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These multiple versions for aclocal, autoconf, automake etc, are for compatability reasons. but a simple apt-get remove ( --purge optional to get rid of any config files ) will remove them. aclocal is part of the automake package.
Also emacs20 emacs20-7 are probably the same package. emacs20 points to emacs20-7.
I did use the command, dselect and then in that remove any used software, as well as configure software, etc. after running them only, I found multiple versions of same software, or maybe as you said.
If you want an interface to apt that works well, try aptitude. Its curses based, so it should run on just about anything, and makes package management a whole lot easier. (apt-get install aptitude)
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