This our general problem resolution for Team City: There are times when the projects will seem to be stuck in "Updating sources: Building and caching clean patch for VCS root: .....".
Our usual method of dealing with this is give it about 15 minutes if it does not show any change - we stop the build.
If this doesn't work, you could always reinstall cydia by re-applying the jailbreak. Just CONNECT it to ITUNES then click RESTORE BACKUP.
NEVER RESTORE IPHONE cause it will force you to update your iphone and its hard to find latest jailbreaks for that.
The issue can occur when Cydia tries to fully refresh its sources at the time of a repository sync, and I’m sure some of you have probably stumbled upon this same error one time or another.
Give it a while and then the lock screen will appear.
Here are a few simple steps to troubleshoot the Cydia refreshing issue: Though it may not be an ideal solution to remove the repo, there is no other option available to fix the issue at the moment.