Use Qubes OS. It will help you in different ways. Firstly, if a problem happens, only the specific environment is affected (such as the project you're working o

Use Qubes OS. It will help you in different ways. Firstly, if a problem happens, only the specific environment is affected (such as the project you're working on), secondly any changes outside of the home directory will be reverted (this was not an issue in example in question but it can happen in other cases, such as a sudo make install deleting stuff from /usr/bin), finally if something really bad happens you can always revert the specific vm where the problem happened. A lot of information about Qubes talk about protection against attacks, but it's also useful against unintentional issues, and I'd argue that's a much more common case where Qubes shines.