Improve argument handling and clean up unecessary files

run_analysis.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python3
+
+from auto_namd.functions import analysis_parser
+from auto_namd.job import get_next_job, get_jobs_from_path, create_job_instances
+
+
+def main(jobs_path, ffs_path, steps, namdbin, params):
+
+    jobs_path = abs_path(jobs_path)
+    job_dirs_l = get_jobs_from_path(jobs_path)
+    jobs = create_job_instances(job_dirs_l)
+
+
+
+if __name__ == '__main__':
+    main()