improve "check" command and update phar binary

The "check" command now has three commandline options:
- bootstrap: a file that is required before running the checks
- config: the config file with check definitions (not implemented yet)
- include_path: path to prepend to include_path PHP ini setting

The three default Configurator checks are configured via an array to
prepare this part of the CheckCommand for a config file parser or
something like that.