[FEATURE] Improve and simplify the command line interfaces

[arnaud-m]

Is your feature request related to a problem? Please describe. They are too many options in the command line interfaces.

• Many of them concern internal/advanced parameters that do not interest much the end user.
• Their naming scheme is not consistent.
• The documentation is incomplete.

Describe the solution you'd like

• Define and explain the naming scheme.
• Improve the management of boolean options.
• Use the hidden keyword for internal options.
• Use the depends and forbids keywords if possible.
• Complete the documentation of the commands.

[arnaud-m]

• http://docopt.org/
• https://clig.dev/