Fall cleanup

[malihass]

• Use pathlib instead of makedirs to handle intermediate directory creation
• Remove the folderManagement module
• Remove label plot module (was only used for sparger paper)
• Remove older sys.path.append
• Fix warning logs
• Make sure size group are correctly read
• Add test for size group reading
• Make bissection tool more general
• Fix CI (move from miniconda to mamba)