move mem_fill_scmat() to bwa.{h,c}
bwa-sw: use bwa_gen_cigar() for cigar generation
bwa-sw: ditch stdaln
replace aln_global in bwase.c
r329: ditch stdaln.{c,h}; no changes to bwa-mem

stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.