treewide: use runtimeShell instead of stdenv.shell whenever possible

[Mic92]

Whenever we create scripts that are installed to $out, we must use runtimeShell
in order to get the shell that can be executed on the machine we create the
package for. This is relevant for cross-compiling. The only use case for
stdenv.shell are scripts that are executed as part of the build system.
Usages in checkPhase are borderline however to decrease the likelyhood
of people copying the wrong examples, I decided to use runtimeShell as well.

Motivation for this change

Things done

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)

• Built on platform(s)

  • NixOS
  • macOS
  • other Linux distributions

• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)

• Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"

  Only vessel and worldofgoo cannot be tested since they require files that I do not have.

• Tested execution of all binary files (usually in ./result/bin/)

• Determined the impact on package closure size (by running nix path-info -S before and after)

• Assured whether relevant documentation is up to date

• Fits CONTRIBUTING.md.

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[FRidh]

This is in line with a1a5ea5 where checkInputs were made native.

[FRidh]

By the way, how come this is not an attribute of stdenv?

[tobim]

Could probably also be done for ccls and cquery.

[Mic92]

@FRidh from my understanding only packages needed for build are in stdenv like coreutils, the build shell and the compiler.

[Ericson2314]

Woo! Marked that this should definitely go to 19.03 too.