run_demo2.sh calls PBstat with wrong input files

run_demo2.sh calls PBstat with a fasta file as input file while PBstat
expects a count file. This commit fix the calls to PBstat in
run_demo2.sh. It also create demo2/md_traj_{1,2,3}.PB.count. These files
have been generated with:

    cd demo2
    ../PBcount.py -f md_traj_1.PB.fasta -o md_traj_1
    ../PBcount.py -f md_traj_2.PB.fasta -o md_traj_2
    ../PBcount.py -f md_traj_3.PB.fasta -o md_traj_3

Notice that the demo still does not complete because of issue #1.

This commit also small typos in run_demo2.sh.
changed output file name for --logo option
changed output file name for PB logo
changed output file name for map and Neq
fixed #1 - homogenized documentation and demo script
with --residue-min and --residue-max options
Merge branch 'pull1' of https://github.com/jbarnoud/PBxplore into jbarnoud-pull1

Conflicts:
	run_demo2.sh
updated demo script 2
deleted demo2/md_traj.PB.transfac