grep: turn off gitlink detection for --no-index

If we are running "git grep --no-index" outside of a git
repository, we behave roughly like "grep -r", examining all
files in the current directory and its subdirectories.
However, because we use fill_directory() to do the
recursion, it will skip over any directories which look like
sub-repositories.

For a normal git operation (like "git grep" in a repository)
this makes sense; we do not want to cross the boundary out
of our current repository into a submodule. But for
"--no-index" without a repository, we should look at all
files, including embedded repositories.

There is one exception, though: we probably should _not_
descend into ".git" directories. Doing so is inefficient and
unlikely to turn up useful hits.

This patch drops our use of dir.c's gitlink-detection, but
we do still avoid ".git". That makes us more like tools such
as "ack" or "ag", which also know to avoid cruft in .git.

As a bonus, this also drops our usage of the ref code
when we are outside of a repository, making the transition
to pluggable ref backends cleaner.

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

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