The mirror function should keep the original symlink target and not the real path.
When having a link that is already in a linked directory, the mirror function set the mirrored link with the realpath and not the original target directory of the symlink.

To reproduce:

I am in a project, the webapp directory in /var/www is an alias:

[14:01:30] COil@COil:/var/www/myproject$ ll
total 12K
4,0K drwxr-xr-x 3 COil COil 4,0K oct.  10 11:03 .
4,0K drwxr-xr-x 9 COil COil 4,0K déc.  26 13:50 ..
   0 lrwxrwxrwx 1 COil COil   38 juil. 10 11:40 webapp -> /home/workspace/myproject/frontend/

The /var/www/myproject/webapp/apps/symfony2 directory contains a symfony2 application, a command
mirrors the /var/www/myproject/webapp/apps/template dir to /var/www/myproject/webapp/apps/newapp.

In this new directory /var/www/myproject/webapp/apps/newapp there are symlinks:

fcBehatPlugin -> /home/workspace/myproject/frontend/apps/template/plugins/fcBehatPlugin

As you can see the symlink is incorrect as it should be the same (relative) it was in the initial template directory that was mirrored.

Same task with the patch applied, we have:

fcBehatPlugin -> ../../../vendor/server/Mycompany/fcBehatPlugin

PR #9867