environment: move `set_git_dir()` and related into setup layer

environment: move `set_git_dir()` and related into setup layer

The functions `set_git_dir()` and friends are used to set up
repositories. As such, they are quite clearly part of the setup
subsystem, but still live in "environment.c". Move them over, which also
helps to get rid of dependencies on `the_repository` in the environment
subsystem.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>