Annotation, multithreading when separate_db and better

Some major improvements with only one new functionality: annotation

• Adds external annotation via csv files -- see user.yml for more information
• Multithreading jobs when separating databases
• Implemented benchmarking in script.rb (see src/script.rb to add benchmarking)
• Better documentation of config files
• All paths in user.yml are relative to this file
• Adds origin sequence from BLAST db (in addition to aligned portion)
• Download taxonomy only for working dir in scripts
• Searches databases by calling blastdbcmd instead of looking for files with extensions *.nhr and *.phr