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Concerning the Joomla core (not the third party extension);
You can update the Joomla with the "extension manager" / update
OR unzip the standard joomla distribution in the root of your master.
Before unzip the joomla distribution, rename the existing "/installation" into "/installation_jms".
Unzip the joomla.tar.gz or joomla.zip
Rename the "/installation" into "/installation_original"
Login in the back-end of the master (/administrator/index.php)
Go in JMS and re-install the patches
When done, you have a new "/installation" directory restored.
Remove or rename this one to re-use the original one (in case you have a specific language version - not the english one).
Rename "/installation" into "/installation_jms25"
Rename "/installation_original" into "/installation"
When done, return in JMS patches to install the patch into the "installation".
After that, go in the new "extension manager" / database checking and fix the DB layout.
Repeat the "extension maanager" / database / fix for each slave sites.
After that, you should have all your websites updated with Joomla 2.5 and the new database layout.
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