Since PDT was introduced we used .projectOptions file in order to save some of the project properties like the project nature and PHP include path.
We have changed this behavior to use Eclipse standard preferences mechanism.
Backward compatibility is being preserved; .projectOptions files are being read and deployed into the preferences mechanism.
This behavior was integrated to the latest integration build (I20070808), please let me know if you’ve encountered any problems with it.
Team Leader, Development Tools