Apache Commons VFS with Quercus

On an unmodified install, how can I configure Quercus so that PHP file functions use Apache Commons VFS to access files?

That's quite a bit of development! More than can fit in an answer here. In outline, there are two main obstacles to overcome here:

1. implementing functions in PHP that use VFS I/O rather than regular I/O
2. replacing the standard file functions (fopen/fread/fwrite/fclose) with the functions above.

Implementing a Quercus module is fairly straightforward - you define functions to be available in php. The main work of the module is to provide the interface to VFS.

class VFSModule extends AbstractQuercusModule
{

    FileSystemManager fsManager = VFS.getManager();

    public Object vfs_fopen(String filename, String mode) {            
        FileObject file =  fsManager.resolveFile(filename);
        if (mode.equals("r"))
            return file.getContent().getInputStream();
        else if (mode.equals("w"))
            return file.getContent().getOutputStream();
        throw new IllegalArgumentException("unsupported mode; "+mode);                
    }

    function String vfs_fread(Object stream, int length) {
        InputStream in = (InputStream)stream;
        byte[] buffer = new byte[length];
        int read = in.read(buffer);
        // todo - handle smaller than length reads
        return buffer;
    }

    function void vfs_fwrite(Object stream, int length, byte[] data) {
        OutputStream out = (OutputStream)stream;
        out.write(data);
    }

} 

(IOException handling is left out to avoid clutter.)

Once the module is coded, as a sanity test, write some php script that calls the custom vfs functions from this module.

Since you can call java (and vfs) directly from PHP, you could do this without a module by coding the equivalent VFS calls in PHP.

$mgr = org.apache.commons.vfs2.VFS.getManager();

function vfs_open($filename, $mode) {
   if ($mode=="r") {
      return $mgr->resolveFile($filename)->content->getInputStream();
   }
   else if ($mode=="w") {
      return $mgr->resolveFile($filename)->content->getOutputStream();
   }
  // todo - handle other mode combinations
}
function vfs_read($resource, $length) {
   $buf = str_repeat(" ", 1024);
   $lenRead = $resource->read($buf, 0, 1024);
   if ($lenRead<0) return "";
   return substr($buf, 0, $lenRead);
}

The next part is mapping these functions to the standard php file functions. This can be done several ways, as described in redefine buit-in php functions.