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While starting a 3.0 workspace with I200407271028 build, I see that new .settings folder appears in projects I have set specific compiler options. This is normal as using 3.1, we have migrated projects compiler options from self-hand made to new Platform/Core Preferences API... However, looking at one .prefs file contents, I see that only modified options are stored in this file. This is not correct as all compiler preferences, even those values are the same than workspace ones, should be present in this file.
While migrating preferences, we do not write preference which have a default value in Javaproject.updatePreferences(IEclipsePreferences)... This test must be removed.
Fixed and released in HEAD. All compiler options for a project are now stored in IEclipsePreferences while migrating a 3.0 or earlier workspace. [jdt-core-internal] Change done in JavaProject.updatePreferences(IEclipsePreferences) method. I've tested this change (ie. open a 3.0 workspace with I200407271028 + this fix), but no test case was added as it's not really possible to simulate this migration using JUnit...
*** Bug 68988 has been marked as a duplicate of this bug. ***
Verified in I200409230100.