Restructure .cocoapods directory to contain repos as a subdirectory.

Intended to be a solution for #1150.

I'm unsure of the naming and I wasn't entirely sure what the best way to go about doing a migration for existing repos. Would appreciate recommendations on the latter. Was thinking maybe just checking `cocoapods_dir` for repo directories if the `master_repo_dir` doesn't exist and moving them over and rechecking before creating anew.

- [x] Initial implementation
- [x] Migration of old repos over to new structure via `pod setup`
- [x] Test for migration.