Looking at the title of your question, I see that git says that ../../file.name needs to be git-deleted. So it seems that you did the git add in a directory two levels below the one that holds file.name. However, this won't work. git add works on the current directory and directories below that one, not in directories higher up in the hierarchy. Unless you specify a path, of course.
Update:
This is documented, although the hint is a bit hidden. From man git-add:
  A, --all
  
  Update files that git already knows
  about (same as --update) and add all
  untracked files that are not ignored
  by .gitignore mechanism.
and
  -u, --update
  
  Update only files that git already
  knows about, staging modified content
  for commit and marking deleted files
  for removal. This is similar to what
  "git commit -a" does in preparation
  for making a commit, except that the
  update is limited to paths specified
  on the command line. If no paths are
  specified, all tracked files in the
  current directory and its
  subdirectories are updated.