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Follow up of 87742. SCENARIO 1 1. Create a Hello world plugin 'com.example.xyz' 2. Export the plugin into a directory (D:/Temp). Leave the 'Package each plug- in in a JAR archive' option unchecked. Everything will export fine. Now for the problem. SCENARIO 2 1. Export the same plugin into the SAME directory (D:/Temp), but this time do check the 'Package each plug-in in a JAR archive' option. 2. You will see that the JAR is correctly created into D:/Temp/plugins, BUT... the directory created from scenario 1 has been deleted.
Even if the plug-in was not deleted, its content would still be changed (overwritten) since the assemble script first gather the files into a flat form. What happens then is due to the behavior of the jar'up target which jar'up the plugin from the folder, and eventually delete the folder. For now I don't see any easy way to fix this kind of problem. An approach would be to export into a tmp folder, then copy it over the folder specified by the user.
Currently we are not actively enhancing PDE build anymore. Therefore, I close this bug as WONTFIX. Please reopen, if you plan to provide a fix.