What seems to work for us is handling the Custom directories for the environment. This allows us to keep the .tsenv file and any dependencies of the environment in .git so we can have multiple environments setup each having its own search directories, adapters etc. The search directories, adapters etc are stored in the Cfg folder so you can have one for each environment that you set up. It has the benefit that you could also modify and prepare your deployment machines from your development environment, just by starting TS in the corresponding environment.
Hope this helps!