # Claude Code-compatible fallback └── .mcp.json # Claude Code-compatible fallback
``` ```
@@ -66,7 +73,7 @@ directory name is also customizable via the `COYOTE_WORKSPACE_CONFIG_DIR`
[environment variable](Environment-Variables), so you can point Coyote at another tool's config directory [environment variable](Environment-Variables), so you can point Coyote at another tool's config directory
(e.g. `.cursor/`, which holds an `mcp.json`) entirely. (e.g. `.cursor/`, which holds an `mcp.json`) entirely.
The workspace file uses the exact same format as the global `functions/mcp.json`, including [Vault](Vault) secret The workspace file uses the exact same format as the global `mcp.json`, including [Vault](Vault) secret
interpolation via `{{SECRET_NAME}}` syntax. Workspace server names shadow global ones on collision. This means that interpolation via `{{SECRET_NAME}}` syntax. Workspace server names shadow global ones on collision. This means that
if both files define a server named `my-db`, the workspace version takes precedence. if both files define a server named `my-db`, the workspace version takes precedence.
@@ -473,7 +480,7 @@ to:
| Value | File | | Value | File |
|-------------|-----------------------------------------------------------------------------------------------| |-------------|-----------------------------------------------------------------------------------------------|
| `user` | `~/.config/coyote/functions/mcp.json` (global; the default) | | `user` | `~/.config/coyote/mcp.json` (global; the default) |
| `workspace` | `.coyote/mcp.json` (project-local; created if missing) | | `workspace` | `.coyote/mcp.json` (project-local; created if missing) |
For workspace scope, Coyote reads from the first existing file in the precedence order documented in For workspace scope, Coyote reads from the first existing file in the precedence order documented in
@@ -529,7 +536,7 @@ If you decline a prompt, the add is aborted and no config changes are written.
time. time.
# Default MCP Servers # Default MCP Servers
Coyote ships with a `functions/mcp.json` file that includes some useful MCP servers: Coyote ships with an `mcp.json` file that includes some useful MCP servers:
* [atlassian](https://github.com/atlassian/atlassian-mcp-server) - Interact with and manage Atlassian tools like Confluence and Jira. * [atlassian](https://github.com/atlassian/atlassian-mcp-server) - Interact with and manage Atlassian tools like Confluence and Jira.
* [github](https://github.com/github/github-mcp-server) - Interact with GitHub repositories, issues, pull requests, and more. * [github](https://github.com/github/github-mcp-server) - Interact with GitHub repositories, issues, pull requests, and more.
@@ -695,7 +702,7 @@ Enabling a server in any of these contexts exposes its capability-gated meta-fun
[Interacting with MCP Servers](#interacting-with-mcp-servers) above. [Interacting with MCP Servers](#interacting-with-mcp-servers) above.
***Note:** The names of each MCP server referenced in the below configuration properties directly corresponds ***Note:** The names of each MCP server referenced in the below configuration properties directly corresponds
to the names given in the `functions/mcp.json` configuration file. So if you change the name of an MCP server to the names given in the `mcp.json` configuration file. So if you change the name of an MCP server
from `slack` to `lucem-slack`, then you need to also update your Coyote configuration accordingly. from `slack` to `lucem-slack`, then you need to also update your Coyote configuration accordingly.
## Global Configuration ## Global Configuration
@@ -717,7 +724,7 @@ enabled_mcp_servers: null # Which MCP servers to enable by default.
``` ```
A special note about `enabled_mcp_servers`: a user can set this to `all` (or include `all` in the list) to enable all A special note about `enabled_mcp_servers`: a user can set this to `all` (or include `all` in the list) to enable all
configured MCP servers in the `functions/mcp.json` configuration. configured MCP servers in the `mcp.json` configuration.
(See the [Configuration Example](https://github.com/Dark-Alex-17/coyote/blob/main/config.example.yaml) file for an example global configuration with all options.) (See the [Configuration Example](https://github.com/Dark-Alex-17/coyote/blob/main/config.example.yaml) file for an example global configuration with all options.)
Skills.md
+1 -1
@@ -92,7 +92,7 @@ This is useful for project-specific workflows: a `db-migration` skill with your
skill that loads the project's deployment MCP server, or any other task-specific overlay that doesn't belong in your skill that loads the project's deployment MCP server, or any other task-specific overlay that doesn't belong in your
global configuration. global configuration.
Workspace skills can reference MCP servers from both the global `functions/mcp.json` and the workspace `.coyote/mcp.json` Workspace skills can reference MCP servers from both the global `mcp.json` and the workspace `.coyote/mcp.json`
(see [Workspace-Local MCP Servers](MCP-Servers#workspace-local-mcp-servers)). (see [Workspace-Local MCP Servers](MCP-Servers#workspace-local-mcp-servers)).
## Frontmatter ## Frontmatter
Vault.md
+1 -1
@@ -211,7 +211,7 @@ At the time of writing, the following files support Coyote secret injection:
| File Type | Description | Limitations | | File Type | Description | Limitations |
|-------------------------|------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------| |-------------------------|------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
| `config.yaml` | The main Coyote configuration file | Cannot use secret injection on the `vault_password_file` field or anywhere inside the `secrets_provider` block | | `config.yaml` | The main Coyote configuration file | Cannot use secret injection on the `vault_password_file` field or anywhere inside the `secrets_provider` block |
| `functions/mcp.json` | The MCP server configuration file | | | `mcp.json` | The MCP server configuration file | |
| `<agent>/tools.<py/sh>` | Tool files for agents | Specific configuration and only supported for Agents, not all global tools ([see below](#environment-variable-secret-injection-in-agents)) | | `<agent>/tools.<py/sh>` | Tool files for agents | Specific configuration and only supported for Agents, not all global tools ([see below](#environment-variable-secret-injection-in-agents)) |