Ok, everything is I've multiple php sites all running on a single server utilizing the same Content management systems. There's no alternation in the core code or modules for that Content management systems between sites so want to have sites make use of the same code repository to really make it simpler to help keep all of the sites running exactly the same version.

This part is simple enough to complete using symbolic links, but ideally I'd like the files simply to be cached by APC once therefore the core code has already been cached for the sites.

The setup is PHP 5.2, APC, apache.

Not understanding much about APC i am speculating the pathing is performed in the symbolic link so that they appear as different files between your sites. Using the Content management systems inside my last job it used pointer files to incorporate the primary code, but want to avoid this because it is untidy and causes it to be harder to keep. Another real question is whether different sites may use exactly the same cache, in searching for this issue I've observed difficulties with fastcgi the inability to share between processes.

Any help could be greatly appreciated.

I have considered that by utilizing pointer files, personal files within the primary web site to include each relevant file, however the content management systems is around 100 files, plus much more for just about any modules used. For that content management systems itself to operate correctly, the files have to be in some manner physically within the subdirectory from the primary site. I am thinking it is not really possible, shame, because it could have been nice whether it was. Presently running on the VPS so memory is restricted.