diff --git a/doc/manual/package.nix b/doc/manual/package.nix
index 2e6fcede3..f8133f2e1 100644
--- a/doc/manual/package.nix
+++ b/doc/manual/package.nix
@@ -3,7 +3,7 @@
 
 , meson
 , ninja
-, lowdown
+, lowdown-unsandboxed
 , mdbook
 , mdbook-linkcheck
 , jq
@@ -42,7 +42,7 @@ mkMesonDerivation (finalAttrs: {
   passthru.externalNativeBuildInputs = [
     meson
     ninja
-    (lib.getBin lowdown)
+    (lib.getBin lowdown-unsandboxed)
     mdbook
     mdbook-linkcheck
     jq
diff --git a/flake.lock b/flake.lock
index b5d0b881c..ce484a67a 100644
--- a/flake.lock
+++ b/flake.lock
@@ -3,11 +3,11 @@
     "flake-compat": {
       "flake": false,
       "locked": {
-        "lastModified": 1696426674,
-        "narHash": "sha256-kvjfFW7WAETZlt09AgDn1MrtKzP7t90Vf7vypd3OL1U=",
+        "lastModified": 1733328505,
+        "narHash": "sha256-NeCCThCEP3eCl2l/+27kNNK7QrwZB1IJCrXfrbv5oqU=",
         "owner": "edolstra",
         "repo": "flake-compat",
-        "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33",
+        "rev": "ff81ac966bb2cae68946d5ed5fc4994f96d0ffec",
         "type": "github"
       },
       "original": {
@@ -23,11 +23,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1719994518,
-        "narHash": "sha256-pQMhCCHyQGRzdfAkdJ4cIWiw+JNuWsTX7f0ZYSyz0VY=",
+        "lastModified": 1733312601,
+        "narHash": "sha256-4pDvzqnegAfRkPwO3wmwBhVi/Sye1mzps0zHWYnP88c=",
         "owner": "hercules-ci",
         "repo": "flake-parts",
-        "rev": "9227223f6d922fee3c7b190b2cc238a99527bbb7",
+        "rev": "205b12d8b7cd4802fbcb8e8ef6a0f1408781a4f9",
         "type": "github"
       },
       "original": {
@@ -48,11 +48,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1721042469,
-        "narHash": "sha256-6FPUl7HVtvRHCCBQne7Ylp4p+dpP3P/OYuzjztZ4s70=",
+        "lastModified": 1734279981,
+        "narHash": "sha256-NdaCraHPp8iYMWzdXAt5Nv6sA3MUzlCiGiR586TCwo0=",
         "owner": "cachix",
         "repo": "git-hooks.nix",
-        "rev": "f451c19376071a90d8c58ab1a953c6e9840527fd",
+        "rev": "aa9f40c906904ebd83da78e7f328cd8aeaeae785",
         "type": "github"
       },
       "original": {
@@ -61,35 +61,18 @@
         "type": "github"
       }
     },
-    "libgit2": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1715853528,
-        "narHash": "sha256-J2rCxTecyLbbDdsyBWn9w7r3pbKRMkI9E7RvRgAqBdY=",
-        "owner": "libgit2",
-        "repo": "libgit2",
-        "rev": "36f7e21ad757a3dacc58cf7944329da6bc1d6e96",
-        "type": "github"
-      },
-      "original": {
-        "owner": "libgit2",
-        "ref": "v1.8.1",
-        "repo": "libgit2",
-        "type": "github"
-      }
-    },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1723688146,
-        "narHash": "sha256-sqLwJcHYeWLOeP/XoLwAtYjr01TISlkOfz+NG82pbdg=",
+        "lastModified": 1734359947,
+        "narHash": "sha256-1Noao/H+N8nFB4Beoy8fgwrcOQLVm9o4zKW1ODaqK9E=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "c3d4ac725177c030b1e289015989da2ad9d56af0",
+        "rev": "48d12d5e70ee91fe8481378e540433a7303dbf6a",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
-        "ref": "nixos-24.05",
+        "ref": "release-24.11",
         "repo": "nixpkgs",
         "type": "github"
       }
@@ -131,7 +114,6 @@
         "flake-compat": "flake-compat",
         "flake-parts": "flake-parts",
         "git-hooks-nix": "git-hooks-nix",
-        "libgit2": "libgit2",
         "nixpkgs": "nixpkgs",
         "nixpkgs-23-11": "nixpkgs-23-11",
         "nixpkgs-regression": "nixpkgs-regression"
diff --git a/flake.nix b/flake.nix
index 44a764dd7..83bdc5ecc 100644
--- a/flake.nix
+++ b/flake.nix
@@ -1,11 +1,11 @@
 {
   description = "The purely functional package manager";
 
-  inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs/release-24.11";
+
   inputs.nixpkgs-regression.url = "github:NixOS/nixpkgs/215d4d0fd80ca5163643b03a33fde804a29cc1e2";
   inputs.nixpkgs-23-11.url = "github:NixOS/nixpkgs/a62e6edd6d5e1fa0329b8653c801147986f8d446";
   inputs.flake-compat = { url = "github:edolstra/flake-compat"; flake = false; };
-  inputs.libgit2 = { url = "github:libgit2/libgit2/v1.8.1"; flake = false; };
 
   # dev tooling
   inputs.flake-parts.url = "github:hercules-ci/flake-parts";
@@ -18,7 +18,7 @@
   inputs.git-hooks-nix.inputs.flake-compat.follows = "";
   inputs.git-hooks-nix.inputs.gitignore.follows = "";
 
-  outputs = inputs@{ self, nixpkgs, nixpkgs-regression, libgit2, ... }:
+  outputs = inputs@{ self, nixpkgs, nixpkgs-regression, ... }:
 
 
     let
@@ -36,7 +36,8 @@
         "armv6l-unknown-linux-gnueabihf"
         "armv7l-unknown-linux-gnueabihf"
         "riscv64-unknown-linux-gnu"
-        "x86_64-unknown-netbsd"
+        # Disabled because of https://github.com/NixOS/nixpkgs/issues/344423
+        # "x86_64-unknown-netbsd"
         "x86_64-unknown-freebsd"
         "x86_64-w64-mingw32"
       ];
@@ -163,7 +164,6 @@
             if prev.stdenv.hostPlatform.system == "i686-linux"
             then (prev.pre-commit.override (o: { dotnet-sdk = ""; })).overridePythonAttrs (o: { doCheck = false; })
             else prev.pre-commit;
-
         };
 
     in {
diff --git a/packaging/dependencies.nix b/packaging/dependencies.nix
index a8005ce16..2c7cf701f 100644
--- a/packaging/dependencies.nix
+++ b/packaging/dependencies.nix
@@ -114,14 +114,6 @@ scope: {
     requiredSystemFeatures = [ ];
   };
 
-  libseccomp = pkgs.libseccomp.overrideAttrs (_: rec {
-    version = "2.5.5";
-    src = pkgs.fetchurl {
-      url = "https://github.com/seccomp/libseccomp/releases/download/v${version}/libseccomp-${version}.tar.gz";
-      hash = "sha256-JIosik2bmFiqa69ScSw0r+/PnJ6Ut23OAsHJqiX7M3U=";
-    };
-  });
-
   boehmgc = pkgs.boehmgc.override {
     enableLargeConfig = true;
   };
@@ -140,8 +132,6 @@ scope: {
   });
 
   libgit2 = pkgs.libgit2.overrideAttrs (attrs: {
-    src = inputs.libgit2;
-    version = inputs.libgit2.lastModifiedDate;
     cmakeFlags = attrs.cmakeFlags or []
       ++ [ "-DUSE_SSH=exec" ];
     nativeBuildInputs = attrs.nativeBuildInputs or []
@@ -169,36 +159,6 @@ scope: {
       ];
   });
 
-  busybox-sandbox-shell = pkgs.busybox-sandbox-shell or (pkgs.busybox.override {
-    useMusl = true;
-    enableStatic = true;
-    enableMinimal = true;
-    extraConfig = ''
-      CONFIG_FEATURE_FANCY_ECHO y
-      CONFIG_FEATURE_SH_MATH y
-      CONFIG_FEATURE_SH_MATH_64 y
-
-      CONFIG_ASH y
-      CONFIG_ASH_OPTIMIZE_FOR_SIZE y
-
-      CONFIG_ASH_ALIAS y
-      CONFIG_ASH_BASH_COMPAT y
-      CONFIG_ASH_CMDCMD y
-      CONFIG_ASH_ECHO y
-      CONFIG_ASH_GETOPTS y
-      CONFIG_ASH_INTERNAL_GLOB y
-      CONFIG_ASH_JOB_CONTROL y
-      CONFIG_ASH_PRINTF y
-      CONFIG_ASH_TEST y
-    '';
-  });
-
-  # TODO change in Nixpkgs, Windows works fine. First commit of
-  # https://github.com/NixOS/nixpkgs/pull/322977 backported will fix.
-  toml11 = pkgs.toml11.overrideAttrs (old: {
-    meta.platforms = lib.platforms.all;
-  });
-
   inherit resolvePath filesetToSource;
 
   mkMesonDerivation =
diff --git a/tests/nixos/default.nix b/tests/nixos/default.nix
index ff1220f35..a9a438a32 100644
--- a/tests/nixos/default.nix
+++ b/tests/nixos/default.nix
@@ -26,6 +26,8 @@ let
 
         # Evaluate VMs faster
         documentation.enable = false;
+        # this links against nix and might break with our git version.
+        system.tools.nixos-option.enable = false;
       };
       _module.args.nixpkgs = nixpkgs;
       _module.args.system = system;