This fixes#117438.
If paths in dependency file are not absoulte, make (or ninja) will
canonicalize them.
While their canonicalization does not involves symbolic links expansion
(for IO performance concerns), leaving a non-absolute path in dependency
file may lead to unexpected canonicalization.
For example, '/a/../b', where '/a' is a symlink to '/c/d', it should be
'/c/b' but make (and ninja) canonicalizes it as '/b', and fails for file
not found.
ca2ab74838