Why am I getting a "destination path '.' already exists" error when trying clone from my webfaction server?

Simply:

git clone [email protected]:github-username/github-repo.git

That will create a new folder github-repo in ../webapps/nameofwebapp/.

In your case:

cd ../webapps/nameofwebapp/
git clone [email protected]:github-username/github-repo.git -b develop ./

If you already did the clone:

cd github-repo
git checkout -b develop origin/develop