bazel: remove wrapProgram and move it to system configuration

This way, custom configurations are all at the same place. Also, user
may override these settings using the command line.

pkgs/development/tools/build-managers/bazel/default.nix

@@ -132,6 +132,7 @@ let
     text = ''
       build --override_repository=${remote_java_tools.name}=${remote_java_tools}
       build --distdir=${distDir}
+      startup --server_javabase=${runJdk}
     '';
   };
 
@@ -484,8 +485,6 @@ stdenv.mkDerivation rec {
     cp ./bazel_src/scripts/packages/bazel.sh $out/bin/bazel
     mv ./bazel_src/output/bazel $out/bin/bazel-real
 
-    wrapProgram "$out/bin/bazel" --add-flags --server_javabase="${runJdk}"
-
     # shell completion files
     mkdir -p $out/share/bash-completion/completions $out/share/zsh/site-functions
     mv ./bazel_src/output/bazel-complete.bash $out/share/bash-completion/completions/bazel