Update documentation to help transition from manage_externals -> git submodules

[mnlevy1981]

https://ncar.github.io/CUPiD/#installing walks new users through the process of cloning CUPiD and setting everything up, but existing users who try to run git pull to update their sandbox may run into issues. I just tried this, going from a fresh copy of v0.1.0 to main, and all I saw was a warning that manage_externals was not removed:

$ git checkout main
warning: unable to rmdir 'manage_externals': Directory not empty
Previous HEAD position was 5c2b957 Merge pull request #123 from TeaganKing/cupid_analysis_env
Switched to branch 'main'
Your branch is up to date with 'origin/main'.

But I'm pretty sure there's a situation where the checkout fails altogether - maybe if a file has been modified in ADF or mom6-tools? I think we want the instructions to recommend removing externals/ before checking out main, then doing the git submodule update and also removing manage_externals (if it is still there after git submodule update --init)