Reference

Page	What it lists
Command line	Every `bogen` command, its options, and the environment variables.
MCP tools	Every tool your agent can call, with its arguments, plus the resources, prompts, guides and the instructions a client receives. Generated from a running server.
HTTP and WebSocket	The server's routes and events, as the editor, the CLI and paired devices use them.

Keeping the MCP reference current

mcp-tools.md is written by a script that starts a server in the same process, on a free port and with a temporary data folder that it removes afterwards, and asks it for tools/list, resources/templates/list, resources/list and prompts/list. It never touches your own data folder or a running Bogen. From the root of a checkout:

npx tsx scripts/gen-docs-reference.ts           # writes docs/guide/reference/mcp-tools.md
npx tsx scripts/gen-docs-reference.ts --check   # exits 1 when the page is out of date

The groups on that page are listed at the top of the script. A new tool that is in no group yet lands under "Other tools", and the script names it on stderr.