Factor out clone-repo logic

[zepumph]

From phetsims/aqua#226, it will be easier to add logic to clone scenerystack org repos if this is factored out.

[brettfiedler]

Not sure if related, but I had tried to add a file argument in clone-missing-repos for example-sim dependencies and scenerystack repos. It's in the pull requests for this repo. On a side not, we can probably clear out that pull request.

#354

[zepumph]

Lol. Amazing! I'll assign to JO to note while adding some more lists over in phetsims/aqua#226.