Reproduce problem:
1. Make a job using repo scm plugin.
2. Create a local manifest in the job
3. Execute job and wait for finish
4. Clear the local manifest for the job
5. Execute job again

Error:
The local manifest is not removed. In the workspace/.repo/ there is a local_manifest.xml still present.

Expected result:
The local_manifest.xml should be deleted when the job is run with a empty local_manifest.xml box

Workaround:
Delete local_manifest.xml manually in the workspace after clearing the local manifest box in the job configuration.