diff --git a/flake.lock b/flake.lock
index 9726a9a06..607e10f9c 100644
--- a/flake.lock
+++ b/flake.lock
@@ -1,5 +1,105 @@
 {
   "nodes": {
+    "crane": {
+      "inputs": {
+        "flake-compat": "flake-compat",
+        "flake-utils": [
+          "putter",
+          "flake-utils"
+        ],
+        "nixpkgs": [
+          "putter",
+          "nixpkgs"
+        ],
+        "rust-overlay": "rust-overlay"
+      },
+      "locked": {
+        "lastModified": 1697588719,
+        "narHash": "sha256-n9ALgm3S+ygpzjesBkB9qutEtM4dtIkhn8WnstCPOew=",
+        "owner": "ipetkov",
+        "repo": "crane",
+        "rev": "da6b58e270d339a78a6e95728012ec2eea879612",
+        "type": "github"
+      },
+      "original": {
+        "owner": "ipetkov",
+        "ref": "v0.14.3",
+        "repo": "crane",
+        "type": "github"
+      }
+    },
+    "flake-compat": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1696267196,
+        "narHash": "sha256-AAQ/2sD+0D18bb8hKuEEVpHUYD1GmO2Uh/taFamn6XQ=",
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "4f910c9827911b1ec2bf26b5a062cd09f8d89f85",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-compat_2": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1673956053,
+        "narHash": "sha256-4gtG9iQuiKITOjNQQeQIpoIB6b16fm+504Ch3sNKLd8=",
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "35bb57c0c8d8b62bbfd284272c928ceb64ddbde9",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1694529238,
+        "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "gitignore": {
+      "inputs": {
+        "nixpkgs": [
+          "putter",
+          "pre-commit-hooks",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1660459072,
+        "narHash": "sha256-8DFJjXG8zqoONA1vXtgeKXy68KdJL5UaXR8NtVMUbx8=",
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "rev": "a20de23b925fd8264fd7fad6454652e142fd7f73",
+        "type": "github"
+      },
+      "original": {
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "type": "github"
+      }
+    },
     "nixpkgs": {
       "locked": {
         "lastModified": 1765472234,
@@ -16,9 +116,133 @@
         "type": "github"
       }
     },
+    "nixpkgs-stable": {
+      "locked": {
+        "lastModified": 1685801374,
+        "narHash": "sha256-otaSUoFEMM+LjBI1XL/xGB5ao6IwnZOXc47qhIgJe8U=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "c37ca420157f4abc31e26f436c1145f8951ff373",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-23.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1699094435,
+        "narHash": "sha256-YLZ5/KKZ1PyLrm2MO8UxRe4H3M0/oaYqNhSlq6FDeeA=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "9d5d25bbfe8c0297ebe85324addcb5020ed1a454",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pre-commit-hooks": {
+      "inputs": {
+        "flake-compat": "flake-compat_2",
+        "flake-utils": [
+          "putter",
+          "flake-utils"
+        ],
+        "gitignore": "gitignore",
+        "nixpkgs": [
+          "putter",
+          "nixpkgs"
+        ],
+        "nixpkgs-stable": "nixpkgs-stable"
+      },
+      "locked": {
+        "lastModified": 1698852633,
+        "narHash": "sha256-Hsc/cCHud8ZXLvmm8pxrXpuaPEeNaaUttaCvtdX/Wug=",
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "rev": "dec10399e5b56aa95fcd530e0338be72ad6462a0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "type": "github"
+      }
+    },
+    "putter": {
+      "inputs": {
+        "crane": "crane",
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs_2",
+        "pre-commit-hooks": "pre-commit-hooks"
+      },
+      "locked": {
+        "lastModified": 1704013409,
+        "narHash": "sha256-v7CTHSKcD6vnIwXRPav+3XETf+uNJz3G+RUF/SHZ+vE=",
+        "ref": "refs/heads/master",
+        "rev": "4d773d3aa9feca3af4578dc62cc6f91ebb16b002",
+        "revCount": 33,
+        "type": "git",
+        "url": "file:///home/rycee/devel/putter"
+      },
+      "original": {
+        "type": "git",
+        "url": "file:///home/rycee/devel/putter"
+      }
+    },
     "root": {
       "inputs": {
-        "nixpkgs": "nixpkgs"
+        "nixpkgs": "nixpkgs",
+        "putter": "putter"
+      }
+    },
+    "rust-overlay": {
+      "inputs": {
+        "flake-utils": [
+          "putter",
+          "crane",
+          "flake-utils"
+        ],
+        "nixpkgs": [
+          "putter",
+          "crane",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1696299134,
+        "narHash": "sha256-RS77cAa0N+Sfj5EmKbm5IdncNXaBCE1BSSQvUE8exvo=",
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "611ccdceed92b4d94ae75328148d84ee4a5b462d",
+        "type": "github"
+      },
+      "original": {
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "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"
       }
     }
   },
diff --git a/flake.nix b/flake.nix
index 96e572f40..809e1d9d9 100644
--- a/flake.nix
+++ b/flake.nix
@@ -2,11 +2,13 @@
   description = "Home Manager for Nix";
 
   inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+  inputs.putter.url = "git+file:///home/rycee/devel/putter";
 
   outputs =
     {
       self,
       nixpkgs,
+      putter,
       ...
     }:
     {
diff --git a/modules/files.nix b/modules/files.nix
index db63fced8..a91d0fff2 100644
--- a/modules/files.nix
+++ b/modules/files.nix
@@ -2,6 +2,7 @@
   pkgs,
   config,
   lib,
+  putter,
   ...
 }:
 
@@ -30,6 +31,8 @@ let
         name = sourceName;
       };
 
+  putterStatePath = "${config.xdg.stateHome}/home-manager/putter-state.json";
+
 in
 
 {
@@ -45,6 +48,14 @@ in
       internal = true;
       description = "Package to contain all home files";
     };
+
+    home.internal = {
+      filePutterConfig = lib.mkOption {
+        type = lib.types.package;
+        internal = true;
+        description = "Putter configuration.";
+      };
+    };
   };
 
   config = {
@@ -91,156 +102,17 @@ in
 
     # This verifies that the links we are about to create will not
     # overwrite an existing file.
-    home.activation.checkLinkTargets = lib.hm.dag.entryBefore [ "writeBoundary" ] (
-      let
-        # Paths that should be forcibly overwritten by Home Manager.
-        # Caveat emptor!
-        forcedPaths = lib.concatMapStringsSep " " (p: ''"$HOME"/${lib.escapeShellArg p}'') (
-          lib.mapAttrsToList (n: v: v.target) (lib.filterAttrs (n: v: v.force) cfg)
-        );
+    home.activation.checkLinkTargets = lib.hm.dag.entryBefore [ "writeBoundary" ] ''
+      ${lib.getExe putter} check -v \
+        --state-file "${putterStatePath}" \
+        ${config.home.internal.filePutterConfig}
+    '';
 
-        storeDir = lib.escapeShellArg builtins.storeDir;
-
-        check = pkgs.replaceVars ./files/check-link-targets.sh {
-          inherit (config.lib.bash) initHomeManagerLib;
-          inherit forcedPaths storeDir;
-        };
-      in
-      ''
-        function checkNewGenCollision() {
-          local newGenFiles
-          newGenFiles="$(readlink -e "$newGenPath/home-files")"
-          find "$newGenFiles" \( -type f -or -type l \) \
-              -exec bash ${check} "$newGenFiles" {} +
-        }
-
-        checkNewGenCollision || exit 1
-      ''
-    );
-
-    # This activation script will
-    #
-    # 1. Remove files from the old generation that are not in the new
-    #    generation.
-    #
-    # 2. Symlink files from the new generation into $HOME.
-    #
-    # This order is needed to ensure that we always know which links
-    # belong to which generation. Specifically, if we're moving from
-    # generation A to generation B having sets of home file links FA
-    # and FB, respectively then cleaning before linking produces state
-    # transitions similar to
-    #
-    #      FA   →   FA ∩ FB   →   (FA ∩ FB) ∪ FB = FB
-    #
-    # and a failure during the intermediate state FA ∩ FB will not
-    # result in lost links because this set of links are in both the
-    # source and target generation.
-    home.activation.linkGeneration = lib.hm.dag.entryAfter [ "writeBoundary" ] (
-      let
-        link = pkgs.writeShellScript "link" ''
-          ${config.lib.bash.initHomeManagerLib}
-
-          newGenFiles="$1"
-          shift
-          for sourcePath in "$@" ; do
-            relativePath="''${sourcePath#$newGenFiles/}"
-            targetPath="$HOME/$relativePath"
-            if [[ -e "$targetPath" && ! -L "$targetPath" ]] ; then
-              if [[ -n "$HOME_MANAGER_BACKUP_COMMAND" ]] ; then
-                verboseEcho "Running $HOME_MANAGER_BACKUP_COMMAND $targetPath."
-                run $HOME_MANAGER_BACKUP_COMMAND "$targetPath" || errorEcho "Running `$HOME_MANAGER_BACKUP_COMMAND` on '$targetPath' failed."
-              elif [[ -n "$HOME_MANAGER_BACKUP_EXT" ]] ; then
-                # The target exists, back it up
-                backup="$targetPath.$HOME_MANAGER_BACKUP_EXT"
-                if [[ -e "$backup" && -n "$HOME_MANAGER_BACKUP_OVERWRITE" ]]; then
-                  run rm $VERBOSE_ARG "$backup"
-                fi
-                run mv $VERBOSE_ARG "$targetPath" "$backup" || errorEcho "Moving '$targetPath' failed!"
-              fi
-            fi
-
-            if [[ -e "$targetPath" && ! -L "$targetPath" ]] && cmp -s "$sourcePath" "$targetPath" ; then
-              # The target exists but is identical – don't do anything.
-              verboseEcho "Skipping '$targetPath' as it is identical to '$sourcePath'"
-            else
-              # Place that symlink, --force
-              # This can still fail if the target is a directory, in which case we bail out.
-              run mkdir -p $VERBOSE_ARG "$(dirname "$targetPath")"
-              run ln -Tsf $VERBOSE_ARG "$sourcePath" "$targetPath" || exit 1
-            fi
-          done
-        '';
-
-        cleanup = pkgs.writeShellScript "cleanup" ''
-          ${config.lib.bash.initHomeManagerLib}
-
-          # A symbolic link whose target path matches this pattern will be
-          # considered part of a Home Manager generation.
-          homeFilePattern="$(readlink -e ${lib.escapeShellArg builtins.storeDir})/*-home-manager-files/*"
-
-          newGenFiles="$1"
-          shift 1
-          for relativePath in "$@" ; do
-            targetPath="$HOME/$relativePath"
-            if [[ -e "$newGenFiles/$relativePath" ]] ; then
-              verboseEcho "Checking $targetPath: exists"
-            elif [[ ! "$(readlink "$targetPath")" == $homeFilePattern ]] ; then
-              warnEcho "Path '$targetPath' does not link into a Home Manager generation. Skipping delete."
-            else
-              verboseEcho "Checking $targetPath: gone (deleting)"
-              run rm $VERBOSE_ARG "$targetPath"
-
-              # Recursively delete empty parent directories.
-              targetDir="$(dirname "$relativePath")"
-              if [[ "$targetDir" != "." ]] ; then
-                pushd "$HOME" > /dev/null
-
-                # Call rmdir with a relative path excluding $HOME.
-                # Otherwise, it might try to delete $HOME and exit
-                # with a permission error.
-                run rmdir $VERBOSE_ARG \
-                    -p --ignore-fail-on-non-empty \
-                    "$targetDir"
-
-                popd > /dev/null
-              fi
-            fi
-          done
-        '';
-      in
-      ''
-        function linkNewGen() {
-          _i "Creating home file links in %s" "$HOME"
-
-          local newGenFiles
-          newGenFiles="$(readlink -e "$newGenPath/home-files")"
-          find "$newGenFiles" \( -type f -or -type l \) \
-            -exec bash ${link} "$newGenFiles" {} +
-        }
-
-        function cleanOldGen() {
-          if [[ ! -v oldGenPath || ! -e "$oldGenPath/home-files" ]] ; then
-            return
-          fi
-
-          _i "Cleaning up orphan links from %s" "$HOME"
-
-          local newGenFiles oldGenFiles
-          newGenFiles="$(readlink -e "$newGenPath/home-files")"
-          oldGenFiles="$(readlink -e "$oldGenPath/home-files")"
-
-          # Apply the cleanup script on each leaf in the old
-          # generation. The find command below will print the
-          # relative path of the entry.
-          find "$oldGenFiles" '(' -type f -or -type l ')' -printf '%P\0' \
-            | xargs -0 bash ${cleanup} "$newGenFiles"
-        }
-
-        cleanOldGen
-        linkNewGen
-      ''
-    );
+    home.activation.linkGeneration = lib.hm.dag.entryAfter [ "writeBoundary" ] ''
+      ${lib.getExe putter} apply $VERBOSE_ARG -v ''${DRY_RUN:+--dry-run} \
+        --state-file "${putterStatePath}" \
+        ${config.home.internal.filePutterConfig}
+    '';
 
     home.activation.checkFilesChanged = lib.hm.dag.entryBefore [ "linkGeneration" ] (
       let
@@ -286,6 +158,18 @@ in
       '') (lib.filter (v: v.onChange != "") (lib.attrValues cfg))
     );
 
+    home.internal.filePutterConfig =
+      let
+        putter = import ./lib/putter.nix { inherit lib; };
+        manifest = putter.mkPutterManifest {
+          inherit putterStatePath;
+          sourceBaseDirectory = config.home-files;
+          targetBaseDirectory = config.home.homeDirectory;
+          fileEntries = attrValues cfg;
+        };
+      in
+      pkgs.writeText "hm-putter.json" manifest;
+
     # Symlink directories and files that have the right execute bit.
     # Copy files that need their execute bit changed.
     home-files =
diff --git a/modules/home-environment.nix b/modules/home-environment.nix
index 32c3ce6b5..0c6460f9d 100644
--- a/modules/home-environment.nix
+++ b/modules/home-environment.nix
@@ -906,6 +906,7 @@ in
             --subst-var-by GENERATION_DIR $out
 
           ln -s ${config.home-files} $out/home-files
+          ln -s ${config.home.internal.filePutterConfig} $out/putter.json
           ln -s ${cfg.path} $out/home-path
 
           cp "$extraDependenciesPath" "$out/extra-dependencies"
diff --git a/modules/lib/putter.nix b/modules/lib/putter.nix
new file mode 100644
index 000000000..2fe42ecc1
--- /dev/null
+++ b/modules/lib/putter.nix
@@ -0,0 +1,81 @@
+# Contains some handy functions for generating Putter file manifests.
+
+{ lib }:
+
+let
+
+  inherit (lib)
+    concatMap
+    concatLists
+    mapAttrsToList
+    hasPrefix
+    filter
+    ;
+
+in
+{
+  # Converts a Home Manager style list of file specifications into a Putter
+  # configuration.
+  #
+  # Note, the interface of this function is not considered stable, it may change
+  # as the needs of Home Manager change.
+  mkPutterManifest =
+    {
+      putterStatePath,
+      sourceBaseDirectory,
+      targetBaseDirectory,
+      fileEntries,
+    }:
+    let
+      # Convert a directory to a Putter configuration. Basically, this will
+      # create a file entry for each file in the directory. Any sub-directories
+      # will be handled recursively.
+      mkDirEntry =
+        f:
+        concatLists (
+          mapAttrsToList (
+            n: v:
+            let
+              f' = f // {
+                source = "${f.source}/${n}";
+                target = "${f.target}/${n}";
+              };
+            in
+            mkEntriesForType f' v
+          ) (builtins.readDir f.source)
+        );
+
+      mkEntriesForType =
+        f: t:
+        if t == "regular" || t == "symlink" then
+          mkFileEntry f
+        else if t == "directory" then
+          mkDirEntry f
+        else
+          throw "unexpected file type ${t}";
+
+      # Create a file entry for the given file.
+      mkFileEntry = f: [
+        {
+          collision.resolution = if f.force then "force" else "abort";
+          action.type = "symlink";
+          source = "${sourceBaseDirectory}/${f.target}";
+          target = (if hasPrefix "/" f.target then "" else "${targetBaseDirectory}/") + f.target;
+        }
+      ];
+
+      # Given a Home Manager file entry, produce a list of Putter entries. For
+      # recursive HM file entries, we recursively traverse the source directory
+      # and generate a Putter entry for each file we encounter.
+      mkEntries = f: if f.recursive then mkEntriesForType f "directory" else mkFileEntry f;
+
+      putterJson = {
+        version = "1";
+        state = putterStatePath;
+        files = concatMap mkEntries (filter (f: f.enable) fileEntries);
+      };
+
+      putterJsonText = builtins.toJSON putterJson;
+    in
+    putterJsonText;
+}