Initial steps to get unit tests running again.

- Added PHPUnit configuration
- Added common bootstrap and updated test cases accordingly
Added missing default value for $noInclude constructor argument
Fix configuration output directory test.

Assertions regarding output directory formatting does not seem to match
the current code nor the expectations when calling getOutputDir().
Fix flag string form test

Output formatting now depends on the environment and not a fixed number
of tabs. Consequently we only test to assure that the values are
actually present and will correspond to a line in the console.
Fix array type determination tests.

Now ArrayOfObject and Object[] becomes Object[] and not array.
Merge branch 'fix-unit-tests'