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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
# Function Calling Configuration
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
- web_search
- 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.
# MCP Server Configuration
Coyote stores the MCP server configuration file, `functions/mcp.json`, in the `functions` directory. You can find
this directory using the following command:
Coyote stores the user-scope MCP server configuration file, `mcp.json`, directly in the Coyote configuration
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
coyote --info | grep functions_dir | awk '{print $2}'
coyote --info | grep mcp_config_file | awk '{print $2}'
```
The syntax for the `functions/mcp.json` file matches [Claude Code's `.mcp.json` configuration format](https://docs.claude.com/en/docs/claude-code/mcp),
> [!NOTE]
> **Historical location:** older Coyote versions stored this file at `functions/mcp.json` inside the `functions`
> directory. That location is still fully supported: if `<config-dir>/mcp.json` does not exist but
> `<config-dir>/functions/mcp.json` does, Coyote keeps using the historical file. Existing installs continue to
> work unchanged, and there is no need to move the file. If both files exist, `<config-dir>/mcp.json` wins.
The syntax for the `mcp.json` file matches [Claude Code's `.mcp.json` configuration format](https://docs.claude.com/en/docs/claude-code/mcp),
with one small difference: the `type` field is **always required** in Coyote, even for stdio servers (Claude Code
allows it to be omitted and infers `stdio` from the presence of a `command`). So any time you're looking to add
a new server, look at its docs and find the Claude Code configuration example. You should be able to use the
exact same configuration in your `functions/mcp.json` file. Just make sure every entry has an explicit `type`.
exact same configuration in your `mcp.json` file. Just make sure every entry has an explicit `type`.
**Note:** Coyote does not support Claude Code's `"streamable-http"` alias (use `"http"` instead) or `envFile`.
For secrets, use [Coyote Vault](Vault) interpolation rather than Claude Code's `${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
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.
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>/
├── .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
```
@@ -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
(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
if both files define a server named `my-db`, the workspace version takes precedence.
@@ -473,7 +480,7 @@ to:
| 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) |
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.
# 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.
* [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.
***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.
## 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
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.)
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
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)).
## 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 |
|-------------------------|------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
| `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)) |