`made-deps-path-based` would sometimes create invalid relative paths when `third_party/packages` was involved because it was using the sibling directory of `packages` as the base. This updates the logic to always make the paths relative to the repository root; this is often a longer relative path than necessary, but that's harmless, and always using the repo root makes it easier to reason about.
Also fixes the fact that paths that were already path based (which is always the case for `some_package/example`'s dependency on `some_package`) were being overridden, causing CI to do some unnecessary duplicate analysis work.
030dd4eafa