Script ensures step completed before moving on to next step

Tests were added to ensure that the output files from the previous step
exist before moving on to next step. This should make debugging much
easier when a run dies.

Fixed bug in which NPT run with constrained protein atoms started from
EM results instead of NVT results.

Cleaned up some cosmetic formatting issues.
Added primitive analysis script

Runs all of the common analysis operations. It's primitive because it
doesn't check to make sure files exist, file names are hard-coded,
and the user has to enter a lot of correct options without prompting.

Also added more output file extensions to .gitignore