You may not necessarily want to change the file format. Are you
working from a version control system (cvs, subversion, git, etc.)
with other people? If so, then changing the file format from dos to
unix would result in every line of the file being edited (all the line
endings) and if another user ends up changing it back to dos then
every line is edited again. Those kind of full file edits could cause
some issues with the version control (i.e. annotate/blame could become
useless).
What I find odd is that the file format after the correction is still
dos, but at that point you start to see the ^Ms. What Os are you
running on? Could you perhaps send me a simple file which exhibits
this issue?
Also, could you try starting vim (or gvim if that's what you are
using) like so and run the correction again to see if the problem
still occurs:
$ vim -u NONE -U NONE --cmd "set nocp | sy on | filetype plugin on | ru plugin/eclim.vim"
or
$ gvim -u NONE -U NONE --cmd "set nocp | sy on | filetype plugin on | ru plugin/eclim.vim"
--
eric