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For building commercial products based on eclipse a hook for obfuscation in an automated build is needed. This includes also the build of update-sites. At the moment there is only a possibility to enable/disable signing of jars but ONLY for "packaged" builds - not for update-site-builds What would be usefull is a hook which is called every time a jar was generated.
Please check the page http://help.eclipse.org/help32/topic/org.eclipse.pde.doc.user/guide/tasks/pde_custom_callbacks.htm These hooks have been added to address this kind of problems. Closing for now, but please let us know if this is still a problem.
We are aware of these hooks. The problem is, that most obfsucators work on jars and not on class files. Note that the build.jars target does not build any jar files in the PDE context (!) Instead of that, the jar files are created by several zip targets in different places e.g. build.update.jars and in the main task of the packager's ant file. There is neither a common place where the jar files for plugins are created nor is there a hook to be called directly after the creation of a jar file, no matter if you are building a packaged product or an update site.
Hooks have been added in HEAD, see org.eclipse.pde.build/templates/headless-build/customAssembly.xml. This file must be copied into the builder directory. There are pre.jarsigning and post.jarUp targets which may be used to obfuscate.
