Merge update and init options and improve help message

- deprecates the init option
- replace the keyword "all" by an option "--all"
- rename debug into dev like in the client

issue4165
review7571003
Add documentation about database setup

review7571003
Fix wrong is_module_to_install test introduced in changeset b0a271549ddd
Add support for domain_<field name> method

issue4126
review6501002
Monitor also the configuration file

issue4157
review7561002