fix(start-work): restore atlas-first slash discovery

Static slash-command discovery runs before agent registration, so /start-work regressed to Sisyphus even though config-time wiring still needed Atlas-aware fallback. Split builtin command resolution so discovery stays Atlas-first while command config remains availability-aware.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/plugin-handlers/command-config-handler.ts

@@ -30,7 +30,9 @@ export async function applyCommandConfig(params: {
   ctx: { directory: string };
   pluginComponents: PluginComponents;
 }): Promise<void> {
-  const builtinCommands = loadBuiltinCommands(params.pluginConfig.disabled_commands);
+  const builtinCommands = loadBuiltinCommands(params.pluginConfig.disabled_commands, {
+    useRegisteredAgents: true,
+  });
   const systemCommands = (params.config.command as Record<string, unknown>) ?? {};
 
   const includeClaudeCommands = params.pluginConfig.claude_code?.commands ?? true;