Ok, here's a quick status as to where I got.

 - Picked through our remaining ambiguous "javax" string references and fixed 
them by checking in the affected file at the library version we're using, then 
took a look at their master branch to see how they've adapter for the "jakarta" 
namespace and applied that fix to our copy.

 - Updated the tomee-patch-plugin to update strings in files and in the case of 
JSF update the path of the file; there are some '*-resources/javax.faces/" 
files.  Those were all renamed.

 - Applied any bytecode transformations that the Eclipse Transformer missed.  
Strings in annotation values were not being updated, nor were any module-info 
classes.  After that there were a few small string tweaks it probably could 
handle with the right configuration, but I just wanted to get this over with so 
I put them in the tomee-patch-plugin for now.

 - Updated the tomee-patch-plugin to remove any signatures that are on any jars.
 
The server boots and looks pretty good at least from a cursory perspective.  We 
need to do some more testing.

Here's the PR which I think is ready to be merged so others can continue down 
this path.

 - https://github.com/apache/tomee/pull/662


-David

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