We created a clone from the dev server for the jenkis CI to improve our work, we configurated it and the tests started working as we wanted. Then we find out that the git plugin in the jenkins is not liked with the project's workspace. It's a PHP REST api project, every server has it's own configuration. So we gave to the jenkins the path of the project to use that - this is the "Checkout to a sub-directiory" option. Then when a new PR is created, then jenkins is tiggered and it's start the build, and at first it's trying to delete the complete workspace. I wouldn't think that it would be impossible to run tests on an already existing project with the jenkins, but this is ablosutly not the way how to do it. Every server has it's own configurations, so those are not part of the git repo, plus there is a base installation for the framework, and that's also not part of the git repository.
Now my question is what information are we missing, and how could we configure the git pluggin to make the jenkins start working on our existing project?