Expand on individual commands

[GavinHuttley]

Break the cli.rst file into usage descriptions for the individual commands, how do they relate to each other etc..

Explain, define, terminology in this doc too

[helmutsimon]

CLI documentation page should be self-contained.

[helmutsimon]

Need to show how you use calculate_threshold with test_neutrality_from_vcf, in particular. Perhaps combine these and output SFS, n, seg_sites etc.