Fix shadowing rules in ClasspathBuilder for jars.

Files in jars coming earlier in a classpath should shadow files
with the same *relative* path to their jar coming later in a
classpath. This behavior was broken in
d97f7d090f44a8399df72e82f876e822a9fc27d7 and so here's the fix.
Merge pull request #537 from sjrd/fix-classpath-shadowing

Fix shadowing rules in ClasspathBuilder for jars.