prepare to replace the SAM printing code

This move is dangerous as SAM printing is very complex, but it will benefit in
the long run. The planned change will reduce the redundancy, improves clarity
and most importantly makes it much easier to output multiple primary hits in an
optional tag.
drop an unnecessary member from mem_aln_t
to test the new sam writer...
new code works for SE
replace PE; BUGGY right now!!
drop the old SAM writer
SAM almost identical to 0.7.2
r359: identical output to 0.7.2 (without -a)
r360: output alternative primary alignments in XA
r361: flag proper pair even if multi-primary

Up to here, all the features in my checklist have been implemented.
r362: bugfix - occasionally wrong TLEN

Use the 0.7.2 way to compute TLEN
r363: XA=>XP; output mapQ in XP

In BWA, XA gives hits "shadowed" by the primary hit. In BWA-MEM, we output
primary hits only. Primary hits may have non-zero mapping quality.
Added Makefile.bak and bwamem-lite to .gitignore
Merge branch 'master' into master_fixes

Conflicts:
	bwamem.c
	bwamem_pair.c
	example.c