To fix this problem you can set up you CI server to merge into the base branch automatically before running the code (in fact you should probably do this by default for other reasons).
This way your devs won't have to merge, they can just rerun their tests, which should be the same workflow as if your CI config is separate from your codebase.
This way your devs won't have to merge, they can just rerun their tests, which should be the same workflow as if your CI config is separate from your codebase.