This plugin provides filters for SCM API based plugins that work based on the presence or absence of specific file paths in the branch.
After installing this plugin, two new options will appear in the branch filters:
- Filter by absence of a path
- Filter by presence of a path
Each filter takes a single path and excludes or includes respectively the branch / tag / change request if the path exists.
You have two Jenkins instances with an organization folder pointing at the same organization.
Both of these instances will discover the same repositories and the same branches / tags / change requests leading to competing builds.
One solution is to put a marker file in the root of all the repositories that indicates which Jenkins instance should build and then use the Filter by presence of a path filter on each Jenkins to look for their respective marker file.
Another solution is to use the presence / absence of a single file to indicate which Jenkins instance should build.

