Restoring confirming abs directories existence at setup

Renaming pasu -> pathways

Streamlining errors definitions

Renaming pathology -> pasu

Adding GetRelDir to get relative path to be used as a suffix

Fixing missing rel to abs initialization in setup

Moving over common setup code

Refactoring SetUserOverrides to work on a map, not file

Fixing default dirs to use filepath.Join

Simplifying SetAbsDirs and separating that from user overrides

Fixing userDirectoriesFilename missing being a fatal error

Fixing userDirs being not initialized by the time it's commonly first…

… used