Jesse C explains the requested feature nicely in the mailing list:
"In the older version of sbt-eclipse it set the eclipse target directory to something other than the sbt target directory. In the current version it appears to be using the same target directory in eclipse as in sbt and I do not see a preference for changing this.
Is there any way to get back the functionality where it generates eclipse code into a different directory?
I consider anything that eclipse does to be throwaway, since it is missing a large chunk of the actual build process (all it is doing is compiling some java and scala files) so I don't want it mucking around with my actual target directory. I like having eclipse compile, since it gives me a nice graphical interface for dealing with errors. So what I'd prefer is to have eclipse compile to somewhere other than my target directory and leave sbt alone."
closes #80: Add setting for different target directories