Different project branches should have different configurations. The configuration section in a multi-branch project is currently shared among all branches, which is only functional in simplistic environments where all branches share the same configuration and build rules.

The configuration should be moved into each branch and not be shared. A possible enhancement to this change would be to add a button to copy configuration from another branch.

The most glaring example of this problem is where each branch adds a new feature, and therefore has different upstream dependencies to watch as build triggers. This cannot be done with Jenkins at present.

Another example is where a particular branch is changing the build rules, and the changes cannot be used in other feature branches until merged.
Workaround (crude): It is possible to execute a different set of build rules that are saved in the branch, but this stuff should be in Jenkins, not the source code.