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Rob Stryker wrote:

 

If opening and closing the project fixes the situation, this would most-likely indicate a bug in upsteram's J2EEDeployableFactory and JEEDeployableFactory.

As Sneza mentioned, it's probably this thing: https://bugs.eclipse.org/bugs/show_bug.cgi?id=279360 It would supposedly be fixed in WTP 3.2, but an interesting entry was added just today:

It was not working for deploy because we never computed the variable and
external jar entries for a single root project.  However, I recently addressed
in issue with this in bug 306534 and now variables and external jars will be
returned as child modules as long as they qualify.  However, it is up to server
tools to get these child modules and process them properly.  Not sure if this
is happening in all cases.  Classpath containers, which get added into the
classpath file with the dependency attribute, are now checked in the single
root util.  If found it now returns false.

Rob Stryker wrote:

 

If you have any small example test project that replicates this i'd be glad to test it.

At the moment I don't have such an example really. I tried to create a small test project, but here everything just worked and it 'seemed' (I'm not 100% sure) that publishing this to the server was also an impulse for the missing libs in the other project to be deployed again. As soon as I have something I will surely attach it here. Thanks for the offer to test it.