Mega refactor - with focus on improving the CLI and setup.

Changes
-------
We now have an equivalent CLI switch for every option one could set via
configuration file. If the same option is set in configuration file and
passed from command line, command line will take precedence.

Database dir is now a compulsory option and it's the only compulsory option.

Host is now configurable.

format-databases subcommand has been removed in favour of -m switch.
And -l & -u will respectively list BLAST+ databases and FASTA files
yet to be converted into a BLAST+ database.

Can update configuration file from command line using -s switch.

Can run SequenceServer in interactive mode (-i).

When using SequenceServer for the first time:
  - If BLAST+ not installed, offer to install.
  - If no BLAST+ database in database dir, offer to create BLAST+ databases.

Simple plug-in architecture:
  - Optionally load a Ruby script after initialisation.

Refactoring
-----------
SequenceServer module defines all functionality needed to setup, start and run.
  - Removed DatabaseFormatter module. Made the functions a part of SequenceServer
    module.
  - Blast module is now mixed into SequenceServer instead of SequenceServer::App.
  - SequenceServer::App is now just a controller. Rack entry point is
    `SequenceServer.call`

Squashed sequencehelpers.rb and sequence.rb into one - sequence.rb.

Rename sinatralikelogformatter.rb to logger.rb and have it define a custom
logger with the same logging format.

Switched to Slop in bin/sequenceserver.

SequenceServer#verbose? -> true if development mode.

Symbolize keys from config.yml.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>