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Ok, maybe we need to analyze the pros and cons of doing it that way.
This is your solution:
var/lib/Zend/ /ZendFramework-0.0.9 /Zend /ZendFramework-1.0.0 /Zend /ZendFramework-1.0.1 /Zend
Magento1/ lib/ Varien/
Magento2/ lib/ Varien/
File: Magento1/app/Manage.php
ini_set('include_path', ini_get('include_path').PS.BP.'/lib'.PS.BP.'/app/code/core'.PS.'/var/lib/Zend/ZendFramework-0.0.9/Zend');
File: Magento2/app/Manage.php
ini_set('include_path', ini_get('include_path').PS.BP.'/lib'.PS.BP.'/app/code/core'.PS.'/var/lib/Zend/ZendFramework-1.0.0/Zend');
Ok, the symlinks are gone. Now we have a new problem. The developers working on the Magento2 website don’t have access to the Zend framework. They only have access to the /home/sites/Magento2 directory. Only root and Core developers can access the ZF directory. So, Magento2 developers have no way of viewing the core components of the system.
Maybe a normal user will not face this problem, but maybe a Web development agency will.
Here is a good example of an App coexisting with the Zend Framework: Trex. Figure 1.3 - Directory Structure.
My solutions, the same solution provided in Trex:
var/lib/Zend/ /ZendFramework-0.0.9 /Zend /ZendFramework-1.0.0 /Zend /ZendFramework-1.0.1 /Zend
Magento1/ lib/ Varien/ Zend-0.0.9/ (symlink to ZendFramework-0.0.9) /Zend
Magento2/ lib/ Varien/ Zend-1.0.0/ (symlink) /Zend
File: Magento1/app/Manage.php
ini_set('include_path', ini_get('include_path').PS.BP.'/lib'.PS.BP.'/app/code/core'.PS..BP.'/lib/Zend-0.0.9/Zend');
File: Magento2/app/Manage.php
ini_set('include_path', ini_get('include_path').PS.BP.'/lib'.PS.BP.'/app/code/core'.PS..BP.'/lib/Zend-1.0.0/Zend');
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