diff --git a/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05 b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05
new file mode 120000
index 0000000..05692dc
--- /dev/null
+++ b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05
@@ -0,0 +1 @@
+/nix/store/wzx1ba5hqqfa23vfrvqmfmkpj25p37mr-source
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#dtach b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#dtach
new file mode 120000
index 0000000..04c699d
--- /dev/null
+++ b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#dtach
@@ -0,0 +1 @@
+/nix/store/v7qy11nyx968dgw93c6c03l0m7bvi4cl-dtach-0.9
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
new file mode 120000
index 0000000..a2a0f06
--- /dev/null
+++ b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
@@ -0,0 +1 @@
+/nix/store/yw7xxl0kgha3f9gk4yn9sf0k9v45l26q-nixfmt-0.6.0-bin
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#singularity b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#singularity
new file mode 120000
index 0000000..64f48c4
--- /dev/null
+++ b/examples/flake_subdependency/after/.gcroots/github:NixOS_nixpkgs_24.05#singularity
@@ -0,0 +1 @@
+/nix/store/cdvdij4yvz9hj9mhycaz56jfjizxqbg7-singularity-ce-4.1.3
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/.gitignore b/examples/flake_subdependency/after/.gitignore
new file mode 100644
index 0000000..1c7574c
--- /dev/null
+++ b/examples/flake_subdependency/after/.gitignore
@@ -0,0 +1,5 @@
+result
+    run_scripts/
+    .*.json
+    .gc_roots
+    
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/flake.lock b/examples/flake_subdependency/after/flake.lock
new file mode 100644
index 0000000..ac8423b
--- /dev/null
+++ b/examples/flake_subdependency/after/flake.lock
@@ -0,0 +1,213 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1726560853,
+        "narHash": "sha256-X6rJYSESBVr3hBoH0WbKE5KvhPU5bloyZ2L4K60/fPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "c1dfcf08411b08f6b8615f7d8971a2bfa81d5e8a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nix-github-actions": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1729742964,
+        "narHash": "sha256-B4mzTcQ0FZHdpeWcpDYPERtyjJd/NIuaQ9+BV1h+MpA=",
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "rev": "e04df33f62cdcf93d73e9a04142464753a16db67",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1717179513,
+        "narHash": "sha256-vboIEwIQojofItm2xGCdZCzW96U85l9nDW3ifMuAIdM=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "63dacb46bf939521bdc93981b4cbb7ecb58427a0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "24.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1730157240,
+        "narHash": "sha256-P8wF4ag6Srmpb/gwskYpnIsnspbjZlRvu47iN527ABQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "75e28c029ef2605f9841e0baa335d70065fe7ae2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable-small",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "rust-overlay": "rust-overlay",
+        "test": "test"
+      }
+    },
+    "rust-overlay": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1731897198,
+        "narHash": "sha256-Ou7vLETSKwmE/HRQz4cImXXJBr/k9gp4J4z/PF8LzTE=",
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      },
+      "original": {
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_3": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "id": "systems",
+        "type": "indirect"
+      }
+    },
+    "test": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nix-github-actions": "nix-github-actions",
+        "nixpkgs": "nixpkgs_2",
+        "systems": "systems_3",
+        "treefmt-nix": "treefmt-nix"
+      },
+      "locked": {
+        "lastModified": 1731205797,
+        "narHash": "sha256-F7N1mxH1VrkVNHR3JGNMRvp9+98KYO4b832KS8Gl2xI=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
+        "type": "github"
+      }
+    },
+    "treefmt-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1730120726,
+        "narHash": "sha256-LqHYIxMrl/1p3/kvm2ir925tZ8DkI0KA10djk8wecSk=",
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "rev": "9ef337e492a5555d8e17a51c911ff1f02635be15",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/examples/flake_subdependency/after/flake.nix b/examples/flake_subdependency/after/flake.nix
new file mode 100644
index 0000000..0345fcd
--- /dev/null
+++ b/examples/flake_subdependency/after/flake.nix
@@ -0,0 +1,73 @@
+{
+  description = "Anysnake2 generated flake";
+  inputs = rec {
+
+    flake-utils = {
+      url =
+        "github:numtide/flake-utils/b1d9ab70662946ef0850d488da1c9019f3a9752a";
+
+    };
+    nixpkgs = {
+      url = "github:NixOS/nixpkgs/24.05";
+
+    };
+    rust-overlay = {
+      url =
+        "github:oxalica/rust-overlay/0be641045af6d8666c11c2c40e45ffc9667839b5";
+      inputs.nixpkgs.follows = "nixpkgs";
+
+    };
+    test = {
+      url =
+        "github:nix-community/poetry2nix/f554d27c1544d9c56e5f1f8e2b8aff399803674e";
+
+    };
+  };
+
+  outputs = { self, flake-utils, nixpkgs, rust-overlay, test }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs {
+          inherit system overlays;
+          config = { allowUnfree = false; };
+        };
+        R_tracked = null;
+        overlays = [ (import rust-overlay) ];
+        rust = pkgs.rust-bin.stable."1.55.0".minimal.override {
+          extensions = [ "rustfmt" "clippy" ];
+        };
+        _args = with pkgs; {
+          name = "anysnake2_container";
+          #later entries beat earlier entries in terms of /bin symlinks
+          script = ''
+                      ${coreutils}
+                      ${bashInteractive_5}
+                      ${bash}
+            ${cacert}
+            ${fish}
+            ${rust}
+            ${stdenv.cc}
+          '';
+        };
+        helpers = import ./functions.nix { inherit pkgs; };
+      in rec {
+        defaultPackage = (helpers.buildSymlinkImage _args).derivation;
+        oci_image = helpers.buildOCIimage _args;
+        devShell = pkgs.stdenv.mkDerivation {
+          name = "anysnake2-devshell";
+          shellHook = ''
+            export PATH=${defaultPackage}/rootfs/bin:$PATH;
+            if test -f "develop_python_path.bash"; then
+              source "develop_python_path.bash"
+            fi
+          '' + (if R_tracked != null then ''
+            export R_LIBS_SITE=${R_tracked}/lib/R/library/
+          '' else
+            "");
+          nativeBuildInputs = with pkgs;
+            [
+              #%DEVSHELL_INPUTS%
+            ];
+        };
+      });
+}
diff --git a/examples/flake_subdependency/after/functions.nix b/examples/flake_subdependency/after/functions.nix
new file mode 100644
index 0000000..ba667e4
--- /dev/null
+++ b/examples/flake_subdependency/after/functions.nix
@@ -0,0 +1,160 @@
+{pkgs}: rec {
+  buildSymlinkImage = {
+    name,
+    script,
+  }: let
+  in rec {
+    script_file = pkgs.writeScript "reqs.sh" script;
+    derivation = pkgs.runCommand "${name}-2" {} ''
+      set -o pipefail
+      shopt -s nullglob
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/share
+      cp ${script_file} $out/reqs.sh
+
+      # so singularity fills in the outside users
+      mkdir -p $out/rootfs/etc
+      touch $out/rootfs/etc/passwd
+      touch $out/rootfs/etc/group
+
+      mkdir -p $out/rootfs/{bin,etc,share,tmp,var/tmp}
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/lib/share
+      mkdir -p $out/rootfs/R_libs
+
+      set -x
+      # the later entries shadow the earlier ones.
+      # symlink the direct dependencies ...
+      for path in $(tac ${script_file});
+         do
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/bin $out/rootfs/bin/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/etc $out/rootfs/etc || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib $out/rootfs/usr/lib/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/share $out/rootfs/usr/share/ || true
+         if [ -d $path/lib/R/library/ ]; then
+           ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib/R/library $out/rootfs/R_libs/ || true
+         fi
+      done
+
+      ln -s $out/rootfs/bin $out/rootfs/usr/bin
+
+      mkdir -p $out/rootfs/etc/profile.d
+      echo "export SSL_CERT_FILE=/etc/ssl/certs/ca-bundle.crt" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      echo "export SSL_CERT_DIR=/etc/ssl/certs" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      #echo "export PATH=/python_env/bin:/bin:/usr/bin/" >>$out/rootfs/etc/bashrc
+      #echo "export PYTHONPATH=$PYTHONPATH:/python_env/lib/python%PYTHON_MAJOR_DOT_MINOR%/site-packages" >>$out/rootfs/etc/bashrc
+
+
+    '';
+  };
+
+  # can't use pkgs.ociTools.buildContainerImage
+  # because it a) does not work from a rootfs
+  # and b) doesn't actually build an image, just a runtime bundle
+  buildOCIimage = {
+    name,
+    script,
+  }: let
+    symlink_image = buildSymlinkImage {
+      inherit name script;
+    };
+    umoci = pkgs.umoci;
+  in
+    pkgs.runCommand "${name}.oci" {} ''
+    set -o pipefail
+    shopt -s nullglob
+    ${umoci}/bin/umoci init --layout "${name}"
+    ${umoci}/bin/umoci new --image "${name}:latest"
+    mkdir tmp-oci-unpack
+
+    mkdir fakeroot/etc -p
+    touch fakeroot/etc/resolv.conf
+
+    # umoci tries to read /etc/resolv.conf, so let's give it one..
+    ${pkgs.bubblewrap}/bin/bwrap \
+           --proc /proc \
+            --dev /dev \
+           --bind /build /build \
+           --ro-bind /build/fakeroot/etc /etc \
+           --ro-bind /nix /nix \
+      ${umoci}/bin/umoci unpack --image "${name}:latest" tmp-oci-unpack --rootless
+
+    echo "rsyncing symlink forest"
+    ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ tmp-oci-unpack/rootfs/
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    echo "rsyncing necessary nix paths"
+    ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+        pkgs.writeClosure [symlink_image.script_file]
+      } / tmp-oci-unpack/rootfs/
+
+
+    # check that we have a rootfs/bin/sh
+    if [ ! -e tmp-oci-unpack/rootfs/bin/sh ]; then
+      echo "No rootfs/bin/sh found"
+      exit 1
+    fi
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    ${umoci}/bin/umoci repack --image "${name}:latest" tmp-oci-unpack
+    ${umoci}/bin/umoci config --image "${name}:latest"
+    # strip the first component
+    cd "${name}" && tar cf $out .
+
+
+    '';
+
+  # this never quite worked and since like 22.05, singularity image building on nixos seems broken
+  #   buildSingularityImage = {
+  #     name,
+  #     script,
+  #   }: let
+  #     symlink_image = buildSymlinkImage {
+  #       inherit name script;
+  #     };
+  #   in
+  #     pkgs.runCommand name {} ''
+  #       set -o pipefail
+  #       shopt -s nullglob
+  #       mkdir -p $out/rootfs/
+
+  #       ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ $out/rootfs/
+  #       chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       #make sure we got everything from the nix store, right?
+  #       ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+  #         pkgs.writeClosure [symlink_image.script_file]
+  #       } / $out/rootfs/
+
+  #       rm $out/rootfs/${symlink_image.script_file}
+  #       chmod 755 $out/rootfs
+
+  #       # # singularity tries to read resolv.conf, hosts and user definitions
+  #       # # when converting the container
+  #       # # so let's fake them
+  #       mkdir $out/etc
+  #       mkdir $out/build
+  #       touch $out/etc/resolv.conf
+  #       touch $out/etc/hosts
+  #       echo "nixbld:x:1000:2000:imtseq:/home/installer:/bin/bash\n" >$out/etc/passwd
+  #       echo "xxx:x: 2000:\n" >$out/etc/group
+  #       echo ${pkgs.singularity}/bin/singularity
+  #       ${pkgs.coreutils}/bin/whoami
+
+  #       # # also consider NIX_REDIRECT and libredirect for this
+  #       # the bash binding is needed for singularity to find 'sh'
+  #       ${pkgs.bubblewrap}/bin/bwrap \
+  #          --proc /proc \
+  #          --dev /dev \
+  #         --bind $out/ $out/ \
+  #         --bind $out/build /build \
+  #         --ro-bind $out/etc /etc \
+  #         --ro-bind /nix /nix \
+  #         --ro-bind "${pkgs.bash}/bin" /usr/bin \
+  #         ${pkgs.singularity}/bin/singularity build  /build/${name}.sif $out/rootfs -v
+  #       mv $out/build/*.sif $out/
+  #       rm -rf $out/build
+  #       rm -rf $out/etc
+  #       # chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       # rm -rf $out/rootfs
+  #     '';
+}
diff --git a/examples/flake_subdependency/after/run_scripts/run/outer_run.sh b/examples/flake_subdependency/after/run_scripts/run/outer_run.sh
new file mode 100644
index 0000000..292d61d
--- /dev/null
+++ b/examples/flake_subdependency/after/run_scripts/run/outer_run.sh
@@ -0,0 +1,2 @@
+#/bin/bash
+bash -i /anysnake2/run.sh
diff --git a/examples/flake_subdependency/after/run_scripts/run/post_run.sh b/examples/flake_subdependency/after/run_scripts/run/post_run.sh
new file mode 100644
index 0000000..e69de29
diff --git a/examples/flake_subdependency/after/run_scripts/run/run.sh b/examples/flake_subdependency/after/run_scripts/run/run.sh
new file mode 100644
index 0000000..20b92ab
--- /dev/null
+++ b/examples/flake_subdependency/after/run_scripts/run/run.sh
@@ -0,0 +1 @@
+shaeu
\ No newline at end of file
diff --git a/examples/flake_subdependency/after/run_scripts/run/singularity.bash b/examples/flake_subdependency/after/run_scripts/run/singularity.bash
new file mode 100644
index 0000000..b2dfd93
--- /dev/null
+++ b/examples/flake_subdependency/after/run_scripts/run/singularity.bash
@@ -0,0 +1,24 @@
+nix shell \
+    github:NixOS/nixpkgs/24.05#dtach \
+    -c \
+    dtach \
+    -c \
+    .anysnake2_flake/dtach/run_2024-11-18_15:04:24 \
+    nix \
+    shell \
+    github:NixOS/nixpkgs/24.05#singularity \
+    -c \
+    singularity exec \
+    --userns \
+    --cleanenv \
+    --home /home/finkernagel \
+    --bind /nix/store:/nix/store:ro \
+    --bind .anysnake2_flake/run_scripts/run/run.sh:/anysnake2/run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/post_run.sh:/anysnake2/post_run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/outer_run.sh:/anysnake2/outer_run.sh:ro \
+    --bind /home/finkernagel/upstream/anysnake2/examples/flake_subdependency:/project:rw \
+    --env ANYSNAKE2=1 \
+    --env PATH=/bin \
+    .anysnake2_flake/result/rootfs \
+    /bin/bash \
+    /anysnake2/outer_run.sh \
diff --git a/examples/flake_subdependency/anysnake2.toml b/examples/flake_subdependency/anysnake2.toml
new file mode 100644
index 0000000..f5be799
--- /dev/null
+++ b/examples/flake_subdependency/anysnake2.toml
@@ -0,0 +1,60 @@
+# test case for test_flake_change_updates_dependant_flakes
+# package settings
+[anysnake2]
+	rev = "dev" # pre 2.0 - 2.0+ uses url2
+	url = "github:TyberiusPrime/anysnake2_release_flakes" # pre 2.0 - 2.0+ uses url2
+	url2 = "dev"
+
+
+[nixpkgs]
+# the nixpkgs used inside the container
+	packages = [
+		"bash",
+		"fish"]
+	url = "github:NixOS/nixpkgs/master/24.05"
+
+
+[rust]
+	url = "github:oxalica/rust-overlay/master/0be641045af6d8666c11c2c40e45ffc9667839b5"
+	version="1.55.0"
+
+
+[flakes.test]
+	packages = []
+	url = "github:nix-community/poetry2nix/master/8810f7d31d4d8372f764d567ea140270745fe173"
+
+
+[container.env]
+	ANYSNAKE2="1"
+
+
+# container settings
+[container.volumes_rw]
+	"." = "/project" # map the current folder to /project
+
+
+[dev_shell]
+	inputs = []
+	shell = "bash"
+
+
+[outside_nixpkgs]
+# the nixpkgs used to run singularity and nixfmt
+	url = "github:NixOS/nixpkgs/master/24.05"
+
+
+[ancient_poetry]
+	url = "git+https://codeberg.org/TyberiusPrime/ancient-poetry.git?ref=main&rev=54a06abec3273f42f9d86a36f184dbb3089cd9c9"
+
+
+[poetry2nix]
+	url = "github:nix-community/poetry2nix/master/8810f7d31d4d8372f764d567ea140270745fe174"
+
+
+[flake-util]
+	url = "github:numtide/flake-utils/main/b1d9ab70662946ef0850d488da1c9019f3a9752a"
+
+
+[devshell]
+	inputs = []
+	shell = "bash"
diff --git a/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05 b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05
new file mode 120000
index 0000000..05692dc
--- /dev/null
+++ b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05
@@ -0,0 +1 @@
+/nix/store/wzx1ba5hqqfa23vfrvqmfmkpj25p37mr-source
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#dtach b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#dtach
new file mode 120000
index 0000000..04c699d
--- /dev/null
+++ b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#dtach
@@ -0,0 +1 @@
+/nix/store/v7qy11nyx968dgw93c6c03l0m7bvi4cl-dtach-0.9
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
new file mode 120000
index 0000000..a2a0f06
--- /dev/null
+++ b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
@@ -0,0 +1 @@
+/nix/store/yw7xxl0kgha3f9gk4yn9sf0k9v45l26q-nixfmt-0.6.0-bin
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#singularity b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#singularity
new file mode 120000
index 0000000..64f48c4
--- /dev/null
+++ b/examples/flake_subdependency/before/.gcroots/github:NixOS_nixpkgs_24.05#singularity
@@ -0,0 +1 @@
+/nix/store/cdvdij4yvz9hj9mhycaz56jfjizxqbg7-singularity-ce-4.1.3
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/.gitignore b/examples/flake_subdependency/before/.gitignore
new file mode 100644
index 0000000..1c7574c
--- /dev/null
+++ b/examples/flake_subdependency/before/.gitignore
@@ -0,0 +1,5 @@
+result
+    run_scripts/
+    .*.json
+    .gc_roots
+    
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/flake.lock b/examples/flake_subdependency/before/flake.lock
new file mode 100644
index 0000000..65e1a93
--- /dev/null
+++ b/examples/flake_subdependency/before/flake.lock
@@ -0,0 +1,213 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1694529238,
+        "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nix-github-actions": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1698974481,
+        "narHash": "sha256-yPncV9Ohdz1zPZxYHQf47S8S0VrnhV7nNhCawY46hDA=",
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "rev": "4bb5e752616262457bc7ca5882192a564c0472d2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1717179513,
+        "narHash": "sha256-vboIEwIQojofItm2xGCdZCzW96U85l9nDW3ifMuAIdM=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "63dacb46bf939521bdc93981b4cbb7ecb58427a0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "24.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1699229614,
+        "narHash": "sha256-0n8d9Nx+J8v2o9Oog5MPPtM2YAq+gDeirQpj9l02YuQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "ae52f963b8f098befb9914cc9220c29c93eb845f",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "master",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "rust-overlay": "rust-overlay",
+        "test": "test"
+      }
+    },
+    "rust-overlay": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1731897198,
+        "narHash": "sha256-Ou7vLETSKwmE/HRQz4cImXXJBr/k9gp4J4z/PF8LzTE=",
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      },
+      "original": {
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_3": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "id": "systems",
+        "type": "indirect"
+      }
+    },
+    "test": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nix-github-actions": "nix-github-actions",
+        "nixpkgs": "nixpkgs_2",
+        "systems": "systems_3",
+        "treefmt-nix": "treefmt-nix"
+      },
+      "locked": {
+        "lastModified": 1699231189,
+        "narHash": "sha256-sW+/iiWdew5mftukqVm7AXPimyAWd6dMOfDkqnyBIec=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "8810f7d31d4d8372f764d567ea140270745fe173",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "8810f7d31d4d8372f764d567ea140270745fe173",
+        "type": "github"
+      }
+    },
+    "treefmt-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1698438538,
+        "narHash": "sha256-AWxaKTDL3MtxaVTVU5lYBvSnlspOS0Fjt8GxBgnU0Do=",
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "rev": "5deb8dc125a9f83b65ca86cf0c8167c46593e0b1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/examples/flake_subdependency/before/flake.nix b/examples/flake_subdependency/before/flake.nix
new file mode 100644
index 0000000..2281750
--- /dev/null
+++ b/examples/flake_subdependency/before/flake.nix
@@ -0,0 +1,73 @@
+{
+  description = "Anysnake2 generated flake";
+  inputs = rec {
+
+    flake-utils = {
+      url =
+        "github:numtide/flake-utils/b1d9ab70662946ef0850d488da1c9019f3a9752a";
+
+    };
+    nixpkgs = {
+      url = "github:NixOS/nixpkgs/24.05";
+
+    };
+    rust-overlay = {
+      url =
+        "github:oxalica/rust-overlay/0be641045af6d8666c11c2c40e45ffc9667839b5";
+      inputs.nixpkgs.follows = "nixpkgs";
+
+    };
+    test = {
+      url =
+        "github:nix-community/poetry2nix/8810f7d31d4d8372f764d567ea140270745fe173";
+
+    };
+  };
+
+  outputs = { self, flake-utils, nixpkgs, rust-overlay, test }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs {
+          inherit system overlays;
+          config = { allowUnfree = false; };
+        };
+        R_tracked = null;
+        overlays = [ (import rust-overlay) ];
+        rust = pkgs.rust-bin.stable."1.55.0".minimal.override {
+          extensions = [ "rustfmt" "clippy" ];
+        };
+        _args = with pkgs; {
+          name = "anysnake2_container";
+          #later entries beat earlier entries in terms of /bin symlinks
+          script = ''
+                      ${coreutils}
+                      ${bashInteractive_5}
+                      ${bash}
+            ${cacert}
+            ${fish}
+            ${rust}
+            ${stdenv.cc}
+          '';
+        };
+        helpers = import ./functions.nix { inherit pkgs; };
+      in rec {
+        defaultPackage = (helpers.buildSymlinkImage _args).derivation;
+        oci_image = helpers.buildOCIimage _args;
+        devShell = pkgs.stdenv.mkDerivation {
+          name = "anysnake2-devshell";
+          shellHook = ''
+            export PATH=${defaultPackage}/rootfs/bin:$PATH;
+            if test -f "develop_python_path.bash"; then
+              source "develop_python_path.bash"
+            fi
+          '' + (if R_tracked != null then ''
+            export R_LIBS_SITE=${R_tracked}/lib/R/library/
+          '' else
+            "");
+          nativeBuildInputs = with pkgs;
+            [
+              #%DEVSHELL_INPUTS%
+            ];
+        };
+      });
+}
diff --git a/examples/flake_subdependency/before/functions.nix b/examples/flake_subdependency/before/functions.nix
new file mode 100644
index 0000000..ba667e4
--- /dev/null
+++ b/examples/flake_subdependency/before/functions.nix
@@ -0,0 +1,160 @@
+{pkgs}: rec {
+  buildSymlinkImage = {
+    name,
+    script,
+  }: let
+  in rec {
+    script_file = pkgs.writeScript "reqs.sh" script;
+    derivation = pkgs.runCommand "${name}-2" {} ''
+      set -o pipefail
+      shopt -s nullglob
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/share
+      cp ${script_file} $out/reqs.sh
+
+      # so singularity fills in the outside users
+      mkdir -p $out/rootfs/etc
+      touch $out/rootfs/etc/passwd
+      touch $out/rootfs/etc/group
+
+      mkdir -p $out/rootfs/{bin,etc,share,tmp,var/tmp}
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/lib/share
+      mkdir -p $out/rootfs/R_libs
+
+      set -x
+      # the later entries shadow the earlier ones.
+      # symlink the direct dependencies ...
+      for path in $(tac ${script_file});
+         do
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/bin $out/rootfs/bin/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/etc $out/rootfs/etc || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib $out/rootfs/usr/lib/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/share $out/rootfs/usr/share/ || true
+         if [ -d $path/lib/R/library/ ]; then
+           ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib/R/library $out/rootfs/R_libs/ || true
+         fi
+      done
+
+      ln -s $out/rootfs/bin $out/rootfs/usr/bin
+
+      mkdir -p $out/rootfs/etc/profile.d
+      echo "export SSL_CERT_FILE=/etc/ssl/certs/ca-bundle.crt" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      echo "export SSL_CERT_DIR=/etc/ssl/certs" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      #echo "export PATH=/python_env/bin:/bin:/usr/bin/" >>$out/rootfs/etc/bashrc
+      #echo "export PYTHONPATH=$PYTHONPATH:/python_env/lib/python%PYTHON_MAJOR_DOT_MINOR%/site-packages" >>$out/rootfs/etc/bashrc
+
+
+    '';
+  };
+
+  # can't use pkgs.ociTools.buildContainerImage
+  # because it a) does not work from a rootfs
+  # and b) doesn't actually build an image, just a runtime bundle
+  buildOCIimage = {
+    name,
+    script,
+  }: let
+    symlink_image = buildSymlinkImage {
+      inherit name script;
+    };
+    umoci = pkgs.umoci;
+  in
+    pkgs.runCommand "${name}.oci" {} ''
+    set -o pipefail
+    shopt -s nullglob
+    ${umoci}/bin/umoci init --layout "${name}"
+    ${umoci}/bin/umoci new --image "${name}:latest"
+    mkdir tmp-oci-unpack
+
+    mkdir fakeroot/etc -p
+    touch fakeroot/etc/resolv.conf
+
+    # umoci tries to read /etc/resolv.conf, so let's give it one..
+    ${pkgs.bubblewrap}/bin/bwrap \
+           --proc /proc \
+            --dev /dev \
+           --bind /build /build \
+           --ro-bind /build/fakeroot/etc /etc \
+           --ro-bind /nix /nix \
+      ${umoci}/bin/umoci unpack --image "${name}:latest" tmp-oci-unpack --rootless
+
+    echo "rsyncing symlink forest"
+    ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ tmp-oci-unpack/rootfs/
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    echo "rsyncing necessary nix paths"
+    ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+        pkgs.writeClosure [symlink_image.script_file]
+      } / tmp-oci-unpack/rootfs/
+
+
+    # check that we have a rootfs/bin/sh
+    if [ ! -e tmp-oci-unpack/rootfs/bin/sh ]; then
+      echo "No rootfs/bin/sh found"
+      exit 1
+    fi
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    ${umoci}/bin/umoci repack --image "${name}:latest" tmp-oci-unpack
+    ${umoci}/bin/umoci config --image "${name}:latest"
+    # strip the first component
+    cd "${name}" && tar cf $out .
+
+
+    '';
+
+  # this never quite worked and since like 22.05, singularity image building on nixos seems broken
+  #   buildSingularityImage = {
+  #     name,
+  #     script,
+  #   }: let
+  #     symlink_image = buildSymlinkImage {
+  #       inherit name script;
+  #     };
+  #   in
+  #     pkgs.runCommand name {} ''
+  #       set -o pipefail
+  #       shopt -s nullglob
+  #       mkdir -p $out/rootfs/
+
+  #       ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ $out/rootfs/
+  #       chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       #make sure we got everything from the nix store, right?
+  #       ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+  #         pkgs.writeClosure [symlink_image.script_file]
+  #       } / $out/rootfs/
+
+  #       rm $out/rootfs/${symlink_image.script_file}
+  #       chmod 755 $out/rootfs
+
+  #       # # singularity tries to read resolv.conf, hosts and user definitions
+  #       # # when converting the container
+  #       # # so let's fake them
+  #       mkdir $out/etc
+  #       mkdir $out/build
+  #       touch $out/etc/resolv.conf
+  #       touch $out/etc/hosts
+  #       echo "nixbld:x:1000:2000:imtseq:/home/installer:/bin/bash\n" >$out/etc/passwd
+  #       echo "xxx:x: 2000:\n" >$out/etc/group
+  #       echo ${pkgs.singularity}/bin/singularity
+  #       ${pkgs.coreutils}/bin/whoami
+
+  #       # # also consider NIX_REDIRECT and libredirect for this
+  #       # the bash binding is needed for singularity to find 'sh'
+  #       ${pkgs.bubblewrap}/bin/bwrap \
+  #          --proc /proc \
+  #          --dev /dev \
+  #         --bind $out/ $out/ \
+  #         --bind $out/build /build \
+  #         --ro-bind $out/etc /etc \
+  #         --ro-bind /nix /nix \
+  #         --ro-bind "${pkgs.bash}/bin" /usr/bin \
+  #         ${pkgs.singularity}/bin/singularity build  /build/${name}.sif $out/rootfs -v
+  #       mv $out/build/*.sif $out/
+  #       rm -rf $out/build
+  #       rm -rf $out/etc
+  #       # chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       # rm -rf $out/rootfs
+  #     '';
+}
diff --git a/examples/flake_subdependency/before/run_scripts/run/outer_run.sh b/examples/flake_subdependency/before/run_scripts/run/outer_run.sh
new file mode 100644
index 0000000..292d61d
--- /dev/null
+++ b/examples/flake_subdependency/before/run_scripts/run/outer_run.sh
@@ -0,0 +1,2 @@
+#/bin/bash
+bash -i /anysnake2/run.sh
diff --git a/examples/flake_subdependency/before/run_scripts/run/post_run.sh b/examples/flake_subdependency/before/run_scripts/run/post_run.sh
new file mode 100644
index 0000000..e69de29
diff --git a/examples/flake_subdependency/before/run_scripts/run/run.sh b/examples/flake_subdependency/before/run_scripts/run/run.sh
new file mode 100644
index 0000000..20b92ab
--- /dev/null
+++ b/examples/flake_subdependency/before/run_scripts/run/run.sh
@@ -0,0 +1 @@
+shaeu
\ No newline at end of file
diff --git a/examples/flake_subdependency/before/run_scripts/run/singularity.bash b/examples/flake_subdependency/before/run_scripts/run/singularity.bash
new file mode 100644
index 0000000..02b8e1e
--- /dev/null
+++ b/examples/flake_subdependency/before/run_scripts/run/singularity.bash
@@ -0,0 +1,24 @@
+nix shell \
+    github:NixOS/nixpkgs/24.05#dtach \
+    -c \
+    dtach \
+    -c \
+    .anysnake2_flake/dtach/run_2024-11-18_15:02:48 \
+    nix \
+    shell \
+    github:NixOS/nixpkgs/24.05#singularity \
+    -c \
+    singularity exec \
+    --userns \
+    --cleanenv \
+    --home /home/finkernagel \
+    --bind /nix/store:/nix/store:ro \
+    --bind .anysnake2_flake/run_scripts/run/run.sh:/anysnake2/run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/post_run.sh:/anysnake2/post_run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/outer_run.sh:/anysnake2/outer_run.sh:ro \
+    --bind /home/finkernagel/upstream/anysnake2/examples/flake_subdependency:/project:rw \
+    --env ANYSNAKE2=1 \
+    --env PATH=/bin \
+    .anysnake2_flake/result/rootfs \
+    /bin/bash \
+    /anysnake2/outer_run.sh \
diff --git a/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05 b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05
new file mode 120000
index 0000000..05692dc
--- /dev/null
+++ b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05
@@ -0,0 +1 @@
+/nix/store/wzx1ba5hqqfa23vfrvqmfmkpj25p37mr-source
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#dtach b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#dtach
new file mode 120000
index 0000000..04c699d
--- /dev/null
+++ b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#dtach
@@ -0,0 +1 @@
+/nix/store/v7qy11nyx968dgw93c6c03l0m7bvi4cl-dtach-0.9
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
new file mode 120000
index 0000000..a2a0f06
--- /dev/null
+++ b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#nixfmt
@@ -0,0 +1 @@
+/nix/store/yw7xxl0kgha3f9gk4yn9sf0k9v45l26q-nixfmt-0.6.0-bin
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#singularity b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#singularity
new file mode 120000
index 0000000..64f48c4
--- /dev/null
+++ b/examples/flake_subdependency/updated/.gcroots/github:NixOS_nixpkgs_24.05#singularity
@@ -0,0 +1 @@
+/nix/store/cdvdij4yvz9hj9mhycaz56jfjizxqbg7-singularity-ce-4.1.3
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/.gitignore b/examples/flake_subdependency/updated/.gitignore
new file mode 100644
index 0000000..1c7574c
--- /dev/null
+++ b/examples/flake_subdependency/updated/.gitignore
@@ -0,0 +1,5 @@
+result
+    run_scripts/
+    .*.json
+    .gc_roots
+    
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/flake.lock b/examples/flake_subdependency/updated/flake.lock
new file mode 100644
index 0000000..e34cd68
--- /dev/null
+++ b/examples/flake_subdependency/updated/flake.lock
@@ -0,0 +1,213 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1694529238,
+        "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nix-github-actions": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1698974481,
+        "narHash": "sha256-yPncV9Ohdz1zPZxYHQf47S8S0VrnhV7nNhCawY46hDA=",
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "rev": "4bb5e752616262457bc7ca5882192a564c0472d2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1717179513,
+        "narHash": "sha256-vboIEwIQojofItm2xGCdZCzW96U85l9nDW3ifMuAIdM=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "63dacb46bf939521bdc93981b4cbb7ecb58427a0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "24.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1731919951,
+        "narHash": "sha256-vOM6ETpl1yu9KLi/icTmLJIPbbdJCdAVYUXZceO/Ce4=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "04386ac325a813047fc314d4b4d838a5b1e3c7fe",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable-small",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "rust-overlay": "rust-overlay",
+        "test": "test"
+      }
+    },
+    "rust-overlay": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1731897198,
+        "narHash": "sha256-Ou7vLETSKwmE/HRQz4cImXXJBr/k9gp4J4z/PF8LzTE=",
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      },
+      "original": {
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "0be641045af6d8666c11c2c40e45ffc9667839b5",
+        "type": "github"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_3": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "id": "systems",
+        "type": "indirect"
+      }
+    },
+    "test": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nix-github-actions": "nix-github-actions",
+        "nixpkgs": "nixpkgs_2",
+        "systems": "systems_3",
+        "treefmt-nix": "treefmt-nix"
+      },
+      "locked": {
+        "lastModified": 1731205797,
+        "narHash": "sha256-F7N1mxH1VrkVNHR3JGNMRvp9+98KYO4b832KS8Gl2xI=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
+        "type": "github"
+      }
+    },
+    "treefmt-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "test",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1698438538,
+        "narHash": "sha256-AWxaKTDL3MtxaVTVU5lYBvSnlspOS0Fjt8GxBgnU0Do=",
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "rev": "5deb8dc125a9f83b65ca86cf0c8167c46593e0b1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/examples/flake_subdependency/updated/flake.nix b/examples/flake_subdependency/updated/flake.nix
new file mode 100644
index 0000000..0345fcd
--- /dev/null
+++ b/examples/flake_subdependency/updated/flake.nix
@@ -0,0 +1,73 @@
+{
+  description = "Anysnake2 generated flake";
+  inputs = rec {
+
+    flake-utils = {
+      url =
+        "github:numtide/flake-utils/b1d9ab70662946ef0850d488da1c9019f3a9752a";
+
+    };
+    nixpkgs = {
+      url = "github:NixOS/nixpkgs/24.05";
+
+    };
+    rust-overlay = {
+      url =
+        "github:oxalica/rust-overlay/0be641045af6d8666c11c2c40e45ffc9667839b5";
+      inputs.nixpkgs.follows = "nixpkgs";
+
+    };
+    test = {
+      url =
+        "github:nix-community/poetry2nix/f554d27c1544d9c56e5f1f8e2b8aff399803674e";
+
+    };
+  };
+
+  outputs = { self, flake-utils, nixpkgs, rust-overlay, test }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs {
+          inherit system overlays;
+          config = { allowUnfree = false; };
+        };
+        R_tracked = null;
+        overlays = [ (import rust-overlay) ];
+        rust = pkgs.rust-bin.stable."1.55.0".minimal.override {
+          extensions = [ "rustfmt" "clippy" ];
+        };
+        _args = with pkgs; {
+          name = "anysnake2_container";
+          #later entries beat earlier entries in terms of /bin symlinks
+          script = ''
+                      ${coreutils}
+                      ${bashInteractive_5}
+                      ${bash}
+            ${cacert}
+            ${fish}
+            ${rust}
+            ${stdenv.cc}
+          '';
+        };
+        helpers = import ./functions.nix { inherit pkgs; };
+      in rec {
+        defaultPackage = (helpers.buildSymlinkImage _args).derivation;
+        oci_image = helpers.buildOCIimage _args;
+        devShell = pkgs.stdenv.mkDerivation {
+          name = "anysnake2-devshell";
+          shellHook = ''
+            export PATH=${defaultPackage}/rootfs/bin:$PATH;
+            if test -f "develop_python_path.bash"; then
+              source "develop_python_path.bash"
+            fi
+          '' + (if R_tracked != null then ''
+            export R_LIBS_SITE=${R_tracked}/lib/R/library/
+          '' else
+            "");
+          nativeBuildInputs = with pkgs;
+            [
+              #%DEVSHELL_INPUTS%
+            ];
+        };
+      });
+}
diff --git a/examples/flake_subdependency/updated/functions.nix b/examples/flake_subdependency/updated/functions.nix
new file mode 100644
index 0000000..ba667e4
--- /dev/null
+++ b/examples/flake_subdependency/updated/functions.nix
@@ -0,0 +1,160 @@
+{pkgs}: rec {
+  buildSymlinkImage = {
+    name,
+    script,
+  }: let
+  in rec {
+    script_file = pkgs.writeScript "reqs.sh" script;
+    derivation = pkgs.runCommand "${name}-2" {} ''
+      set -o pipefail
+      shopt -s nullglob
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/share
+      cp ${script_file} $out/reqs.sh
+
+      # so singularity fills in the outside users
+      mkdir -p $out/rootfs/etc
+      touch $out/rootfs/etc/passwd
+      touch $out/rootfs/etc/group
+
+      mkdir -p $out/rootfs/{bin,etc,share,tmp,var/tmp}
+      mkdir -p $out/rootfs/usr/lib
+      mkdir -p $out/rootfs/usr/lib/share
+      mkdir -p $out/rootfs/R_libs
+
+      set -x
+      # the later entries shadow the earlier ones.
+      # symlink the direct dependencies ...
+      for path in $(tac ${script_file});
+         do
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/bin $out/rootfs/bin/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/etc $out/rootfs/etc || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib $out/rootfs/usr/lib/ || true
+         ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/share $out/rootfs/usr/share/ || true
+         if [ -d $path/lib/R/library/ ]; then
+           ${pkgs.xorg.lndir}/bin/lndir -ignorelinks $path/lib/R/library $out/rootfs/R_libs/ || true
+         fi
+      done
+
+      ln -s $out/rootfs/bin $out/rootfs/usr/bin
+
+      mkdir -p $out/rootfs/etc/profile.d
+      echo "export SSL_CERT_FILE=/etc/ssl/certs/ca-bundle.crt" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      echo "export SSL_CERT_DIR=/etc/ssl/certs" >>$out/rootfs/etc/bashrc # singularity pulls that from the env otherwise apperantly
+      #echo "export PATH=/python_env/bin:/bin:/usr/bin/" >>$out/rootfs/etc/bashrc
+      #echo "export PYTHONPATH=$PYTHONPATH:/python_env/lib/python%PYTHON_MAJOR_DOT_MINOR%/site-packages" >>$out/rootfs/etc/bashrc
+
+
+    '';
+  };
+
+  # can't use pkgs.ociTools.buildContainerImage
+  # because it a) does not work from a rootfs
+  # and b) doesn't actually build an image, just a runtime bundle
+  buildOCIimage = {
+    name,
+    script,
+  }: let
+    symlink_image = buildSymlinkImage {
+      inherit name script;
+    };
+    umoci = pkgs.umoci;
+  in
+    pkgs.runCommand "${name}.oci" {} ''
+    set -o pipefail
+    shopt -s nullglob
+    ${umoci}/bin/umoci init --layout "${name}"
+    ${umoci}/bin/umoci new --image "${name}:latest"
+    mkdir tmp-oci-unpack
+
+    mkdir fakeroot/etc -p
+    touch fakeroot/etc/resolv.conf
+
+    # umoci tries to read /etc/resolv.conf, so let's give it one..
+    ${pkgs.bubblewrap}/bin/bwrap \
+           --proc /proc \
+            --dev /dev \
+           --bind /build /build \
+           --ro-bind /build/fakeroot/etc /etc \
+           --ro-bind /nix /nix \
+      ${umoci}/bin/umoci unpack --image "${name}:latest" tmp-oci-unpack --rootless
+
+    echo "rsyncing symlink forest"
+    ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ tmp-oci-unpack/rootfs/
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    echo "rsyncing necessary nix paths"
+    ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+        pkgs.writeClosure [symlink_image.script_file]
+      } / tmp-oci-unpack/rootfs/
+
+
+    # check that we have a rootfs/bin/sh
+    if [ ! -e tmp-oci-unpack/rootfs/bin/sh ]; then
+      echo "No rootfs/bin/sh found"
+      exit 1
+    fi
+    chmod +w tmp-oci-unpack/rootfs -R # because we don't have write on the directories
+
+    ${umoci}/bin/umoci repack --image "${name}:latest" tmp-oci-unpack
+    ${umoci}/bin/umoci config --image "${name}:latest"
+    # strip the first component
+    cd "${name}" && tar cf $out .
+
+
+    '';
+
+  # this never quite worked and since like 22.05, singularity image building on nixos seems broken
+  #   buildSingularityImage = {
+  #     name,
+  #     script,
+  #   }: let
+  #     symlink_image = buildSymlinkImage {
+  #       inherit name script;
+  #     };
+  #   in
+  #     pkgs.runCommand name {} ''
+  #       set -o pipefail
+  #       shopt -s nullglob
+  #       mkdir -p $out/rootfs/
+
+  #       ${pkgs.rsync}/bin/rsync -arW ${symlink_image.derivation}/rootfs/ $out/rootfs/
+  #       chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       #make sure we got everything from the nix store, right?
+  #       ${pkgs.rsync}/bin/rsync -arW --exclude=* --files-from=${
+  #         pkgs.writeClosure [symlink_image.script_file]
+  #       } / $out/rootfs/
+
+  #       rm $out/rootfs/${symlink_image.script_file}
+  #       chmod 755 $out/rootfs
+
+  #       # # singularity tries to read resolv.conf, hosts and user definitions
+  #       # # when converting the container
+  #       # # so let's fake them
+  #       mkdir $out/etc
+  #       mkdir $out/build
+  #       touch $out/etc/resolv.conf
+  #       touch $out/etc/hosts
+  #       echo "nixbld:x:1000:2000:imtseq:/home/installer:/bin/bash\n" >$out/etc/passwd
+  #       echo "xxx:x: 2000:\n" >$out/etc/group
+  #       echo ${pkgs.singularity}/bin/singularity
+  #       ${pkgs.coreutils}/bin/whoami
+
+  #       # # also consider NIX_REDIRECT and libredirect for this
+  #       # the bash binding is needed for singularity to find 'sh'
+  #       ${pkgs.bubblewrap}/bin/bwrap \
+  #          --proc /proc \
+  #          --dev /dev \
+  #         --bind $out/ $out/ \
+  #         --bind $out/build /build \
+  #         --ro-bind $out/etc /etc \
+  #         --ro-bind /nix /nix \
+  #         --ro-bind "${pkgs.bash}/bin" /usr/bin \
+  #         ${pkgs.singularity}/bin/singularity build  /build/${name}.sif $out/rootfs -v
+  #       mv $out/build/*.sif $out/
+  #       rm -rf $out/build
+  #       rm -rf $out/etc
+  #       # chmod +w $out/rootfs -R # because we don't have write on the directories
+  #       # rm -rf $out/rootfs
+  #     '';
+}
diff --git a/examples/flake_subdependency/updated/run_scripts/run/outer_run.sh b/examples/flake_subdependency/updated/run_scripts/run/outer_run.sh
new file mode 100644
index 0000000..292d61d
--- /dev/null
+++ b/examples/flake_subdependency/updated/run_scripts/run/outer_run.sh
@@ -0,0 +1,2 @@
+#/bin/bash
+bash -i /anysnake2/run.sh
diff --git a/examples/flake_subdependency/updated/run_scripts/run/post_run.sh b/examples/flake_subdependency/updated/run_scripts/run/post_run.sh
new file mode 100644
index 0000000..e69de29
diff --git a/examples/flake_subdependency/updated/run_scripts/run/run.sh b/examples/flake_subdependency/updated/run_scripts/run/run.sh
new file mode 100644
index 0000000..20b92ab
--- /dev/null
+++ b/examples/flake_subdependency/updated/run_scripts/run/run.sh
@@ -0,0 +1 @@
+shaeu
\ No newline at end of file
diff --git a/examples/flake_subdependency/updated/run_scripts/run/singularity.bash b/examples/flake_subdependency/updated/run_scripts/run/singularity.bash
new file mode 100644
index 0000000..3e9978e
--- /dev/null
+++ b/examples/flake_subdependency/updated/run_scripts/run/singularity.bash
@@ -0,0 +1,24 @@
+nix shell \
+    github:NixOS/nixpkgs/24.05#dtach \
+    -c \
+    dtach \
+    -c \
+    .anysnake2_flake/dtach/run_2024-11-18_15:03:22 \
+    nix \
+    shell \
+    github:NixOS/nixpkgs/24.05#singularity \
+    -c \
+    singularity exec \
+    --userns \
+    --cleanenv \
+    --home /home/finkernagel \
+    --bind /nix/store:/nix/store:ro \
+    --bind .anysnake2_flake/run_scripts/run/run.sh:/anysnake2/run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/post_run.sh:/anysnake2/post_run.sh:ro \
+    --bind .anysnake2_flake/run_scripts/run/outer_run.sh:/anysnake2/outer_run.sh:ro \
+    --bind /home/finkernagel/upstream/anysnake2/examples/flake_subdependency:/project:rw \
+    --env ANYSNAKE2=1 \
+    --env PATH=/bin \
+    .anysnake2_flake/result/rootfs \
+    /bin/bash \
+    /anysnake2/outer_run.sh \
diff --git a/examples/full/anysnake2.toml b/examples/full/anysnake2.toml
index 000a081..0f1d4dd 100644
--- a/examples/full/anysnake2.toml
+++ b/examples/full/anysnake2.toml
@@ -31,14 +31,12 @@
 
 [nixpkgs]
 	allow_unfree = true # set to true to allow unfree packages from nixpkgs
-	packages = [ # use https://search.nixos.org/packages to search
+	packages = [
 		"fish",
-		"netcat",
-		"varscan", # unfree example
 		"gnumake",
 		"gnused",
-	#"docker-client"
-	] # optional
+		"netcat",
+		"varscan"]
 	url = "github:NixOS/nixpkgs/master/24.05"
 
 
diff --git a/src/config.rs b/src/config.rs
index b18ca4d..6a84885 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -664,7 +664,7 @@ pub struct TofuFlake {
     pub url: TofuVCS,
     pub dir: Option<String>,
     pub follows: Option<Vec<String>>,
-    pub packages: Vec<String>,
+    pub packages: Option<Vec<String>>,
 }
 
 #[derive(Deserialize, Debug, Default)]
diff --git a/src/flake_writer.rs b/src/flake_writer.rs
index a6188be..6ad3f46 100644
--- a/src/flake_writer.rs
+++ b/src/flake_writer.rs
@@ -60,13 +60,18 @@ fn get_filenames(flake_dir: impl AsRef<Path>, use_generated_file_instead: bool)
     }
 }
 
+pub struct WriteFlakeResult {
+    pub flake_nix_changed: bool,
+    pub python_lock_changed: bool
+}
+
 pub fn write_flake(
     flake_dir: impl AsRef<Path>,
     parsed_config: &mut config::TofuConfigToml,
     use_generated_file_instead: bool, // which is set if do_not_modify_flake is in effect.
     in_non_spec_but_cached_values: &HashMap<String, String>,
     out_non_spec_but_cached_values: &mut HashMap<String, String>,
-) -> Result<bool> {
+) -> Result<WriteFlakeResult> {
     let template = std::include_str!("nix/flake_template.nix");
     let flake_dir: &Path = flake_dir.as_ref();
 
@@ -200,20 +205,24 @@ pub fn write_flake(
         gitargs.push("poetry/poetry.lock");
     } */
 
-    let mut res = write_flake_contents(
+    let flake_nix_changed = write_flake_contents(
         &old_flake_contents,
         &flake_contents,
         use_generated_file_instead,
         &flake_filename,
         flake_dir,
     )?;
-    res |= python_locks_changed;
 
     run_git_add(&git_tracked_files, flake_dir)?;
     run_git_commit(flake_dir)?; //after nix 2.23 we will need to commit the flake, possibly. At
                                 //least if we wanted to reference it from another flake
 
-    Ok(res)
+    Ok({
+        WriteFlakeResult {
+            flake_nix_changed,
+            python_lock_changed: python_locks_changed,
+        }
+    })
 }
 
 /// format the list of input flakes for the inputs = {} section of a flake.nix
@@ -927,13 +936,13 @@ fn add_flakes(
                 flake.dir.clone(),
                 &rev_follows[..],
             ));
-            if flake.packages.is_empty() {
+            if flake.packages.is_none() {
                 nixpkgs_pkgs.insert(format!(
                     "({}.defaultPackage.x86_64-linux or {}.packages.x86_64-linux.defaults)",
                     name, name
                 ));
-            } else {
-                for pkg in &flake.packages {
+            } else if let Some(pkgs) = &flake.packages{
+                for pkg in pkgs {
                     nixpkgs_pkgs.insert(format!("{name}.{pkg}"));
                 }
             }
diff --git a/src/main.rs b/src/main.rs
index 51346ae..79ad12b 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -366,7 +366,12 @@ fn inner_main() -> Result<()> {
             match sc.subcommand() {
                 Some(("flake", _)) => {
                     info!("Writing just flake/flake.nix");
-                    rebuild_flake(use_generated_file_instead, "flake", &flake_dir)?;
+                    rebuild_flake(
+                        use_generated_file_instead,
+                        "flake",
+                        &flake_dir,
+                        flake_changed.flake_nix_changed,
+                    )?;
                 }
                 Some(("oci", _)) => {
                     info!("Building oci-image in flake/result");
@@ -374,11 +379,17 @@ fn inner_main() -> Result<()> {
                         use_generated_file_instead,
                         "oci_image.x86_64-linux",
                         &flake_dir,
+                        flake_changed.flake_nix_changed,
                     )?;
                 }
                 Some(("rootfs", _)) => {
                     info!("Building rootfs in flake/result");
-                    rebuild_flake(use_generated_file_instead, "", &flake_dir)?;
+                    rebuild_flake(
+                        use_generated_file_instead,
+                        "",
+                        &flake_dir,
+                        flake_changed.flake_nix_changed,
+                    )?;
                 }
                 _ => {
                     info!("Please pass a subcommand as to what to build (use --help to list)");
@@ -404,9 +415,18 @@ fn inner_main() -> Result<()> {
         let build_unfinished_file = flake_dir.join(".build_unfinished"); // ie. the flake build failed
                                                                          //
                                                                          //early error exit if you try to run an non-existant command
-        if flake_changed || !build_output.exists() || build_unfinished_file.exists() {
+        if flake_changed.flake_nix_changed
+            || flake_changed.python_lock_changed
+            || !build_output.exists()
+            || build_unfinished_file.exists()
+        {
             info!("Rebuilding flake");
-            rebuild_flake(use_generated_file_instead, "", &flake_dir)?;
+            rebuild_flake(
+                use_generated_file_instead,
+                "",
+                &flake_dir,
+                flake_changed.flake_nix_changed,
+            )?;
         }
 
         if let Some(python) = &tofued_config.python {
@@ -923,10 +943,22 @@ fn rebuild_flake(
     use_generated_file_instead: bool,
     target: &str,
     flake_dir: impl AsRef<Path>,
+    flake_content_changed: bool,
 ) -> Result<()> {
     debug!("writing flake");
 
     if !use_generated_file_instead {
+        if flake_content_changed {
+            let flake_lock_path = flake_dir.as_ref().join("flake.lock");
+            if flake_lock_path.exists() {
+                fs::remove_file(&flake_lock_path)?;
+            }
+            Command::new("nix")
+                .args(["flake", "lock"])
+                .current_dir(&flake_dir)
+                .status()
+                .context("(Re)-locking flake failed")?;
+        }
         run_without_ctrl_c(|| {
             Command::new("git")
                 .args(["commit", "-m", "autocommit"])
diff --git a/src/tofu.rs b/src/tofu.rs
index 47aaef5..1d0a1ce 100644
--- a/src/tofu.rs
+++ b/src/tofu.rs
@@ -514,7 +514,7 @@ impl Tofu<HashMap<String, config::TofuFlake>> for Option<HashMap<String, config:
                             url: tofued,
                             dir: value.dir,
                             follows: value.follows,
-                            packages: value.packages.unwrap_or_default(),
+                            packages: value.packages,
                         },
                     ))
                 })
diff --git a/tests/integration_tests.rs b/tests/integration_tests.rs
index a6e6585..621e79b 100644
--- a/tests/integration_tests.rs
+++ b/tests/integration_tests.rs
@@ -1,5 +1,5 @@
 use named_lock::NamedLock;
-use std::path::PathBuf;
+use std::path::{Path, PathBuf};
 use std::process::Command;
 use tempfile::TempDir;
 
@@ -166,11 +166,7 @@ fn test_basic() {
 
 #[test]
 fn test_basic_pre_post_single_line() {
-    let (_code, stdout, _stderr) = run_test(
-        "examples/basic",
-        &["test_pre_post_single_line"],
-        true,
-    );
+    let (_code, stdout, _stderr) = run_test("examples/basic", &["test_pre_post_single_line"], true);
     dbg!(&stdout);
     assert!(stdout.contains("posthello from inside"));
     assert!(stdout.contains("posthello from outside"));
@@ -695,3 +691,39 @@ fn test_empty() {
         .unwrap()
         .starts_with("github:TyberiusPrime/anysnake2_release_flakes"));
 }
+
+fn replace_in_file(path: impl AsRef<Path>, query: &str, replacement: &str) {
+    let raw = ex::fs::read_to_string(&path).unwrap();
+    assert!(raw.contains(query));
+    let out = raw.replace(query, replacement);
+    ex::fs::write(path, out).unwrap();
+}
+
+#[test]
+fn test_flake_change_updates_dependant_flakes() {
+    let ((_code, _stdout, _stderr), td) =
+        run_test_tempdir("examples/flake_subdependency", &["run", "--", "bash" ,"--version"]);
+    let before = ex::fs::read_to_string(td.path().join(".anysnake2_flake/flake.lock")).unwrap();
+    assert!(before.contains("8810f7d31d4d8372f764d567ea140270745fe173"));
+    replace_in_file(
+        &td.path().join("anysnake2.toml"),
+        "8810f7d31d4d8372f764d567ea140270745fe173",
+        "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
+    );
+    let updated_anysnake2_toml = ex::fs::read_to_string(td.path().join("anysnake2.toml")).unwrap();
+    assert!(updated_anysnake2_toml.contains("f554d27c1544d9c56e5f1f8e2b8aff399803674e"));
+    run_test(
+        &td.path().to_string_lossy(),
+        &["run", "--", "bash" ,"--version"],
+        false,
+    );
+    let updated = ex::fs::read_to_string(td.path().join(".anysnake2_flake/flake.lock")).unwrap();
+    assert!(updated != before);
+    run_test(
+        &td.path().to_string_lossy(),
+        &["run", "--", "bash" ,"--version"],
+        true,
+    );
+    let after = ex::fs::read_to_string(td.path().join(".anysnake2_flake/flake.lock")).unwrap();
+    assert_eq!(after, updated);
+}