I'm running 10.10 and have stayed within the repositories. When it is time to upgrade to 11.04 are there any "programs" in the 10.10 repository that are a potential conflict with 11.04 and should remove before "Upgrading?"
The update manager handles this for you, you shouldn't have to do anything.
Where it becomes problematic is when people start adding third party applications. The upgrader does it's best to cope by disabling PPAs on upgrades, etc. but you should be good to go!
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