search_and_combine

See merge request ec504/ec504_projects/group4!2

working command-line interface

See merge request ec504/ec504_projects/group4!1

Merge branch 'combine_wip_db_and_MoleculeClass' of agile.bu.edu:ec504/ec504_projects/group4 into combine_wip_db_and_MoleculeClass

Molecule class now implements Serializable, bug: atomArrayList compare; comment out for now, extra prints for each stage of compares in areMoleculesEqual()

clean dependencies, change outer database structure to HashMap, add print database command, implement addMolecule, add check for nonexistent ArrayList in findMolecule, rearrange catch in save and load

add command handlers for user arguments with different number of tokens, better termination logic on timeout

bugfix: pass initial arguments to server, bugfix: correct argument to client, close streams in the same scope after receiving client message