Anyone know how to get rid of those line borders in Eclipse (using Aptana plugin for Rails development).

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I believe those borders fall under “Annotations” in Eclipse. Go to Window -> Preferences -> General -> Editors -> Text Editors -> Annotations and find the offending annotation.
If it is “Occurrences” annotation type that is causing the lines to appear, you can either uncheck the “Text as” box or you can find the “Mark Occurrence” setting and turn it off altogether.