Re-applies clerk.yaml changes to running agents. Use when the user edited clerk.yaml and wants to apply, sync, reconcile, update, or push config changes. Triggers on 'apply the changes', 'sync my config', 'I just edited clerk.yaml', or 'how do I apply changes'.
When the user changes clerk.yaml and wants to apply it, or asks to reconcile/sync config — use this skill to re-apply configuration to one or all agents.
Determine whether to reconcile:
Before reconciling, read the current ~/.clerk/clerk.yaml (or $CLERK_CONFIG) and describe what will be updated:
For one agent (<name>):
agents.<name> and its inherited profile/defaultsstart.sh, settings.json, .mcp.json, .claude/agents/*.md (sub-agents), , systemd timerstelegram/cron-N.shFor all agents:
agents: and note "same files for each"Before reconciling, tell the user what will be updated and ask for confirmation.
Example: "I'll reconcile the dev agent — updating start.sh, settings.json, .mcp.json, and sub-agent files from clerk.yaml. CLAUDE.md will not be touched. Confirm?"
Only proceed after an affirmative reply.
For a single agent:
clerk agent reconcile <name>
For all agents:
clerk agent reconcile --all
If reconcile isn't available, try:
clerk agent apply <name>
Show the output from the reconcile command. Highlight:
If systemd timers were updated, note that they're live immediately — no restart needed for timers.
If start.sh or .mcp.json changed, suggest restarting the affected agents: "The agent's startup script changed. Restart it to apply? (clerk agent restart <name>)"
CLAUDE.md — never overwritten after initial scaffold (protects customizations)telegram/history.db — conversation history preservedaccess.json — access control list preserved| Changed | Action |
|---|---|
model, tools, env, hooks, skills | Reconcile + restart |
schedule (add/remove tasks) | Reconcile only (timers update live) |
system_prompt_append, claude_md_raw | Reconcile + restart (only affects new sessions) |
subagents | Reconcile only (Claude Code reads sub-agent files per-session) |
mcp_servers | Reconcile + restart |