Fix all commands help argument and reformat help texts

[bacali95]

Closes #69

[thevpc]

Using CoreNutsUtils.isIncludesHelpOption is a bad idea, This is why it was commented.
Take the example where "--xml" is part of the options. This call will ignore the option.
Perhaps one can do like in DefaultNutsSettingsInternalExecutable but am not sure it works properly (the version i have now is broken)

[bacali95]

I think that --xml argument and all standard options will not be ignored in this case because it will be already parsed while creating NutsBootWorkspace, so I think usinf that helper is safe.

public NutsBootWorkspace(NutsBootTerminal bootTerminal,String... args) {
    LOG=new PrivateNutsLog(bootTerminal);
    this.options=new PrivateBootWorkspaceOptions(LOG)
            .parseArguments(args)
            .setBootTerminal(bootTerminal)
            .build();
    LOG.setOptions(this.options);
    newInstanceRequirements = 0;
}

[thevpc]

--xml can appear before the command (parsed at boot) or after the command (parsed by the command)

nuts --xml ls --json

in this example, ls is executed in json format and not --xml

Let me add another example:

nuts --xml settings --json --help

[bacali95]

I didn't where the issue here, do we need to take the last format (--json or --xml...) option?

[thevpc]

Do not bother yourself with this limit case. I will accept the changes anyway.