Due to differences between JGit versions, we will not be able to detect if the reason for a missing object is lack of support for submodules or not.
JGit handled Submodules via a separate exception:
org.eclipse.jgit.pgm-0.10.1.sh clone git:java.lang.UnsupportedOperationException: Submodules are not supported
at org.eclipse.jgit.lib.WorkDirCheckout$1.visitEntry(WorkDirCheckout.java:170)
at org.eclipse.jgit.lib.IndexTreeWalker.finishVisitTree(IndexTreeWalker.java:205)
at org.eclipse.jgit.lib.IndexTreeWalker.walk(IndexTreeWalker.java:142)
at org.eclipse.jgit.lib.IndexTreeWalker.walk(IndexTreeWalker.java:120)
at org.eclipse.jgit.lib.WorkDirCheckout.checkoutOutIndexNoHead(WorkDirCheckout.java:166)
at org.eclipse.jgit.lib.WorkDirCheckout.checkout(WorkDirCheckout.java:143)
at org.eclipse.jgit.pgm.Clone.doCheckout(Clone.java:192)
at org.eclipse.jgit.pgm.Clone.run(Clone.java:126)
at org.eclipse.jgit.pgm.TextBuiltin.execute(TextBuiltin.java:139)
at org.eclipse.jgit.pgm.Main.execute(Main.java:191)
at org.eclipse.jgit.pgm.Main.run(Main.java:120)
at org.eclipse.jgit.pgm.Main.main(Main.java:94)
Latest JGit does not and uses MissingObjectException instead:
org.eclipse.jgit.pgm-0.12.0-SNAPSHOT.sh clone git:fatal: Missing unknown 9ada5de967ea8805e7c8142d3647d0500100fa5a
JGit bug has been opened, error message in Git plugin has been improved.