Changed default sampling scheme to be permutation
Cleaned up index_calculations.r
Cleaned up internal.r
Cleaned up distances.r
Deleted useless pdf
rewrote parts of poppr manual to reflect samp change
rewrote man pages
Added rm statements to makefile
Noted change in NEWS
Merge branch 'master' into devel

Conflicts:
	DESCRIPTION
	vignettes/poppr_manual.Rnw
	vignettes/poppr_manual.pdf
	vignettes/poppr_manual.tex