$ mkdir patches subdir

$ cat > editor
< #! /bin/sh
< echo Editing $1
< sed -e 's:foo:bar:' $1 > $1.new
< mv $1.new $1
$ chmod +x editor
$ export EDITOR=%PWD/editor

$ quilt new patch
> Patch patches/patch is now on top

$ echo foobar > foobar
$ quilt edit foobar
> File foobar added to patch patches/patch
> Editing foobar

$ cd subdir
$ echo foo > foo
$ quilt edit foo
> File subdir/foo added to patch ../patches/patch
> Editing subdir/foo

$ cd ..
$ cat foobar
> barbar

$ cat subdir/foo
> bar

$ quilt files
> foobar
> subdir/foo