The two main areas that control the IDE's coloring:
Window | Preference | Java | Editor | Syntax Coloring
Window | Preference | General | Editors | Text Editors
These preferences are saved in:
[workspace]\.metadata\.plugins\org.eclipse.core.runtime\.settings\org.eclipse.jdt.ui.prefs
[workspace]\.metadata\.plugins\org.eclipse.core.runtime\.settings\org.eclipse.ui.editors.prefs
Linux/Mac [workspace]/.metadata/.plugins/org.eclipse.core.runtime/.settings/
Where,org.eclipse.jdt.ui.prefs = Syntax Coloring
org.eclipse.ui.editors.prefs = Text Editors
So from that one can make, import, and export their preferences easily without editing the files manually.