filter_assim refactor

Refactoring filter assim:

• Each process calculates increments vs. previously only one process would do this for each observation. So more elements in the broadcast/send receive, and redundant (but simultaneous) calculation by each process. This is to allow future implementation of new assimilation algorithms

Code readability changes:

• removed timing variables
• get_close caching moved inside subroutine
• adaptive localization moved into subroutine
• cov_factor and adjust_obs_impact moved into subroutine
• Call new subroutines in adaptive_inflate_mod:
• update_single_state_space_inflation, update_varying_state_space_inflation