setup: set startup_info->have_repository more reliably

setup: set startup_info->have_repository more reliably

When setup_git_directory() is called, we set a flag in
startup_info to indicate we have a repository. But there are
a few other mechanisms by which we might set up a repo:

  1. When creating a new repository via init_db(), we
     transition from no-repo to being in a repo. We should
     tweak this flag at that moment.

  2. In enter_repo(), a stricter form of
     setup_git_directory() used by server-side programs, we
     check the repository format config. After doing so, we
     know we're in a repository, and can set the flag.

With these changes, library code can now reliably tell
whether we are in a repository and act accordingly. We'll
leave the "prefix" field as NULL, which is what happens when
setup_git_directory() finds there is no prefix.

Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>