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.