Reference

Use this section when you already know what you need to look up. It is denser than the guides: commands, config ownership, files, environment variables, storage model, and script behavior.

CLI

Global config

Project config

Environment variables

Files and directories

Database schema

Projects and synchronization

Background jobs

Supervisor

Federation commands

Fast lookup

Need	Start here
Exact command groups, read/write behavior, project resolution	CLI reference
Packaged service settings, database URL, providers, MCP, retention	Global config
Repo markers, user-local project overrides, agent behavior	Project config
Runtime and secret variables used by scripts, services, and providers	Environment variables
Where config, env files, runtime state, caches, skills, and docs live	Files and directories
PostgreSQL table groups, migrations, pgvector, and inspection guidance	Database schema
How to interpret success, usage errors, and operational failures	Exit codes

Source-of-truth rule

The current binary is authoritative for flags and subcommands:

codifix --help
codifix <command> --help
codifix <command> <subcommand> --help

The markdown docs remain the deeper workflow reference. The website reference should be scriptable and current, not a copy of every guide.