Refresh_Javas: handle plugins/ & jars/ better

When compiling with a classpath that contains both .jar files in
plugins/ and jars/, and the .jar files in plugins/ have a correct
Class-Path: entry in their manifest (that does *not* include ../jars/),
there are invalid implicit class path entries that -Xlint:path
warns about.

Don't.

Pointed out by Philippe Carl.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>