The following patch addresses this:

[alrubinger@localhost Branch_5_x]$ svn di server/
When using an in-memory archive backed by VFS, we're using an "unjar"; this leaves out any RAM-backed resources. Instead explode the contents, regardless of what's behind the virtual abstraction:

Index: server/src/main/org/jboss/web/deployers/AbstractWarDeployer.java
===================================================================
— server/src/main/org/jboss/web/deployers/AbstractWarDeployer.java (revision 91204)
+++ server/src/main/org/jboss/web/deployers/AbstractWarDeployer.java (working copy)
-357,7 +357,7 @@

VFSDeploymentUnit vfsUnit = (VFSDeploymentUnit)unit;
VirtualFile root = vfsUnit.getRoot();

• VirtualFile unjared = VFSUtils.unjar(root);
  + VirtualFile unjared = VFSUtils.explode(root);
  // file was not unjared yet
  if (root != unjared)
  {

This was exposed by prototyping in EMB-32.