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I want to essentially reset Ubuntu 14.04 to factory settings, but I want to keep my unity preferences and my python packages. I'm thinking I should just uninstall all software that aren't factory installed.

How would I go about doing this, or is there an alternative you suggest?

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I think what you are looking is system restore to as passive state. There is a package available but it must be installed and have a screenshot of state. check this page to get help in installing Time Shift and configuration. Time Shift