Are there any impacts or repercussions if the dos2unix command is run on Java source files, right before they are compiled? The Java files would be downloaded from a CVS repository in Linux and then compiled to a jar by an Ant script. Thanks.
No need to even test this (theoretically): in the Java languages, line breaks bare no semantical meaning. Therefore there presence is irrelevant (to the compiler that is).
So a human reader mind find it very unpleasant to look at source code that has zero newlines, or a newline in just any place where they are legit - for the compiler, as said: it doesn't matter.
Therefore tools like dos2unix are not supposed to make any changes to source code that could make a "semantical" difference.
And of course: the real answer is: don't spend your time worrying about line breaks. Invest it into moving your the whole system from 1999 to 2018 (by getting replacing say CVS with git, and Ant with maven/gradle for example).