Because the virtualization server involves a very deep integration
with Tomcat, there's no guarantee you won't hit problems that
might result from trying to make things work on a non-certified
version. However, if you're going to really take over low-level
administration of this servlet container, let's assume you'll also
take over the QA functions as well for the entire integration
(i.e.: you're happy to "swim at your own risk")….
The easiest approach might be for you to just install WCM
in two disjoint directories: X and Y (i.e.: X & Y are neither
parents, children, nor siblings of each other). Use X as your
"pristine alfresco" source, and Y as where you do your in-place
modifications.
This allows you to create a patch that transforms X –> Y,
and also creates a debugging environment for you, should
your patched version fail; if X works but Y fails, you know
where to start looking for the problem. Also, as Alfresco
issues new releases (e.g.: X'), you can create a patch
that brings you from X –> X', and use that as the basis
of creating your Y –> Y' patch.
Also, if you're on Windows, be sure you install the virt server
as a service, not as a console app (Alfresco's current installer
is defective in this regard, currently). To do this by hand from
a CMD shell, cd into the c:\alfresco-XXX\ directory,
then do this: set JAVA_HOME=c:\alfresco-XXX\java
then do this: bin\service.bat install alfrescoVirtualTomcat
where "c:\alfresco-XXX" corresponds to where ever you've
installed alfresco.