The contents between 'Service Project'\ServiceDefinition.csx\roles\WebRole and 'WebRole Project'\ are different, and think they should be the same.
This would avoid any Refresh issues.
\ServiceDefinition.csx\roles\WebRole currently contains:
a. WebRole contents
b. folder PHP Azure SDK
c. folder PHP core (with php.ini and extensions)
If by default, a WebRole project contains the other two folders, then for advanced users would be able to modify php.ini and add extensions.
Thereby, upon 'Package Application' could be performed with Refresh, which would include a complete copy of contents of WebRole package into
'Service Project'\ServiceDefinition.csx\roles\WebRole folder.