Ground work for processing additional sites sampled from the pool of multinomial negatives

This addresses the need for running AAModel on specific sites, e.g sampled sites from the pool of multinomial negatives. To achieve it, following changes were made :

• Clean up Alignment_run module from legacy functions and move functions specifically related to multinomial scan into their own module Multinomial. Introduce Multinomial.result type that wrap Multinomial_test.result with info about the site (Constant | Variable), to avoid redondant computation of the site state.
• Store site state (Constant | Variable) in the cache alongside scan results
• Implement a conductor to define specific sites to be processed ; also refactor the conductors (see Scan_cmd.Conductor and AAModel). Constant site detection is now delegated to the conductor to take advantage of cached data / multinomial scan.
• Add a flag to the CLI to specify a number of multinomial negatives to be sampled and processed by AAModel