Command indexation

The main changes are:
- now command and --options are *indexed* in documentation (mainly by using @ftable)
- gather from source code the options that are missing in documentation

Other minor changes are:
- consistency fixes
- moved to @samp{} when relevant
- deleted option --wide-register-format and --wide-register-report (cannot be found in source code)
- added @var like in "--option @var{STR}"
- moved options --XXXXXXX-report to naming like --XXXXXXX-format (-report cannot be found in source code)