If anyone else has an issue with the "Path Mapping" popup appearing when debugging a Flex and PHP application on your local Zend Server, here is the solution.
When you first install Flash Builder 4.5 for PHP, it will remind you to download and install Zend Server CE.
Once you have done that, the next time you start Flash Builder, you get this.
Unfortunately, Flash Builder for PHP did not configure Path Mapping for Zend Server CE correctly. When I create a combined Flex and PHP project, and go to debug it, I got this:
The popup appears like 100 times for various php classes in the framework. I would select the bottom option of "Get content from the server for the following path:" I would have to go through 5 minutes of clicking these popups before finally getting my application to launch.
The problem turned out to be the Path Mapping. If you go to Preferences --> PHP --> PHP Servers, you will see that the Local Zend Server has been added as the default. Select it and click the Edit button. Then select the Path Mapping tab.
The entry for Zend Framework will point to a wrong server path.
The "Path on Server" is set to /usr/local/zend/ZendServer/share/ZendFramework/library
It should be set to /usr/local/zend/share/ZendFramework/library
Once I changed it, the popups no longer appeared.