[thwarted]

This would be a lot easier if EVERYTHING that you've ever done is stored in your home directory because you can't write anywhere else (and neither can apps you're running) as your own user. On Windows this is a problem because sometimes apps write to the application folder in Program Files, then there are registry changes, sometimes stuff is stored in Application Data, and some stuff is stored in hidden directories that are, by default, invisible.

I've moved the entire home directory between installs of different versions of linux distributions and between entirely different distributions with only minor issues (related mostly to an old format of a config file not being recognized by the newer application). I've had the same .opera directory for years.

Running applications in their own VM is a good idea for security. It's a good idea to work around system and file management deficiencies in the operating system and the application itself also.