Pretty much agree with tohu for daily usage. The different usage & connotation is imo mainly evident in science & industry. Would explain the weird ngrams chart imo.
blue=prüfung, red=überprüfung

On the google trends graph you can see clearly the peak when Fukushima happened around march 2011. Überprüfung
has the connotation of a independent 3rd person/institution checking a system while a Prüfung
is e.g. a school or phd test inside a institution. The blue google trends line oscillates pretty periodically, at the end of every year there are no Prüfungen
, mostly in the middle.
The rise of überprüfen
in ngrams is imo linked to the continuous arising of technological systems in the last century and more & more Überprüfungen
in our technological society. Here the connotation and meaning of Überprüfung
is imo known and clear, esp. in industry/science.
In science you also say gegenprüfen
, when several scientist/groups independently check the same hypothesis/theory. Ich prüfe meine Daten/Behauptung
vs. Ich überprüfe eine fremde Conclusio/Messdaten
. The prefixes gegen/über
dont say anything about quality or number of tests, but what it refers to. über
simply implies/connotes someone over or outside of the hierarchy of the proved institution/system is checking. In English this distinction doesnt seem to exist according to ger/eng dictionaries.
Your XML-Parser is basically an exterior softare checking your code, so you would say überprüfen
. If you "parse" your source code yourself by looking over it and check spelling, prüfen
would imo be more correct. But here its really überhairsplitting :)
Weiterhin kann man (können Sie) die geparsten Dateien mit einem XML-Schema überprüfen.