The two folders
Every project revolves around two locations:
- A source folder that you actually edit, usually something like
skills-organized/. - A flat target folder that your tool reads, such as
.agents/skills.
The project config binds those two together.
Example layout
For a generic .agents setup, the default shape is:
target: ~/.agents/skills
source: ~/.agents/skills-organized
config: ~/.agents/.skill-organizer.yml
The same pattern applies to tool-specific folders such as ~/.claude/skills, ~/.codex/skills, or ~/.agent/skills.
Why this matters
Most tools only scan one folder level for skills. That makes direct organization awkward once you want to group skills by source, team, or topic.
skill-organizer keeps the organized tree as the source of truth and generates the flat target view that tools can consume.
The config file
The config is intentionally small:
source: /repo/.agents/skills-organized
target: /repo/.agents/skills
That simplicity is what makes sync, status, watch mode, and service management predictable.