1) jdeps doesn't handle the same package name being used in more than one JAR files

$ ./bin/jdeps demo/jfc/Notepad/Notepad.jar demo/jfc/SwingSet2/SwingSet2.jar
demo/jfc/Notepad/Notepad.jar -> /net/scanas404.us.oracle.com/export/java-re/jdk/8/ea/b113/binaries/solaris-x64/jre/lib/rt.jar
   <unnamed> (Notepad.jar)
      -> java.awt
      ...
demo/jfc/SwingSet2/SwingSet2.jar -> demo/jfc/Notepad/Notepad.jar
demo/jfc/SwingSet2/SwingSet2.jar -> /net/scanas404.us.oracle.com/export/java-re/jdk/8/ea/b113/binaries/solaris-x64/jre/lib/rt.jar
   <unnamed> (SwingSet2.jar)
      -> <unnamed> Notepad.jar
      -> java.awt
      ...

2) javax.crypto.* packages are in compact1 but shown as "JDK internal API".

jdeps reads ct.sym to determine which packages are which profiles. javax.crypto.* in compact1 but not in rt.jar (they are in jce.jar) and thus they are not included in ct.sym. So dependency on javax.crypto.* APIs is incorrectly shown as JDK internal API.

ct.sym was designed to work only with rt.jar. Since javac treats jce.jar as in other jars in classpath and javax.crypto.* are in compact1, program using javax.crypto is compiled successfully with -profile compact1. Instead of generating ct.sym to work with multiple jars that would require javac to change too, jdeps will special these APIs in jdeps.

3) -verbose prints all class dependencies including those within the same JAR file. The summary.dot file should show package-level summary which would be more useful for analysis when -verbose is specified.