Kaedenn improvements #13
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Added a gitignore Added a common bash script (work in progress) Added preliminary changes to master_script.sh Added a script to extract programs (work in progress)
Further additions to the common script Fixes and cleanup to the database download, package installation, and test of the master script.
Various improvements to setup_and_test items Added input and output folders to .gitignore
Incorporating improvements from Kaedenn, many programming updates
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Many improvements made by Github user Kaedenn, improving pathing and use of some of the SAMSA2 programs. Rewriting of common paths, easier installation and setup, and improvements to some of the output messages.
Merged mainly from fork https://github.com/Kaedenn/samsa2/ .