tree_dir option can result in confusing situations

The tree_dir option results in some confusing situations, and some error conditions must be special cased explicitly for the option, which only add to its confusion:

  - It can mistakenly be pointed at a wrong branch directory (#1299071)
  - The directory pointed at can be a full working tree, not a lightweight checkout.
  - The option makes security with apparmor harder to control.
  - Not as useful with lightweight checkouts, as we always talk to the remote.

In light of this, it is probably best to remove the tree_dir option, and always use a temporary directory