Refactor two-pass compilation logic to base pom.xml

In ImageJA we use a known two-pass compilation workaround to allow compilation with JDK's pre-Java 9, despite the presence of a module-info.java.

As JPMS integration becomes more ubiquitous throughout the SciJava ecosystem, it would make sense to relocate this fix to the base pom, as a counterpart to the java 9 profile.