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Using M6, here is a reproducable test case. All plugins are imported as binaries except JDT/Core + JDT/Core tests. Go into org.eclipse.jdt.core.formatter.DefaultCodeFormatterConstants. Select for example, FORMATTER_BLANK_LINES_BEFORE_IMPORTS and search for references in the workspace. It finds only two hits in the code formatter code. It should also find a reference in the code formatter preference page code. org.eclipse.jdt.internal.ui.preferences.formatter.BlankLinesTabPage line 86.
I think this has always worked this way. We index the .class files & use their constant pool to find references, so we miss inlined fields. Using the attached source would be considerably slower.