When a re-index is triggered manually on OrganizationFolder the re-index should be propagated to all its children (run a re-index on every MultiBranchProject in the org. folder), but actually it's not happening. This is producing wrong behaviors, for example: if you make a change in the OrganizationFolder configuration (a checkout credentials change, for example) it is not propagated to existing MultiBranchProject s and their existent branch jobs. So if you trigger a build on a branch job, the new credentials configuration is not pickep up.
Possible root cause:
When a re-index is triggered manually on OrganizationFolder a call to computeChildren occurs, this call ends up with a series of calls to SCMSourceObserver.complete(), if the projectName already has a MultiBranchProject in ComputedFolder.items (the multi-branch already exists) then project.scheduleBuild() is never called, so the re-index in that child will never occur.