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I've tracked down the problem was introduced by a change in
{project.build.outputDirectory}MIFOS-5879to allow the project to be built on Java7. Commit 92b18dbaaa4289a88c0e95bc1211e982b997a1aa updated the version of native2ascii-maven-plugin from 1.0-alpha-1 to 1.0-beta-1. To fix the encoding issue we could either rollback the said commit if we need to get a release out right away or change application/pom.xml line 665 from "<src>" to "<workDir>". I haven't dug deep into changes between alpha and beta versions but I suspect the config option "src" has been renamed to "workDir". Because our pom.xml didn't have a "workDir", the default $was used.
For more info about native2ascii plugin and available config options see http://mojo.codehaus.org/native2ascii-maven-plugin/native2ascii-mojo.html.