I also don't understand why the default char encoding in JDev is platform dependent. For example on my Mac it is "MacRoman" which might confuse international Windows users :-) I always set JDev to use UTF-8 as default encoding, but it is really something everyone in your team has to do and preferably before starting a project so all files are created in UTF-8
This new audit rule could check that each XML file is in the UTF-8 encoding and suggest to the user in the audit warning to set UTF-8 as default in JDev's preferences. Anyone is invited to implement this AUDITRULES-26 issue,. It is an open source community project for a reason :-)
Non-XML files (like java source) are impossible to check, unless you introduce byte-order-markers but many tools will fail of a BOM is present. Hopefully suggesting the proper default through an audit rules does the trick.
BTW my suggestion is to only use plain ASCII in Java files. Better use \u1234 so you know everybody can read the java file regardless the character encoding they use when opening the file.