sbteclipse was not created to support this use case.
It might be possible to tweak the sbt settings used by the eclipse
command, but you will have to dig in sbt.
Otherwise, you can create a simple sh script to "fix" the file every time your dependencies change:
sed -i 's%"/root/.ivy2/%"/home/codez/Dev/remote/wm1/root/.ivy2/%' .classpath