Description of problem:
Yum "clean" option is not working correctly if a repository is configured in
/etc/yum.repos.d/

Version-Release number of selected component (if applicable):
yum-3.2.8-9.el5_2.1

How reproducible:
100%

Steps to Reproduce:
1. Create a yum repository configuration file in /etc/yum.repos.d
2. yum clean all
3. Error: Repository <repo> is listed more than once in the configuration
  
Actual results:
The yum cache is not cleared

Expected results:
The yum cache should be cleared

Additional info: