Recompile system app

Recompile system app

Because I'm creating a custom ROM I want to remove some entries from the
settings.apk Because there is no way to hide a preference with XML I have
to change the source code from the apk and have to delete the preference
from the PreferenceScreen. So I decompiled the classes.dex with dex2jar
copied the source code and add the following line:
getPreferenceScreen().removePreference(findPreference("toggle_wifi"));
Now my problem is that I do not know how to recompile the app. I can't
compile it wit Eclipse because it uses some system namespaces (in Eclipse
it is an error so I can't compile) How can I recompile the app? I only
have the *.java files.