Change IO (and restart) for multisystem support

Description

Change all io_* functions that operate on files/directories to have a namespace argument so files are written to a folder inside the corresponding namespace folder.

News snippet

Change IO (and restart) for multisystem support

Checklist

• I have checked that my code follows the Octopus coding standards
• I have added tests for all the new features added in this request.

Closes #189 (closed)