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It's hard to say why there was an issue uninstalling, but to clean up, just follow the manual install steps in reverse, and
Strange. It doesn't really do that much. Anyway, if you want to fully manually uninstall here's how:
Ensure the service is stopped: INEDOPROGETSVC
Uninstall services by executing "ProGet.Service.exe" from an admin command line in the ProGet\Service directory, and followign the prompts
Delete the Service and WebApp directories, (and anything else under ProGet you don't want to keep)
Delete the HKLM\Software\Inedo\ProGet registry key
Delete the HKLM\Software\Microsoft\Windows\CurrentVersion\Uninstall\ProGet registry key
If using IIS, delete the ProGet web app and app pools
If you really want to delete everything , you can also drop the ProGet SQL database