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In 3.0m3, build.properties has a new multipage editor which is nice, but I believe its first editor page really belongs as a tab in the plugin manifest editor. The two files have to be kept in sync anyway (see for example bug 34165). I would even go so far as to suggest that build.properties should be a hidden file like .classpath, automatically maintained by the PDE UI, if possible. There is precedent - the doc says "The information [in the run-time information page] about the source folders that should be compiled to produce the libraries is actually stored in a separate file (build.properties). When you change this information, build.properties will be updated. This can only happen if the file is not in use. If it is, the manifest editor will indicate that the file is in use and you will only be able to browse the information." So there's another problem this would help fix: what happens when you are editing both the build.properties file and the plugin.xml file. Rationale: Build.properties is just such a rich source of problems for plugin developers and I'm tired of answering questions about it :).
The mutual exclusion of editing the plugin.xml and build.properties files has gone away in 3.0M3.
will be addressed in bug 37661 *** This bug has been marked as a duplicate of 37661 ***