vcs: let _run_git_command use base command from Preferences
vcs: Reshape app_is_git_controlled check

The check now _uses_ app_repo's function (in order
to be able to use the command from Preferences).

Therefore I moved the creation of the app_repo object
inside the one-time check of app_is_git_controlled.
vcs: Fix missing else clause in app_is_git_controlled()

Taking an idea from Davide in
https://github.com/wbsoft/frescobaldi/pull/240#issuecomment-26712555
Merge pull request #241 from uliska/git-executable-preference

Add Preference for Git executable