#697: Multiple templates in configuration only executes first one

Due to the way the config is parsed (and the lack of a Query language) was only
the first template picked. With these changes I have enabled a more robust way
of extracting the templates. However; the command handling should be refactored
to be more robust overall.

Included in this commit is the reformatting of the config template and the config
of phpDocumentor itself
#697: Multiple templates in configuration only executes first one

Using the RunCommand did not work because I had provided the wrong Typehint.
Fixed with this commit
The configuration file is dicovered by looking at the current working folder,
because this is a relativce path does the phar look inside the phar archive
and find nothing. By prepending getcwd with the config file names does this
work. During testing a second error was found in the transformation as the
structure.xml was incorrectly retrieved. This is fixed as well.
Merge branch 'master' into plugin_tests
Added unit test for listener abstract