diff --git a/README.md b/README.md
index a4c62ab0..c1f38272 100644
--- a/README.md
+++ b/README.md
@@ -9,11 +9,9 @@ store.
 
 ## Setting up a new dev environment
 
-* Create a new `*.nix` file in the shells directory that describes the environment (this is the hard part).
+* Add a shell to the devShells output in `flake.nix`.
 
-* Execute `use_nix > .envrc` to initialize the `.envrc` file.
-
-* Execute `ln -s /path/to/correct/file.nix shell.nix`.
+* Execute `use_flake /path/to/repo#name-of-shell > .envrc` to initialize the `.envrc` file.
 
 * Execute `direnv allow` to load the `.envrc` file which in turn loads your environment.
 
diff --git a/flake.nix b/flake.nix
index 394a1fe2..1eebfef3 100644
--- a/flake.nix
+++ b/flake.nix
@@ -90,21 +90,7 @@
       };
       hostDefaults = {
         modules = [
-          ({ lib, pkgs, ... }: {
-            environment.etc = lib.mapAttrs'
-              (key: val: {
-                name = "channels/${key}";
-                value = {
-                  source = pkgs.runCommandNoCC "${key}-channel" { } ''
-                    mkdir $out
-                    echo "${val.rev or (toString val.lastModified)}" > $out/.version-suffix
-                    echo "import ${val.outPath}/default.nix" > $out/default.nix
-                  '';
-                };
-              })
-              inputs;
-            nix.nixPath = [ "/etc/channels" ];
-          })
+          { nix.generateRegistryFromInputs = true; }
           accentor.nixosModule
           agenix.nixosModules.age
           home-manager.nixosModule
@@ -132,6 +118,63 @@
                 agenix.defaultPackage.x86_64-linux
               ];
             };
+            accentor-api-client-js = pkgs.devshell.mkShell {
+              name = "Accentor API client in JavaScript";
+              packages = with pkgs; [ nodejs yarn ];
+            };
+            dodona = pkgs.devshell.mkShell {
+              name = "Dodona";
+              imports = [ "${devshell}/extra/language/c.nix" ];
+              packages = with pkgs; [
+                (pkgs.lowPrio binutils)
+                chromedriver
+                findutils
+                gnumake
+                nodejs
+                ruby_3_0
+                yarn
+              ];
+              env = [
+                { name = "DATABASE_URL"; value = "mysql2://root:dodona@127.0.0.1:3306/dodona"; }
+                { name = "TEST_DATABASE_URL"; value = "mysql2://root:dodona@127.0.0.1:3306/dodona_test"; }
+                { name = "GEM_HOME"; eval = "$PRJ_DATA_DIR/bundle/$(ruby -e 'puts RUBY_VERSION')"; }
+                { name = "PATH"; prefix = "$GEM_HOME/bin"; }
+              ];
+              commands = [
+                {
+                  name = "start-dockers";
+                  category = "general commands";
+                  help = "Start mysql and memcached in docker containers";
+                  command = ''
+                    trap "systemd-run --user --no-block docker stop dodona-db dodona-cache" 0
+                    docker run -d --name dodona-db -p 3306:3306 --rm -v dodona-db-data:/var/lib/mysql -e MYSQL_ROOT_PASSWORD=dodona mariadb:latest
+                    docker run -d --name dodona-cache -p 11211:11211 --rm memcached:latest
+                    while [ 1 -eq 1 ]
+                    do
+                      sleep 1000
+                    done
+                  '';
+                }
+              ];
+              language.c = {
+                compiler = pkgs.gcc;
+                includes = [ pkgs.libmysqlclient pkgs.zlib ];
+                libraries = [ pkgs.libmysqlclient pkgs.zlib ];
+              };
+            };
+            dodona-docs = pkgs.devshell.mkShell {
+              name = "Dodona Docs";
+              env = [{ name = "PUPPETEER_EXECUTABLE_PATH"; eval = "${pkgs.ungoogled-chromium}/bin/chromium"; }];
+              packages = with pkgs; [ nodejs yarn ];
+            };
+            dodona-judge-r = pkgs.devshell.mkShell {
+              name = "R judge";
+              packages = [
+                (pkgs.rWrapper.override {
+                  packages = with pkgs.rPackages; [ base64enc dplyr dslabs jsonlite knitr lintr R6 rlang styler ];
+                })
+              ];
+            };
           };
         };
     };
diff --git a/modules/development/git/default.nix b/modules/development/git/default.nix
index 78a74bde..819aa572 100644
--- a/modules/development/git/default.nix
+++ b/modules/development/git/default.nix
@@ -32,11 +32,9 @@
             tag.gpgSign = true;
           };
           ignores = [
+            ".data"
             ".direnv"
             ".envrc"
-            "shell.nix"
-            # Ruby dependencies in source tree
-            "/vendor/bundle"
           ];
           signing = {
             key = "charlotte@vanpetegem.me";
diff --git a/shells/accentor-android.nix b/shells/accentor-android.nix
deleted file mode 100644
index fc204814..00000000
--- a/shells/accentor-android.nix
+++ /dev/null
@@ -1,64 +0,0 @@
-let
-  pkgs = import <nixpkgs> { config.android_sdk.accept_license = true; };
-  buildToolsVersion = "29.0.2";
-  composed = pkgs.androidenv.composeAndroidPackages {
-    toolsVersion = "26.1.1";
-    platformToolsVersion = "29.0.6";
-    buildToolsVersions = [ buildToolsVersion ];
-    # includeEmulator = false;
-    # emulatorVersion = "27.2.0";
-    platformVersions = [ "29" ];
-    includeSources = true;
-    includeDocs = true;
-    # includeSystemImages = false;
-    # systemImageTypes = [ "default" ];
-    # abiVersions = [ "armeabi-v7a" ];
-    # lldbVersions = [ "2.0.2558144" ];
-    # cmakeVersions = [ "3.6.4111459" ];
-    # includeNDK = false;
-    # ndkVersion = "16.1.4479499";
-    # useGoogleAPIs = false;
-    # useGoogleTVAddOns = false;
-    # includeExtras = [ "extras;google;gcm" ];
-  };
-  gradle-fhs-nix = pkgs.writeText "gradle-fhs.nix" ''
-    { run }:
-    let
-      pkgs = import <nixpkgs> {};
-    in
-      (pkgs.buildFHSUserEnv {
-        name = "android-sdk-env";
-        targetPkgs = pkgs: (with pkgs; [ glibc ]);
-        profile = '''
-          export ANDROID_SDK_ROOT="${composed.androidsdk}/libexec/android-sdk/"
-        ''';
-        runScript = "bash -c '''''${run}'''";
-      }).env
-  '';
-  gradle-run-script = pkgs.writeShellScriptBin "gradle" ''
-    REPO_ROOT="$(git rev-parse --show-toplevel)"
-    nix-shell --argstr run "\"$REPO_ROOT/gradlew $@\"" "${gradle-fhs-nix}"
-  '';
-  sign-release = pkgs.writeShellScriptBin "sign-release" ''
-    BUILD_TOOLS_PATH="${composed.androidsdk}/libexec/android-sdk/build-tools/${buildToolsVersion}"
-    REPO_ROOT="$(git rev-parse --show-toplevel)"
-    APK_DIR="$REPO_ROOT/app/build/outputs/apk/release"
-
-    rm "$APK_DIR/"*
-    ${gradle-run-script}/bin/gradle assembleRelease
-    "$BUILD_TOOLS_PATH/zipalign" -v -p 4 "$APK_DIR/app-release-unsigned.apk" "$APK_DIR/app-release-unsigned-aligned.apk"
-
-    "$BUILD_TOOLS_PATH/apksigner" sign --ks "$REPO_ROOT/keystore.jks" --out "$APK_DIR/app-release.apk" "$APK_DIR/app-release-unsigned-aligned.apk"
-    "$BUILD_TOOLS_PATH/apksigner" verify "$APK_DIR/app-release.apk"
-  '';
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    gradle-run-script
-    sign-release
-    jdk11
-  ];
-  shellHook = ''
-    export ANDROID_SDK_ROOT="${composed.androidsdk}/libexec/android-sdk/"
-  '';
-}
diff --git a/shells/accentor-api.nix b/shells/accentor-api.nix
deleted file mode 100644
index 05707c22..00000000
--- a/shells/accentor-api.nix
+++ /dev/null
@@ -1,29 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    ffmpeg
-    imagemagick
-    postgresql
-    ruby_3_1
-    taglib
-    zlib
-    (
-      pkgs.writeShellScriptBin "start-db" ''
-        trap "systemd-run --user --no-block docker stop accentor-db" 0
-        docker run -d --name accentor-db -p 5432:5432 --rm -v accentor-db-data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=accentor postgres:latest
-
-        while [ 1 -eq 1 ]
-        do
-          sleep 1000
-        done
-      ''
-    )
-  ];
-  shellHook = ''
-    export DATABASE_URL="postgres://postgres:accentor@127.0.0.1:5432/accentor"
-    export GEM_HOME="$PWD/vendor/bundle/$(ruby -e 'puts RUBY_VERSION')"
-    export PATH="$GEM_HOME/bin:$PATH"
-  '';
-}
diff --git a/shells/accentor-web.nix b/shells/accentor-web.nix
deleted file mode 100644
index 3856032f..00000000
--- a/shells/accentor-web.nix
+++ /dev/null
@@ -1,10 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    nodejs-12_x
-    python38
-    yarn
-  ];
-}
diff --git a/shells/dodona-docs.nix b/shells/dodona-docs.nix
deleted file mode 100644
index 2099dc92..00000000
--- a/shells/dodona-docs.nix
+++ /dev/null
@@ -1,12 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    nodejs-12_x
-    yarn
-  ];
-  shellHook = ''
-    export PUPPETEER_EXECUTABLE_PATH="${pkgs.ungoogled-chromium}/bin/chromium"
-  '';
-}
diff --git a/shells/dodona.nix b/shells/dodona.nix
deleted file mode 100644
index 19884f16..00000000
--- a/shells/dodona.nix
+++ /dev/null
@@ -1,32 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    chromedriver
-    libmysqlclient
-    nodejs-14_x
-    ruby_3_0
-    yarn
-    zlib
-    (
-      pkgs.writeShellScriptBin "start-dockers" ''
-        trap "systemd-run --user --no-block docker stop dodona-db dodona-cache" 0
-
-        docker run -d --name dodona-db -p 3306:3306 --rm -v dodona-db-data:/var/lib/mysql -e MYSQL_ROOT_PASSWORD=dodona mariadb:latest
-        docker run -d --name dodona-cache -p 11211:11211 --rm memcached:latest
-
-        while [ 1 -eq 1 ]
-        do
-          sleep 1000
-        done
-      ''
-    )
-  ];
-  shellHook = ''
-    export TEST_DATABASE_URL="mysql2://root:dodona@127.0.0.1:3306/dodona_test"
-    export DATABASE_URL="mysql2://root:dodona@127.0.0.1:3306/dodona"
-    export GEM_HOME="$PWD/vendor/bundle/$(ruby -e 'puts RUBY_VERSION')"
-    export PATH="$GEM_HOME/bin:$PATH"
-  '';
-}
diff --git a/shells/idea-code-with-me.nix b/shells/idea-code-with-me.nix
deleted file mode 100644
index 11ac8d68..00000000
--- a/shells/idea-code-with-me.nix
+++ /dev/null
@@ -1,7 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-(pkgs.buildFHSUserEnv {
-  name = "idea-env";
-  targetPkgs = pkgs: [ pkgs.jdk11 pkgs.wget pkgs.bash pkgs.zlib pkgs.xlibs.libXext pkgs.xlibs.libX11 pkgs.xlibs.libXrender pkgs.xlibs.libXtst pkgs.xlibs.libXi pkgs.freetype pkgs.fontconfig ];
-}).env
diff --git a/shells/javafx.nix b/shells/javafx.nix
deleted file mode 100644
index 7d1a2651..00000000
--- a/shells/javafx.nix
+++ /dev/null
@@ -1,19 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = with pkgs; [
-    (
-      pkgs.writeShellScriptBin "compile" ''
-        find src -name '*.java' -print0 | xargs --no-run-if-empty -0 ${jdk17}/bin/javac -d out -sourcepath src
-        find src -type d -printf '%P\0' | xargs -0 -I \{\} mkdir -p out/\{\}
-        find resources -type d -printf '%P\0' | xargs -0 -I \{\} mkdir -p out/\{\}
-        find src -type f -not -name '*.java' -printf '%P\0' | xargs -0 -I \{\} cp src/\{\} out/\{\}
-        find resources -type f -not -name '*.java' -printf '%P\0' | xargs -0 -I \{\} cp resources/\{\} out/\{\}
-        (cd out && ${jdk17}/bin/java polis.Main)
-      ''
-    )
-    jdk17
-    openjfx17
-  ];
-}
diff --git a/shells/r.nix b/shells/r.nix
deleted file mode 100644
index 360e1985..00000000
--- a/shells/r.nix
+++ /dev/null
@@ -1,20 +0,0 @@
-let
-  pkgs = import <nixpkgs> { };
-in
-pkgs.mkShell {
-  buildInputs = [
-    (pkgs.rWrapper.override {
-      packages = with pkgs.rPackages; [
-        base64enc
-        dplyr
-        dslabs
-        jsonlite
-        knitr
-        lintr
-        R6
-        rlang
-        styler
-      ];
-    })
-  ];
-}