Allow linking of entire repositories
Don't copy over .git when linking whole repos
Add guards for using whole directory mode in bad ways
Add documentation for whole directory linking
Merge branch 'whole-repo'

* whole-repo:
  Add documentation for whole directory linking
  Add guards for using whole directory mode in bad ways
  Don't copy over .git when linking whole repos
  Allow linking of entire repositories
Merge remote-tracking branch 'upstream/master'