[chef] usage of 'site-cookbooks' for template customizing

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Hello,

We have used the following documentation section in order to customize
templates from the mysql and php cookbooks:
http://wiki.opscode.com/display/chef/Cookbooks#Cookbooks-CustomizingTemplatesandFiles

so we created a site-cookbooks folder, added it to the cookbook_path config 
for
knife, and created apache et mysql directory structure for the templates in
order to override my.cnf.erb for mysql and debian/php.ini.erb for php

but when running the command

knife cookbook upload -a

we got the following warning:

WARNING: * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * *
WARNING: The cookbooks: mysql, php exist in multiple places in your
cookbook_path.
A composite version of these cookbooks has been compiled for uploading.

IMPORTANT: In a future version of Chef, this behavior will be removed and you
will no longer
be able to have the same version of a cookbook in multiple places in your
cookbook_path.
WARNING: The affected cookbooks are located:
mysql:
    /root/svnChef/trunk/chef-repo/cookbooks/mysql
    /root/svnChef/trunk/chef-repo/site-cookbooks/mysql
php:
    /root/svnChef/trunk/chef-repo/cookbooks/php
    /root/svnChef/trunk/chef-repo/site-cookbooks/php
WARNING: * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * *

Could you let us know what we are doing wrong please ?

Thanks in advance for your answers.

Best regards,
Christophe