Copy instead of link haskell-backend binaries in nix derivation (#4106)

Following up on #4096,
[evm-semantics#2739](runtimeverification/evm-semantics#2739),
[evm-semantics#2745](runtimeverification/evm-semantics#2745),
and
[kontrol#1013](runtimeverification/kontrol#1013),
I measured the install time of `kontrol` with `kup` on a fresh Ubuntu
virtual machine. Compared to a previous measurement, the install time
has been reduced to 10 minutes from previously 20 minutes.

During the latest measurement I noticed that Haskell dependencies are
still being downloaded, even though the import-from-derivation
anti-pattern has already been removed in #4096. I investigated and
noticed that the Haskell dependencies are also considered runtime
dependencies. This is caused by the `withZ3` wrapper that links to
binaries in Haskell derivations. These Haskell derivations also contain
references to Haskell dependencies, namely `kore` and
`hs-backend-booster`.

This pull request changes the `withZ3` wrapper to copy the respective
binary prior to wrapping.

E.g., for `kore-rpc-booster`, this reduces the total size to download by
more than 5GB, when installing from nix cache. In addition, these
downloads were spread among many smaller derivations to download.

<details><summary>Output of `nix-tree` before the change:
</summary>
<p>
<pre>

┌─────────────────────────────────────────────────────┬────────────────────────────────────────────────────┬────────────────────────────────────────────────────┐
│kore-rpc-booster 5.15 GiB (5.15 GiB)│hs-backend-booster-0.1.0 5.12 GiB
(5.08 GiB)│kore-0.1.0 4.89 GiB (1.31 GiB)│
│ │z3-4.13.4 72.03 MiB (32.24 MiB)│kore-rpc-types-0.1.0 3.34 GiB (80.65
MiB)│
│ │bash-5.2p26 32.51 MiB (1.54 MiB)│json-rpc-1.0.4 3.21 GiB (15.82 MiB)│
│ │ │aeson-pretty-0.8.10 3.04 GiB (21.2 MiB)│
│ │ │deriving-aeson-0.2.9 3.02 GiB (605.28 KiB)│
│ │ │aeson-2.1.2.1 3.02 GiB (52.64 MiB)│
│ │ │monad-logger-0.3.40 2.98 GiB (4.6 MiB)│
│ │ │stm-conduit-4.0.1 2.97 GiB (2.49 MiB)│
│ │ │conduit-extra-1.3.6 2.95 GiB (5.0 MiB)│
│ │ │cereal-conduit-0.8.0 2.88 GiB (441.2 KiB)│
│ │ │conduit-1.3.5 2.88 GiB (13.4 MiB)│
│ │ │semialign-1.3 2.86 GiB (3.73 MiB)│
│ │ │mono-traversable-1.0.17.0 2.85 GiB (22.06 MiB)│
│ │ │recursion-schemes-5.2.2.5 2.82 GiB (6.79 MiB)│
│ │ │cryptonite-0.30 2.81 GiB (54.26 MiB)│
│ │ │free-5.2 2.81 GiB (22.79 MiB)│
│ │ │vector-algorithms-0.9.0.1 2.81 GiB (25.24 MiB)│
│ │ │witherable-0.4.2 2.8 GiB (4.6 MiB)│
│ │ │indexed-traversable-instances- 2.79 GiB (358.65 KiB)│
│ │ │bitvec-1.1.5.0 2.78 GiB (10.49 MiB)│
│ │ │vector-0.13.1.0 2.77 GiB (49.75 MiB)│
│ │ │semigroupoids-6.0.1 2.77 GiB (12.16 MiB)│
│ │ │language-c-0.9.3 2.76 GiB (63.64 MiB)│
│ │ │profunctors-5.6.2 2.75 GiB (10.68 MiB)│
│ │ │memory-0.18.0 2.74 GiB (5.69 MiB)│
│ │ │basement-0.0.16 2.74 GiB (28.09 MiB)│
│ │ │bifunctors-5.6.2 2.73 GiB (16.04 MiB)│
│ │ │optparse-applicative-0.18.1.0 2.72 GiB (8.72 MiB)│
│ │ │streaming-commons-0.2.2.6 2.72 GiB (4.91 MiB)│
│ │ │attoparsec-0.14.4 2.72 GiB (17.16 MiB)│
│ │ │QuickCheck-2.14.3 2.72 GiB (19.19 MiB)│
│ │ │network-run-0.2.8 2.72 GiB (1.29 MiB)│
│ │ │hpp-0.6.5 2.71 GiB (13.35 MiB)│

└─────────────────────────────────────────────────────┴────────────────────────────────────────────────────┴────────────────────────────────────────────────────┘
/nix/store/y51pfqn8fcmnimhkswfc1fda2pan3kmj-hs-backend-booster-0.1.0
NAR Size: 108.81 MiB | Closure Size: 5.12 GiB | Added Size: 5.08 GiB
Immediate Parents (1): kore-rpc-booster
</pre>
</p>
</details> 

<details><summary>Output of `nix-tree` after the change:</summary>
<p>
<pre>

┌─────────────────────────────────────────────────────┬────────────────────────────────────────────────────┬────────────────────────────────────────────────────┐
│kore-rpc-booster 113.87 MiB (113.87 MiB)│z3-4.13.4 72.03 MiB (32.24
MiB)│gcc-13.2.0-lib 39.78 MiB (8.81 MiB)│
│ │elfutils-0.191 58.27 MiB (16.82 MiB)│glibc-2.39-52 30.96 MiB (28.88
MiB)│
│ │gmp-with-cxx-6.3.0 40.51 MiB (741.04 KiB)│ │
│ │ncurses-6.4 34.51 MiB (3.54 MiB)│ │
│ │bash-5.2p26 32.51 MiB (1.54 MiB)│ │
│ │secp256k1-0.4.1 32.22 MiB (1.25 MiB)│ │
│ │zlib-1.3.1 31.09 MiB (125.16 KiB)│ │
│ │libffi-3.4.6 31.03 MiB (71.87 KiB)│ │
│ │glibc-2.39-52 30.96 MiB (28.88 MiB)│ │
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└─────────────────────────────────────────────────────┴────────────────────────────────────────────────────┴────────────────────────────────────────────────────┘
/nix/store/ih51sgk8g57fnkbd5r82ddi8k5vln8cl-z3-4.13.4
NAR Size: 32.24 MiB | Closure Size: 72.03 MiB | Added Size: 32.24 MiB
Immediate Parents (1): kore-rpc-booster
</pre>
</p>
</details>

Author: juliankuners

flake.nix

@@ -139,11 +139,18 @@
 
       withZ3 = pkgs: pkg: exe: pkgs.stdenv.mkDerivation {
         name = exe;
-        phases = [ "installPhase" ];
+        dontUnpack = true;
+        dontPatch = true;
+        dontConfigure = true;
+        dontBuild = true;
+        
         buildInputs = with pkgs; [ makeWrapper ];
         installPhase = ''
           mkdir -p $out/bin
-          makeWrapper ${pkg}/bin/${exe} $out/bin/${exe} --prefix PATH : ${pkgs.z3}/bin
+          cp ${pkg}/bin/${exe} $out/bin/${exe}
+        '';
+        postFixup = ''
+          wrapProgram $out/bin/${exe} --prefix PATH : ${pkgs.z3}/bin
         '';
       };
     in {