When upgrading magento via ssh, it upgrades to the same version... Here is an example:
./mage list-upgrades
returns 'Mage_All_Latest: 1.8.1.0 => 1.9.1.1' then I do:
./mage install http://connect20.magentocommerce.com/community Mage_All_Latest --force
which returns 'Package community/Mage_All_Latest 1.8.1.0 installed successfully'
TL;DR: Magento packages upgrade to the version they are already on, instead of upgrading to the newest version available.
You just need to upgrade list of modules by ./mage upgrade-all. You might have to replace mage with pear though.
When the process is complete you'll see a list of modules saying 'already installed', 'package upgraded' etc...
Some of links which will help you.
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