Add an explicit GIT_DIR to the list of excludes

When an explicit '--git-dir' option points to a directory inside
the work tree, git treats it as if it were any other directory.
In particular, 'git status' lists it as untracked, while 'git add -A'
stages the metadata directory entirely

Add GIT_DIR to the list of excludes in setup_standard_excludes(),
while checking that GIT_DIR is not just '.git', in which case it
would be ignored by default, and that GIT_DIR is inside GIT_WORK_TREE

Although an analogous comparison of any given path against '.git'
is done in treat_path(), this does not seem to be the right place
to compare against GIT_DIR. Instead, the excludes provide an
effective mechanism of ignoring a file/directory, and adding GIT_DIR
as an exclude is equivalent of putting it into '.gitignore'. Function
setup_standard_excludes() was chosen because that is the place where
the excludes are initialized by the commands that are concerned about
excludes

Signed-off-by: Pasha Bolokhov <pasha.bolokhov@gmail.com>