Minor fixes to the FreeBSD contributions

On one code path, a reference to `af` should have been `self`.  There is
also a semantic change to handle odd uses of dependency-generation flags
that arises in libtool/autotools-based build systems.  These seem to
sometimes include dependency flags (-MT and friends) during
compilation (which probably has no effect).

The problem is that when these flags are really used for dependency
generation (and no code generation), we really should not invoke clang
to generate bitcode since it will fail.  On the other hand, we can't
just bail out when we see these -M* flags, since they might be misused
in a real compilation step.  This change tries to compromise: we only
skip bitcode generation when we see a -M* dependency flag and NO
accompanying `-c` flag.  This should work in the vast majority of cases,
since real makefile dependency generation should never use the -c flag.
whitespace
fixing a conflict.

Merge branch 'master' of https://github.com/travitch/whole-program-llvm

Conflicts:
	driver/utils.py