Make sure replica runs up to max + del_beta.

max can now therefore be set exactly equal to MAX/2 where
MAX is the max corresponding to the "normal" run.
Make sure mutualinfo also runs up to max+del_beta.
Add bash script mutualinfo.sh for whole runs.
Update Makefile for source file name changes.
mutuainfo should go only upto max, not max+incre.
Update README file with bash script instructions.
Minor edit to README.
Minor update to README.
Minor update to README.
Merge pull request #1 from badshah400/master

Bash script to run and save results in new directory every run