The previous build system patch was incomplete and left the `wrapper.d`
directory empty, leaving Bear unable to pick up any build commands
at all and breaking the functional test suite, which we also weren't
running. Switch to overriding CMake flags instead and add the patches
and dependencies necessary to get the functional tests running to
prevent a future regression.

I've checked that the instructions in Nix's
`doc/manual/src/contributing/hacking.md` work after this change,
which is what started this yak shave in the first place.