Thank you for this work. The fix looks good to me and makes sense to me. It did not occur to me that a module-info file is in the game because it is so well hidden and not present in source.
Have you signed the CLA?
Also, please feel free to add yourself to ACKNOWLEDGMENTS (unless you are already in the list).

Just signed CLA. I will skip ACKNOWLEDGMENTS file for now.

Alright. (We may still record your contribution in ACKNOWLEDGMENTS eventually by means of #308, I hope that's okay for you.)

@juniartisu Does this fix work for you as well?/Can you confirm it fixes #316 in your environment?

@Stewori I will try out the fix and do testing on it and will put update here once it is done.

@Stewori The fix is good. I am not seeing any issue so far. Than you @lifebarier for investigating and fixing it.

@lifebarier could you do me a favor and add the line
- [ GH-316 ] PR313 cause regression
to the NEWS file (line 22) as part of this PR? Then I wouldn't have to make a separate PR for that. When done, I will merge this PR. Thanks again!

@lifebarier @Stewori
i tried to build the jar with ant after this fix. Though the shading is done properly but still i see errors when i am trying to decompile the built jar with Java Decompiler jd-gui-1.6.6.jar.
this error indicate incomplete or corrupted jar.

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 9
at com.sun.nio.zipfs.ZipConstants.SH(ZipConstants.java:192)
at com.sun.nio.zipfs.ZipConstants.LG(ZipConstants.java:196)
at com.sun.nio.zipfs.ZipFileSystem$Entry.readExtra(ZipFileSystem.java:2302)
at com.sun.nio.zipfs.ZipFileSystem$Entry.cen(ZipFileSystem.java:1903)
at com.sun.nio.zipfs.ZipFileSystem$Entry.readCEN(ZipFileSystem.java:1871)
at com.sun.nio.zipfs.ZipFileSystem.getEntry0(ZipFileSystem.java:1329)
at com.sun.nio.zipfs.ZipFileSystem.getFileAttributes(ZipFileSystem.java:317)
at com.sun.nio.zipfs.ZipPath.getAttributes(ZipPath.java:664)
at com.sun.nio.zipfs.ZipFileSystemProvider.readAttributes(ZipFileSystemProvider.java:294)
at java.nio.file.Files.readAttributes(Files.java:1737)
at java.nio.file.Files.isDirectory(Files.java:2192)
at org.jd.gui.model.container.GenericContainer$Entry.isDirectory(GenericContainer.java:110)
at org.jd.gui.model.container.ContainerEntryComparator.compare(ContainerEntryComparator.java:26)

@abhi-rck
Why are you trying to decompile jar?
I would be really surprised if change to exclude 2 module-info files from build would break jar in such way.
Anyhow, for fun I tired to open jython-standalone.jar with that decompiler and it opened just fine.