add support for dir_input and dir_output

[visr]

Until now, the paths to the files were all either absolute or relative to the TOML. This makes is flexible because you can point to wherever you want. One downside, compared to the more rigid approach used before, is that it makes it hard to try quickly send all output to a new directory when trying things out, as you have to change all the output paths in the TOML.

This should relieve that, as you can now just add a dir_input and dir_output key in the TOML. If they are not added, nothing changes, so this is not breaking. These folders are only used for paths that are not absolute. dir_input and dir_output can also be absolute if needed.