The check needs to be in the right subdirectory to be included in the agent.
If I put for Linux files in check_mk/agents/custom/check_name/lib/plugins/ the file is copped in the plugin’s folder on the target system and makes it possible to replace checkmk build in checks (e.g. with a patched version).
That is why I thought the folder structure needs to represent the folder structure on the target system.
For me, the problem is solved. Maybe the documentation could be improved, but on the other side I thought that I had tested the solution which works now and must have done something wrong in the first test.