diff --git a/README.md b/README.md
index b5ed92b35..0b946a98d 100644
--- a/README.md
+++ b/README.md
@@ -9,32 +9,23 @@ read the warning below.
 Words of warning
 ----------------
 
-This project is in early development! I personally use it to manage
+This project is under development. I personally use it to manage
 several user configurations but it may fail catastrophically for you.
 So beware!
 
-To configure programs and services the Home Manager must write various
-things to your home directory and possibly overwrite files you have
-previously created. For example, if you use Home Manager to install
-and configure Git then your `~/.gitconfig` will be replaced by a link
-to a configuration generated by Home Manager:
+In some cases Home Manager cannot detect whether it will overwrite a
+previous manual configuration. For example, the Gnome Terminal module
+will write to your dconf store and cannot tell whether a configuration
+that it is about to be overwrite was from a previous Home Manager
+generation or from manual configuration.
 
-```
-$ ls -gG ~/.gitconfig
-lrwxrwxrwx 1 73 Jan  8 21:59 /home/rycee/.gitconfig -> /nix/store/pk7g12816avnxyhnkbdhqhnlzrw7fsga-home-manager-files/.gitconfig
-```
+Home Manager targets [NixOS][] version 17.03 (the current stable
+version), it may or may not work on other Linux distributions and
+NixOS versions.
 
-So, if you already have a wonderful, painstakingly created
-`~/.gitconfig` it will be gone. Home Manager will _not_ attempt to
-backup the previous `~/.gitconfig` file.
-
-Further, Home Manager targets [NixOS][] version 17.03 (the current
-stable version), it may or may not work on other Linux distributions
-and NixOS versions.
-
-Finally, the `home-manager` tool does not explicitly support rollbacks
-at the moment so if your home directory gets messed up you'll have to
-fix it yourself (you can attempt to run the activation script for the
+Also, the `home-manager` tool does not explicitly support rollbacks at
+the moment so if your home directory gets messed up you'll have to fix
+it yourself (you can attempt to run the activation script for the
 desired generation).
 
 Now when your expectations have been built up and you are eager to try
@@ -132,6 +123,44 @@ $ home-manager build
 which will create a `result` link to a directory containing an
 activation script and the generated home directory files.
 
+File safety
+-----------
+
+To configure programs and services the Home Manager must write various
+things to your home directory. To prevent overwriting any existing
+files when switching to a new generation, Home Manager will attempt to
+detect collisions between existing files and generated files. If any
+such collision is detected the activation will terminate before
+changing anything on your computer.
+
+For example, suppose you have a wonderful, painstakingly created
+`~/.gitconfig` and add
+
+```nix
+{
+  # …
+
+  programs.git = {
+    enable = true;
+    userName = "Jane Doe";
+    userEmail = "jane.doe@example.org";
+  };
+
+  # …
+}
+```
+
+to your configuration. Attempting to switch to the generation will
+then result in
+
+```
+$ home-manager switch
+…
+Activating checkLinkTargets
+Existing file '/home/jdoe/.gitconfig' is in the way
+Please move the above files and try again
+```
+
 [Nix]: https://nixos.org/nix/
 [NixOS]: https://nixos.org/
 [Nixpkgs]: https://nixos.org/nixpkgs/
diff --git a/modules/home-environment.nix b/modules/home-environment.nix
index b270b1cc3..3b62b77f4 100644
--- a/modules/home-environment.nix
+++ b/modules/home-environment.nix
@@ -246,6 +246,37 @@ in
     # script's "check" and the "write" phases.
     home.activation.writeBoundary = dagEntryAnywhere "";
 
+    # This verifies that the links we are about to create will not
+    # overwrite an existing file.
+    home.activation.checkLinkTargets = dagEntryBefore ["writeBoundary"] (
+      let
+        pattern = "-home-manager-files/";
+        check = pkgs.writeText "check" ''
+          newGenFiles="$1"
+          shift
+          for sourcePath in "$@" ; do
+            relativePath="''${sourcePath#$newGenFiles/}"
+            targetPath="$HOME/$relativePath"
+            if [[ -e "$targetPath" \
+                && ! "$(readlink -e "$targetPath")" =~ "${pattern}" ]] ; then
+              echo -e "Existing file '$targetPath' is in the way"
+              collision=1
+            fi
+          done
+
+          if [[ -v collision ]] ; then
+            echo -e "Please move the above files and try again"
+            exit 1
+          fi
+        '';
+      in
+      ''
+        newGenFiles="$(readlink -e "$newGenPath/home-files")"
+        find "$newGenFiles" -type f -print0 -or -type l -print0 \
+                | xargs -0 bash ${check} "$newGenFiles"
+      ''
+    );
+
     home.activation.linkGeneration = dagEntryAfter ["writeBoundary"] (
       let
         link = pkgs.writeText "link" ''