- Allow multiple PHPUnit configuration files

Add code in to allow multiple PHPUnit configuration files to be
specified in the bootstrap config array

- Allow multiple root test directories

Add code in to allow multiple root test directories to be specified in
the bootstrap config array

- Allow arguments to be passed to comand line version

Allow certain bootstrap variables to be passed to the command line
version including xml_configuration_file so that it can work with the
new optional array format

- Pre-emptively warn user of major failure reasons

Warn the user of the following:
* the template cache directory is not writable (required during setup)
* the XML configuration file doesn't contain the PHPUnit_Util_Log_JSON
listener (required when using xml conf files)
* the results retrieved from PHPUnit_TextUI_Command don't contain a
json (required to parse results)