Kigi-CLI/crates/codegen/kigi-tui/docs/user-guide/07-mcp-servers.md

MCP Servers

MCP (Model Context Protocol) servers extend Kigi with external tool integrations. They let Kigi interact with any service that implements the MCP standard.

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What Are MCP Servers?

An MCP server is a process that exposes tools to Kigi over a standardized protocol. When you configure an MCP server, its tools become available to the model alongside Kigi's built-in tools. The model can discover and call these tools during a session.

For example, a GitHub MCP server might expose tools like create_issue, list_pull_requests, and search_code. A database server might expose query, list_tables, and describe_schema.

See the MCP specification for protocol details.

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Configuration

MCP servers are configured in ~/.kigi/config.toml under [mcp_servers.<name>] sections.

stdio Transport (Local Process)

Kigi spawns a local process and communicates over stdin/stdout:

[mcp_servers.my-server]
command = "/path/to/server"           # Server executable
args = ["--flag", "value"]            # Command arguments
env = { API_KEY = "sk-..." }          # Environment variables
enabled = true                        # Enable or disable the server (default: true)
startup_timeout_sec = 30              # Server startup timeout, seconds (default: 30)
tool_timeout_sec = 6000               # Per-tool-call timeout fallback, seconds (default: 6000)
tool_timeouts = { slow_op = 120 }     # Per-tool timeout overrides, seconds

Global startup-timeout override: instead of setting startup_timeout_sec per server, you can change the default for all servers via the MCP_TIMEOUT environment variable (milliseconds, compatible with Claude Code) or KIGI_MCP_STARTUP_TIMEOUT_SECS (seconds). A per-server startup_timeout_sec still takes precedence over both. Cold-start npx/uvx servers that download packages on first launch often need this; the default is 30s.

MCP tool-result size cap: large MCP / use_tool results are truncated inline (full payload spilled under the session mcp/ folder). Default is 20_000 bytes. Override via:

• env KIGI_MAX_MCP_OUTPUT_BYTES or MAX_MCP_OUTPUT_BYTES (bytes; Kigi-native wins if both set; Claude-style name, but we bound by bytes not tokens)
• config.toml — user-level (~/.kigi/config.toml) or repo-level (.kigi/config.toml anywhere on the cwd → git-root chain; the deepest file wins, and the repo value applies only once the folder is trusted):

[mcp]
max_output_bytes = 40000

Precedence: requirements.toml > env > repo .kigi/config.toml > user/managed config > default. Repo edits apply to running sessions in that directory via config hot-reload.

HTTP/SSE Transport (Remote Server)

For remote MCP servers accessible over HTTP:

[mcp_servers.remote-api]
url = "https://mcp.example.com/api"
headers = { "Authorization" = "Bearer token" }

Streamable HTTP with Session ID

[mcp_servers.my-streamable-server]
url = "https://mcp.example.com/api/mcp"
headers = { "x-mcp-session-id" = "{{session_id}}" }

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CLI Management

Manage MCP servers from the command line without editing config files:

# List configured MCP servers
kigi mcp list
kigi mcp list --json          # Machine-readable output

# Add a stdio server. Everything after -- is the server command, so flags
# like -y reach the server instead of being parsed by kigi.
kigi mcp add filesystem -- npx -y @modelcontextprotocol/server-filesystem /path/to/dir

# Add a stdio server with environment variables (-e is repeatable)
kigi mcp add postgres -e DATABASE_URL=postgres://localhost/mydb -- npx -y @modelcontextprotocol/server-postgres

# Add a remote HTTP server
kigi mcp add --transport http sentry https://mcp.sentry.dev/mcp

# Add a remote server with an authentication header (--header is repeatable)
kigi mcp add --transport http api https://mcp.example.com/mcp --header "Authorization: Bearer YOUR_TOKEN"

# Add a remote SSE server
kigi mcp add --transport sse linear https://mcp.linear.app/sse

# Remove a server
kigi mcp remove github

# Diagnose a server's configuration and connectivity
kigi mcp doctor               # Check every configured server
kigi mcp doctor github        # Check one server
kigi mcp doctor --json        # Machine-readable output

The transport defaults to stdio; pass --transport http or --transport sse for remote servers.

By default kigi mcp add writes to ~/.kigi/config.toml (--scope user). Use --scope project to write to .kigi/config.toml in the current directory instead, which can be committed and shared with your team (see Project-Scoped MCP Servers). Header and environment variable values are stored verbatim, so reference secrets as ${VAR} instead of pasting them into a committed project config (see Example Configurations). kigi mcp list shows servers from both scopes, marking project-scoped ones with (project).

kigi mcp remove searches both scopes and exits 0 after removing the server. It exits 1 when the name is not found, or when the name is defined in both user and project scope — pass --scope to say which one to remove.

Breaking changes from earlier releases: --env now takes one KEY=value per flag (use -e A=1 -e B=2, not --env A=1 B=2), and server names may only contain letters, numbers, hyphens, and underscores.

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Project-Scoped MCP Servers

MCP servers can be configured per-project by placing a .kigi/config.toml in your repository:

my-project/
  .kigi/
    config.toml
  src/
  ...

# .kigi/config.toml
[mcp_servers.linear]
url = "https://mcp.linear.app/mcp"
enabled = true

When a server exposes a native HTTP/SSE endpoint, prefer the url form over wrapping it in a stdio proxy such as npx mcp-remote <url>. Kigi handles HTTP/SSE and OAuth directly, so the native form avoids an extra subprocess per session. It also registers Kigi's own OAuth client with the provider.

Kigi walks from the current directory up to the git repo root, loading .kigi/config.toml at each level:

Location	Scope	Priority
~/.kigi/config.toml	All projects	Lowest
<repo-root>/.kigi/config.toml	This repository	Medium
<cwd>/.kigi/config.toml	Current directory	Highest

If a project defines a server with the same name as a global one, the project version replaces it entirely (fields are not merged).

Project-scoped files contribute [mcp_servers], [plugins], and [permission] entries. Kigi reads most other config sections only from ~/.kigi/config.toml.

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Tool Naming

MCP tools are namespaced with the server name to avoid collisions:

• Server filesystem with tool read_file becomes filesystem__read_file
• Server github with tool create_issue becomes github__create_issue

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Toggle Servers at Runtime

You can enable or disable MCP servers during a session without restarting Kigi.

The /mcps Modal

Open the MCP servers modal in the TUI:

• Run /mcps as a slash command
• Or press Ctrl+L (non–VS Code family) and navigate to the MCP Servers tab; on VS Code family use /plugins or /mcp and open the MCP Servers tab

From the modal you can:

• See each server's source, enabled state, and tool count
• Enable or disable a server with Space
• Expand a server to view the tools it provides
• Refresh the list with r after you edit config.toml
• Authenticate an OAuth server with i
• Add a server with a, or remove one with x

Tool Discovery

The model has access to two built-in tools for working with MCP servers:

• search_tool — Discover available integration tools across all enabled MCP servers. Use this to find tools by name or description.
• use_tool — Call an integration tool discovered via search_tool. Specify the fully-qualified tool name (e.g., github__create_issue).

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Compatibility

Kigi loads MCP server configurations from multiple sources for compatibility:

Source	Format	Location	Configurable
config.toml	Native Kigi config	~/.kigi/config.toml, .kigi/config.toml	Always on
.claude.json	Claude Code format	~/.claude.json	[compat.claude] mcps
.cursor/mcp.json	Cursor format	~/.cursor/mcp.json, <project>/.cursor/mcp.json	[compat.cursor] mcps
.mcp.json	MCP standard format	Project root (cwd to git root)	Loaded unless you have imported or dismissed the Claude import prompt (the import marker is set)

All sources are merged in priority order: config.toml > Claude > Cursor > .mcp.json. Servers from higher-priority sources take precedence when names conflict.

The Claude and Cursor MCP sources are scanned by default. To disable scanning for a specific vendor, set [compat.<vendor>] mcps = false in ~/.kigi/config.toml or the corresponding environment variable (KIGI_CURSOR_MCPS_ENABLED, KIGI_CLAUDE_MCPS_ENABLED). See Configuration for details. Use kigi inspect to see which MCP servers were loaded and their vendor origin ([cursor], [claude]).

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MCP OAuth

For MCP servers that require OAuth authentication, Kigi handles the credential flow automatically. When an MCP server requests OAuth credentials, Kigi opens a browser-based authorization flow and stores the resulting tokens for future use.

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Example Configurations

Use the url form for hosted MCP servers and the command / args form for local stdio tools.

Native HTTP (hosted services)

You must authenticate OAuth-based MCP servers before you can use them. Kigi stores the resulting tokens under ~/.kigi/mcp_credentials.json. After you edit config.toml, press r in the /mcps modal to refresh the server list.

[mcp_servers.linear]
url = "https://mcp.linear.app/mcp"
enabled = true

[mcp_servers.sentry]
url = "https://mcp.sentry.dev/mcp"
enabled = true

[mcp_servers.mixpanel]
url = "https://mcp.mixpanel.com/mcp"
enabled = true

For internal or self-hosted servers that authenticate with a static bearer token rather than OAuth, set the Authorization header explicitly:

[mcp_servers.internal-tools]
url = "https://mcp.internal.example.com/mcp"
enabled = true

[mcp_servers.internal-tools.headers]
Authorization = "Bearer <token>"

To avoid putting secrets in the config file, reference an environment variable with ${VAR} (or ${VAR:-default}). Kigi expands string fields in [mcp_servers.*] — url, command, args, and the values in env and headers — at load time:

[mcp_servers.internal-tools]
url = "https://mcp.internal.example.com/mcp"
enabled = true
headers = { "Authorization" = "Bearer ${INTERNAL_MCP_TOKEN}" }

Local stdio

Use stdio for tools that must run locally (filesystem access, local databases, in-house servers).

# Filesystem access scoped to a directory
[mcp_servers.filesystem]
command = "npx"
args = ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/directory"]

# Local Postgres
[mcp_servers.postgres]
command = "npx"
args = ["-y", "@modelcontextprotocol/server-postgres", "postgresql://user:pass@localhost/db"]

# Custom server with a longer startup timeout and tuned per-tool timeouts
[mcp_servers.my-tools]
command = "/usr/local/bin/my-mcp-server"
args = ["--config", "/etc/my-mcp.json"]
startup_timeout_sec = 30
tool_timeout_sec = 120
tool_timeouts = { slow_analysis = 300, quick_lookup = 10 }

On Windows, npm installs launchers like npx, npm, pnpm, and yarn as .cmd batch shims (there is no npx.exe). Kigi resolves a bare command such as npx to its real launcher path on PATH (honoring PATHEXT) before spawning, so these work without manually wrapping them in cmd /c. A command given as an absolute path or one containing a path separator is used as-is.

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Available MCP Servers

A partial list of MCP servers you can configure with the url or command forms shown above. Confirm the current endpoint or package name with each provider before use:

Server	Transport	Endpoint / Package
Linear	HTTP (OAuth)	https://mcp.linear.app/mcp
Sentry	HTTP (OAuth)	https://mcp.sentry.dev/mcp
Mixpanel	HTTP (OAuth)	https://mcp.mixpanel.com/mcp
Filesystem	stdio	@modelcontextprotocol/server-filesystem
Git	stdio	@modelcontextprotocol/server-git
GitHub	stdio	@modelcontextprotocol/server-github
GitLab	stdio	@modelcontextprotocol/server-gitlab
PostgreSQL	stdio	@modelcontextprotocol/server-postgres
SQLite	stdio	@modelcontextprotocol/server-sqlite
Puppeteer	stdio	@modelcontextprotocol/server-puppeteer

See the MCP Server Registry for the full list of community servers and the MCP specification for protocol details.

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Troubleshooting

Server Not Starting

# Test the server command manually
npx -y @modelcontextprotocol/server-filesystem /path

# Increase startup timeout
# In config.toml:
[mcp_servers.filesystem]
startup_timeout_sec = 30

For stdio servers, Kigi captures the process's standard error to ~/.kigi/logs/mcp/<server>.stderr.log, truncated on each launch. Check this file when a server starts but fails to handshake:

tail -f ~/.kigi/logs/mcp/filesystem.stderr.log

Viewing Server Status

Use kigi inspect to see all loaded MCP servers and their sources:

kigi inspect          # Human-readable
kigi inspect --json   # Machine-readable

Debug Logging

RUST_LOG=debug KIGI_LOG_FILE=/tmp/kigi.log kigi
tail -f /tmp/kigi.log

Look for log entries containing mcp to trace server startup, tool discovery, and tool call execution.