[BUGFIX] Adjust to TYPO3 Flow CGL

This adjusts the code base to be more in sync with the Flow Coding
guidelines:
http://docs.typo3.org/flow/TYPO3FlowDocumentation/TheDefinitiveGuide/PartV/CodingGuideLines/PHP.html

While there are mostly cosmetic tweaks this also contains some
fixes to otherwise breaking code, thus the "BUGFIX" prefix.

@Mario: I'm not sure whether you *want* to adapt the Flow CGL, otherwise ignore this. But you should at least take over the fix from MetaDataExtractorCommandController line 182/216. Also please verify that the changed behavior in MetaDataExtractorCommandController::getCachePath() works for you. Modifying the application context on the ConfigurationManager (singleton) can have severe side-effects