When we sign an MV-JAR, the tool does not list classes inside META-INF/versions folder.
Although, if we verify a signed jar, classes in "META-INF/versions" folder are listed.

Jarsigner tool do not list version-specific files while signing.
 E.g. I have MV.jar with classes specific to jdk 8.

jarsigner -verbose -keystore key.jks -storepass password -keypass password MV_GUI.jar alias

Output:

updating: META-INF/MANIFEST.MF
   adding: META-INF/ALIAS.SF
   adding: META-INF/ALIAS.RSA
   signing: NewJFrame$1.class
   signing: NewJFrame.class
jar signed.

But seems like classes we signed, cause when I try to verify they are present and checked:
jarsigner -verbose -verify -keystore key.jks -storepass password -keypass password MV_GUI.jar

s k 503 Mon Mar 02 15:29:32 MSK 2015 META-INF/MANIFEST.MF
          625 Mon Mar 02 15:29:32 MSK 2015 META-INF/ALIAS.SF
         1364 Mon Mar 02 15:29:32 MSK 2015 META-INF/ALIAS.RSA
            0 Tue Jan 27 14:02:16 MSK 2015 META-INF/
            0 Mon Feb 02 18:46:28 MSK 2015 META-INF/versions/
            0 Mon Feb 02 18:46:28 MSK 2015 META-INF/versions/8/
smk 506 Mon Jan 26 19:37:34 MSK 2015 META-INF/versions/8/NewJFrame$1.class
smk 3946 Mon Jan 26 19:37:34 MSK 2015 META-INF/versions/8/NewJFrame.class
smk 509 Mon Jan 26 19:44:32 MSK 2015 NewJFrame$1.class
smk 3896 Mon Jan 26 19:44:32 MSK 2015 NewJFrame.class