Force Vim's mksession to use relative paths?

You can't do that without setting up a wrapper function for it, AFAIK.

E.g. something like:

function! MakeSession()
  let b:sessiondir = getcwd()
  let b:filename = b:sessiondir . '/session.vim'
  exe "mksession! " . b:filename
  exe "edit! " . b:filename
  exe "g:^cd :d"
  exe "x" 
endfunction