Best way to organise external toolboxes or turn them into packages

Hi folks,

I'm working on a project with very different types of analysis involved and I utilise a couple of external toolboxes mainly from File Exchange but hosted on github. What is the best way to organise these? My main problem here is shadowing. Right now I'm adding them all on to my path, but some function shadow Matlab built-in ones and some even shadow functions from other toolboxes. I would love to just convert them into packages and use them by their identifier, but is there any smart or automatic way to do this? Most of these toolbox I follow on github and update them regularly. So I don't want to manually go into all these files and change their function calls to account for the package name, which would be gone with the next commit. Hence also changing the toolbox directory structure is not really an option (to put most of the functions in private folders or something similar) How do you organise lots of external toolboxes?