Allow multiple root test directories

Add code in to allow multiple root test directories to be specified in
the bootstrap config array
Allow multiple PHPUnit configuration files, Allow arguments to be passed to comand line version

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