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This will allow checking common configuration information into CVS (e.g., input jars). It'd be great to store this info in the .project file.
reclassified as enhancement request...
We're planning to implement this functionality in the same way as the JDT does in Eclipse 3.1 (M2 onwards), by having a per-project ".settings" directory, and then files in here contain the settings from different plugins, e.g. org.eclipse.jdt.core.prefs. So we could have org.eclipse.ajdt.core.prefs and/or org.eclipse.ajdt.ui.prefs files.
I've now done the first bit of this. The preference which stores the current build configuration file now has project scope, which means it appears in the .settings directory of the project, and so can be checked in with the project.
It's now all done, and available in the latest development build. Compiler settings are stored, and so are outjar, inpath, aspectpath etc. The preference files appear under a ".settings" directory. JDT uses this directory on Eclipse 3.1, but we now use it across Eclipse 3.0 and 3.1.