praefect: Fix inconsistencies in praefect sub-commands

The change fixes file names for sub-commands as well as moves code into separate files to organise it with file per sub-command layout.
The change also fixes usage of magic literals by using constants instead and relocates code from sub-command specific file into a shared subcmd.go file. The file names also aligned with a common format - snake case named after the sub-command name.
The change also includes a dial timeout configuration for the remove-repository sub-command to speed up the test one of TestRemoveRepository_Exec_gitalies_is_out_of_service.