Document a difference between git and github in extra-deps

[jorpic]

I spent some time trying to understand why github: user/repo in extra-deps does not work if repo contains git submodules.
Probably it worth to explicitly mention the difference between git and github in documentation.

ref #5603

[mpilgrem]

@jorpic, I changed the base branch, because pull requests for improvements to documentation that are applicable to the current released version of Stack should target this repository's stable branch.

[mpilgrem]

@jorpic, post-merging, I made some further changes to this part of the documentation. The help on GitHub archive files was in the wrong location, adding to the confusion.