In Eclipse’s Package Explorer View, objects can have an adornment which consists of an orange rectangle (or cylinder), like so:

I can’t find it in the icon reference for Eclipse Indigo.
What does it mean?
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It means the file is under version control. (i.e. cvs, svn, git or something else)
You can have a look for the meaning here : http://www.rorycullen.com/blog/2009/07/guide-to-subclipse-decorator-icons/
maybe not your version control system, but it’s pretty standard in eclipse.