Handle allow-newer packages when preparing contributions

At the moment, the instructions to build a patch read as follows:

1. `scripts/patch-tool unpack doctest`
2. Modify files in `packages/doctest-$version/` as necessary
3. Build/test as normal, e.g. `cabal build doctest`
4. `scripts/patch-tool update-patches`
5. Commit the patch

In particular, nothing is said about using allow-newer on the boot libraries as CI does.

This omission leads to contributing patches that update bounds of dependencies on some boot libraries which aren't necessary.

Maybe the root cabal.project[.local] file could list these dependencies in allow-newer:.