diff --git a/CHANGES.md b/CHANGES.md
index 47bee9cd6d..3a08bbb66c 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,19 +1,24 @@
 ## Unreleased
 
-### Added
-
 ### Fixed
 
 - **irmin-client**
   - Fix a fd leak when using `clone` (#2322, @samoht)
 - **irmin-git**
   - Fix git sync example (#2327, @art-w)
+  - Fixed issue with two subsequent `Irmin-git` repos, where one
+    repo would lose the ability to find its root path (#2326, @zazedd)
 - **irmin**
   - Fix CI, update dependencies (#2321, @smorimoto)
   - Update documentation (#2323, #2324, #2325, @christinerose)
+- **irmin-cli**
+  - Fix uncaught exception (#2326, @art-w)
 
 ### Removed
 
+- **irmin**
+  - Removed `?allow_duplicate` parameter from the `Conf.key` function (#2326, @zazedd)
+
 ## 3.9.0 (2023-10-05)
 
 ### Added
diff --git a/src/irmin-cli/cli.ml b/src/irmin-cli/cli.ml
index ceadcf7089..10091bb149 100644
--- a/src/irmin-cli/cli.ml
+++ b/src/irmin-cli/cli.ml
@@ -108,7 +108,7 @@ let print_exc exc =
   | e -> Fmt.epr "ERROR: %a\n%!" Fmt.exn e);
   exit 1
 
-let run t = Lwt_main.run (Lwt.catch (fun () -> t) print_exc)
+let run fn = Lwt_main.run (Lwt.catch fn print_exc)
 let mk (fn : 'a) : 'a Term.t = Term.(const (fun () -> fn) $ setup_log)
 
 (* INIT *)
@@ -118,7 +118,7 @@ let init =
     doc = "Initialize a store.";
     man = [];
     term =
-      (let init (S (_, _store, _)) = run Lwt.return_unit in
+      (let init (S (_, _store, _)) = run @@ fun () -> Lwt.return_unit in
        Term.(mk init $ store ()));
   }
 
@@ -143,15 +143,15 @@ let get =
     term =
       (let get (S (impl, store, _)) path =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            S.find t (key S.Path.t path) >>= function
-            | None ->
-                print "<none>";
-                exit 1
-            | Some v ->
-                print "%a" (Irmin.Type.pp S.Contents.t) v;
-                Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         S.find t (key S.Path.t path) >>= function
+         | None ->
+             print "<none>";
+             exit 1
+         | Some v ->
+             print "%a" (Irmin.Type.pp S.Contents.t) v;
+             Lwt.return_unit
        in
        Term.(mk get $ store () $ path));
   }
@@ -170,17 +170,17 @@ let list =
            | Empty -> S.Path.empty
            | Path str -> key S.Path.t str
          in
-         run
-           (let* t = store in
-            let* paths = S.list t path in
-            let pp_step = Irmin.Type.pp S.Path.step_t in
-            let pp ppf (s, k) =
-              match S.Tree.destruct k with
-              | `Contents _ -> Fmt.pf ppf "FILE %a" pp_step s
-              | `Node _ -> Fmt.pf ppf "DIR %a" pp_step s
-            in
-            List.iter (print "%a" pp) paths;
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let* paths = S.list t path in
+         let pp_step = Irmin.Type.pp S.Path.step_t in
+         let pp ppf (s, k) =
+           match S.Tree.destruct k with
+           | `Contents _ -> Fmt.pf ppf "FILE %a" pp_step s
+           | `Node _ -> Fmt.pf ppf "DIR %a" pp_step s
+         in
+         List.iter (print "%a" pp) paths;
+         Lwt.return_unit
        in
        Term.(mk list $ store () $ path_or_empty));
   }
@@ -194,52 +194,52 @@ let tree =
     term =
       (let tree (S (impl, store, _)) =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            let all = ref [] in
-            let todo = ref [ S.Path.empty ] in
-            let rec walk () =
-              match !todo with
-              | [] -> Lwt.return_unit
-              | k :: rest ->
-                  todo := rest;
-                  let* childs = S.list t k in
-                  Lwt_list.iter_p
-                    (fun (s, c) ->
-                      let k = S.Path.rcons k s in
-                      match S.Tree.destruct c with
-                      | `Node _ ->
-                          todo := k :: !todo;
-                          Lwt.return_unit
-                      | `Contents _ ->
-                          let+ v = S.get t k in
-                          all := (k, v) :: !all)
-                    childs
-                  >>= walk
-            in
-            walk () >>= fun () ->
-            let all = !all in
-            let all =
-              List.map
-                (fun (k, v) ->
-                  ( Irmin.Type.to_string S.Path.t k,
-                    Irmin.Type.to_string S.Contents.t v ))
-                all
-            in
-            let max_length l =
-              List.fold_left (fun len s -> max len (String.length s)) 0 l
-            in
-            let k_max = max_length (List.map fst all) in
-            let v_max = max_length (List.map snd all) in
-            let pad = 79 + k_max + v_max in
-            List.iter
-              (fun (k, v) ->
-                let dots =
-                  String.make (pad - String.length k - String.length v) '.'
-                in
-                print "%s%s%s" k dots v)
-              all;
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let all = ref [] in
+         let todo = ref [ S.Path.empty ] in
+         let rec walk () =
+           match !todo with
+           | [] -> Lwt.return_unit
+           | k :: rest ->
+               todo := rest;
+               let* childs = S.list t k in
+               Lwt_list.iter_p
+                 (fun (s, c) ->
+                   let k = S.Path.rcons k s in
+                   match S.Tree.destruct c with
+                   | `Node _ ->
+                       todo := k :: !todo;
+                       Lwt.return_unit
+                   | `Contents _ ->
+                       let+ v = S.get t k in
+                       all := (k, v) :: !all)
+                 childs
+               >>= walk
+         in
+         walk () >>= fun () ->
+         let all = !all in
+         let all =
+           List.map
+             (fun (k, v) ->
+               ( Irmin.Type.to_string S.Path.t k,
+                 Irmin.Type.to_string S.Contents.t v ))
+             all
+         in
+         let max_length l =
+           List.fold_left (fun len s -> max len (String.length s)) 0 l
+         in
+         let k_max = max_length (List.map fst all) in
+         let v_max = max_length (List.map snd all) in
+         let pad = 79 + k_max + v_max in
+         List.iter
+           (fun (k, v) ->
+             let dots =
+               String.make (pad - String.length k - String.length v) '.'
+             in
+             print "%s%s%s" k dots v)
+           all;
+         Lwt.return_unit
        in
        Term.(mk tree $ store ()));
   }
@@ -265,12 +265,12 @@ let set =
        in
        let set (S (impl, store, _)) author message path v =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let message = match message with Some s -> s | None -> "set" in
-            let* t = store in
-            let path = key S.Path.t path in
-            let value = value S.Contents.t v in
-            S.set_exn t ~info:(info (module S) ?author "%s" message) path value)
+         run @@ fun () ->
+         let message = match message with Some s -> s | None -> "set" in
+         let* t = store in
+         let path = key S.Path.t path in
+         let value = value S.Contents.t v in
+         S.set_exn t ~info:(info (module S) ?author "%s" message) path value
        in
        Term.(mk set $ store () $ author $ message $ path $ v));
   }
@@ -284,14 +284,14 @@ let remove =
     term =
       (let remove (S (impl, store, _)) author message path =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let message =
-              match message with Some s -> s | None -> "remove " ^ path
-            in
-            let* t = store in
-            S.remove_exn t
-              ~info:(info (module S) ?author "%s" message)
-              (key S.Path.t path))
+         run @@ fun () ->
+         let message =
+           match message with Some s -> s | None -> "remove " ^ path
+         in
+         let* t = store in
+         S.remove_exn t
+           ~info:(info (module S) ?author "%s" message)
+           (key S.Path.t path)
        in
        Term.(mk remove $ store () $ author $ message $ path));
   }
@@ -312,14 +312,14 @@ let clone =
       (let clone (S (impl, store, f), remote) depth =
          let (module S) = Store.Impl.generic_keyed impl in
          let module Sync = Irmin.Sync.Make (S) in
-         run
-           (let* t = store in
-            let* r = remote in
-            let* x = apply r f in
-            Sync.fetch t ?depth x >>= function
-            | Ok (`Head d) -> S.Head.set t d
-            | Ok `Empty -> Lwt.return_unit
-            | Error (`Msg e) -> failwith e)
+         run @@ fun () ->
+         let* t = store in
+         let* r = remote in
+         let* x = apply r f in
+         Sync.fetch t ?depth x >>= function
+         | Ok (`Head d) -> S.Head.set t d
+         | Ok `Empty -> Lwt.return_unit
+         | Error (`Msg e) -> failwith e
        in
        Term.(mk clone $ remote () $ depth));
   }
@@ -334,14 +334,14 @@ let fetch =
       (let fetch (S (impl, store, f), remote) =
          let (module S) = Store.Impl.generic_keyed impl in
          let module Sync = Irmin.Sync.Make (S) in
-         run
-           (let* t = store in
-            let* r = remote in
-            let branch = branch S.Branch.t "import" in
-            let* t = S.of_branch (S.repo t) branch in
-            let* x = apply r f in
-            let* _ = Sync.pull_exn t x `Set in
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let* r = remote in
+         let branch = branch S.Branch.t "import" in
+         let* t = S.of_branch (S.repo t) branch in
+         let* x = apply r f in
+         let* _ = Sync.pull_exn t x `Set in
+         Lwt.return_unit
        in
        Term.(mk fetch $ remote ()));
   }
@@ -355,21 +355,21 @@ let merge =
     term =
       (let merge (S (impl, store, _)) author message branch =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let message = match message with Some s -> s | None -> "merge" in
-            let branch =
-              match Irmin.Type.of_string S.Branch.t branch with
-              | Ok b -> b
-              | Error (`Msg msg) -> failwith msg
-            in
-            let* t = store in
-            S.merge_with_branch t branch
-              ~info:(info (module S) ?author "%s" message)
-            >|= function
-            | Ok () -> ()
-            | Error conflict ->
-                let fmt = Irmin.Type.pp_json Irmin.Merge.conflict_t in
-                Fmt.epr "CONFLICT: %a\n%!" fmt conflict)
+         run @@ fun () ->
+         let message = match message with Some s -> s | None -> "merge" in
+         let branch =
+           match Irmin.Type.of_string S.Branch.t branch with
+           | Ok b -> b
+           | Error (`Msg msg) -> failwith msg
+         in
+         let* t = store in
+         S.merge_with_branch t branch
+           ~info:(info (module S) ?author "%s" message)
+         >|= function
+         | Ok () -> ()
+         | Error conflict ->
+             let fmt = Irmin.Type.pp_json Irmin.Merge.conflict_t in
+             Fmt.epr "CONFLICT: %a\n%!" fmt conflict
        in
        let branch_name =
          let doc = Arg.info ~docv:"BRANCH" ~doc:"Branch to merge from." [] in
@@ -389,14 +389,14 @@ let pull =
          let (module S) = Store.Impl.generic_keyed impl in
          let message = match message with Some s -> s | None -> "pull" in
          let module Sync = Irmin.Sync.Make (S) in
-         run
-           (let* t = store in
-            let* r = remote in
-            let* x = apply r f in
-            let* _ =
-              Sync.pull_exn t x (`Merge (info (module S) ?author "%s" message))
-            in
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let* r = remote in
+         let* x = apply r f in
+         let* _ =
+           Sync.pull_exn t x (`Merge (info (module S) ?author "%s" message))
+         in
+         Lwt.return_unit
        in
        Term.(mk pull $ remote () $ author $ message));
   }
@@ -411,12 +411,12 @@ let push =
       (let push (S (impl, store, f), remote) =
          let (module S) = Store.Impl.generic_keyed impl in
          let module Sync = Irmin.Sync.Make (S) in
-         run
-           (let* t = store in
-            let* r = remote in
-            let* x = apply r f in
-            let* _ = Sync.push_exn t x in
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let* r = remote in
+         let* x = apply r f in
+         let* _ = Sync.push_exn t x in
+         Lwt.return_unit
        in
        Term.(mk push $ remote ()));
   }
@@ -430,11 +430,11 @@ let snapshot =
     term =
       (let snapshot (S (impl, store, _)) =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            let* k = S.Head.get t in
-            print "%a" S.Commit.pp_hash k;
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let* k = S.Head.get t in
+         print "%a" S.Commit.pp_hash k;
+         Lwt.return_unit
        in
        Term.(mk snapshot $ store ()));
   }
@@ -454,13 +454,13 @@ let revert =
        in
        let revert (S (impl, store, _)) snapshot =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            let hash = commit S.Hash.t snapshot in
-            let* s = S.Commit.of_hash (S.repo t) hash in
-            match s with
-            | Some s -> S.Head.set t s
-            | None -> failwith "invalid commit")
+         run @@ fun () ->
+         let* t = store in
+         let hash = commit S.Hash.t snapshot in
+         let* s = S.Commit.of_hash (S.repo t) hash in
+         match s with
+         | Some s -> S.Head.set t s
+         | None -> failwith "invalid commit"
        in
        Term.(mk revert $ store () $ snapshot));
   }
@@ -560,18 +560,18 @@ let watch =
            at_exit (fun () ->
                match !proc with None -> () | Some p -> p#terminate)
          in
-         run
-           (let* t = store in
-            let* _ =
-              S.watch_key t path
-                (handle_diff
-                   (module S : Irmin.Generic_key.S
-                     with type Schema.Path.t = S.path
-                      and type commit = S.commit)
-                   path command proc)
-            in
-            let t, _ = Lwt.task () in
-            t)
+         run @@ fun () ->
+         let* t = store in
+         let* _ =
+           S.watch_key t path
+             (handle_diff
+                (module S : Irmin.Generic_key.S
+                  with type Schema.Path.t = S.path
+                   and type commit = S.commit)
+                path command proc)
+         in
+         let t, _ = Lwt.task () in
+         t
        in
        let command =
          let doc = Arg.info ~docv:"COMMAND" ~doc:"Command to execute" [] in
@@ -620,33 +620,33 @@ let dot =
            Printf.sprintf "%2d:%2d:%2d" tm.Unix.tm_hour tm.Unix.tm_min
              tm.Unix.tm_sec
          in
-         run
-           (let* t = store in
-            let call_dot = not no_dot_call in
-            let buf = Buffer.create 1024 in
-            Dot.output_buffer ~html:false t ?depth ~full ~date buf >>= fun () ->
-            let oc = open_out_bin (basename ^ ".dot") in
-            let* () =
-              Lwt.finalize
-                (fun () ->
-                  output_string oc (Buffer.contents buf);
-                  Lwt.return_unit)
-                (fun () ->
-                  close_out oc;
-                  Lwt.return_unit)
-            in
-            if call_dot then (
-              let i = Sys.command "/bin/sh -c 'command -v dot'" in
-              if i <> 0 then
-                [%logs.err
-                  "Cannot find the `dot' utility. Please install it on your \
-                   system and be sure it is available in your $PATH."];
-              let i =
-                Sys.command
-                  (Printf.sprintf "dot -Tpng %s.dot -o%s.png" basename basename)
-              in
-              if i <> 0 then [%logs.err "The %s.dot is corrupted" basename]);
-            Lwt.return_unit)
+         run @@ fun () ->
+         let* t = store in
+         let call_dot = not no_dot_call in
+         let buf = Buffer.create 1024 in
+         Dot.output_buffer ~html:false t ?depth ~full ~date buf >>= fun () ->
+         let oc = open_out_bin (basename ^ ".dot") in
+         let* () =
+           Lwt.finalize
+             (fun () ->
+               output_string oc (Buffer.contents buf);
+               Lwt.return_unit)
+             (fun () ->
+               close_out oc;
+               Lwt.return_unit)
+         in
+         if call_dot then (
+           let i = Sys.command "/bin/sh -c 'command -v dot'" in
+           if i <> 0 then
+             [%logs.err
+               "Cannot find the `dot' utility. Please install it on your \
+                system and be sure it is available in your $PATH."];
+           let i =
+             Sys.command
+               (Printf.sprintf "dot -Tpng %s.dot -o%s.png" basename basename)
+           in
+           if i <> 0 then [%logs.err "The %s.dot is corrupted" basename]);
+         Lwt.return_unit
        in
        Term.(mk dot $ store () $ basename $ depth $ no_dot_call $ full));
   }
@@ -737,24 +737,22 @@ let graphql =
        in
        let graphql (S (impl, store, remote_fn)) port addr =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let module Server =
-              Graphql.Server.Make
-                (S)
-                (struct
-                  let remote = remote_fn
-                end)
-            in
-           let* t = store in
-           let server = Server.v (S.repo t) in
-           let* ctx = Conduit_lwt_unix.init ~src:addr () in
-           let ctx = Cohttp_lwt_unix.Net.init ~ctx () in
-           let on_exn exn =
-             [%logs.debug "on_exn: %s" (Printexc.to_string exn)]
-           in
-           Cohttp_lwt_unix.Server.create ~on_exn ~ctx
-             ~mode:(`TCP (`Port port))
-             server)
+         run @@ fun () ->
+         let module Server =
+           Graphql.Server.Make
+             (S)
+             (struct
+               let remote = remote_fn
+             end)
+         in
+         let* t = store in
+         let server = Server.v (S.repo t) in
+         let* ctx = Conduit_lwt_unix.init ~src:addr () in
+         let ctx = Cohttp_lwt_unix.Net.init ~ctx () in
+         let on_exn exn = [%logs.debug "on_exn: %s" (Printexc.to_string exn)] in
+         Cohttp_lwt_unix.Server.create ~on_exn ~ctx
+           ~mode:(`TCP (`Port port))
+           server
        in
        Term.(mk graphql $ store () $ port $ addr));
   }
@@ -803,10 +801,10 @@ let branches =
     term =
       (let branches (S (impl, store, _)) =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            let+ branches = S.Branch.list (S.repo t) in
-            List.iter (Fmt.pr "%a\n" (Irmin.Type.pp S.branch_t)) branches)
+         run @@ fun () ->
+         let* t = store in
+         let+ branches = S.Branch.list (S.repo t) in
+         List.iter (Fmt.pr "%a\n" (Irmin.Type.pp S.branch_t)) branches
        in
        Term.(mk branches $ store ()));
   }
@@ -869,59 +867,59 @@ let log =
        let exception Return in
        let commits (S (impl, store, _)) plain pager num skip reverse =
          let (module S) = Store.Impl.generic_keyed impl in
-         run
-           (let* t = store in
-            let fmt f date =
-              Fmt.pf f "%s %s %02d %02d:%02d:%02d %04d" (weekday date)
-                (month date) date.tm_mday date.tm_hour date.tm_min date.tm_sec
-                (date.tm_year + 1900)
-            in
-            let repo = S.repo t in
-            let skip = ref (Option.value ~default:0 skip) in
-            let num = Option.value ~default:0 num in
-            let num_count = ref 0 in
-            let commit formatter key =
-              if num > 0 && !num_count >= num then raise Return
-              else if !skip > 0 then
-                let () = decr skip in
-                Lwt.return_unit
-              else
-                let+ commit = S.Commit.of_key repo key >|= Option.get in
-                let hash = S.Backend.Commit.Key.to_hash key in
-                let info = S.Commit.info commit in
-                let date = S.Info.date info in
-                let author = S.Info.author info in
-                let message = S.Info.message info in
-                let date = Unix.localtime (Int64.to_float date) in
-                let () =
-                  Fmt.pf formatter "commit %a\nAuthor: %s\nDate: %a\n\n%s\n\n%!"
-                    (Irmin.Type.pp S.hash_t) hash author fmt date message
-                in
-                incr num_count
-            in
-            let* max = S.Head.get t >|= fun x -> [ `Commit (S.Commit.key x) ] in
-            let iter ~commit ~max repo =
-              Lwt.catch
-                (fun () ->
-                  if reverse then S.Repo.iter ~commit ~min:[] ~max repo
-                  else S.Repo.breadth_first_traversal ~commit ~max repo)
-                (function Return -> Lwt.return_unit | exn -> raise exn)
-            in
-            if plain then
-              let commit = commit Format.std_formatter in
-              iter ~commit ~max repo
-            else
-              Lwt.catch
-                (fun () ->
-                  let out = Unix.open_process_out pager in
-                  let commit = commit (Format.formatter_of_out_channel out) in
-                  let+ () = iter ~commit ~max repo in
-                  let _ = Unix.close_process_out out in
-                  ())
-                (function
-                  | Sys_error s when String.equal s "Broken pipe" ->
-                      Lwt.return_unit
-                  | exn -> raise exn))
+         run @@ fun () ->
+         let* t = store in
+         let fmt f date =
+           Fmt.pf f "%s %s %02d %02d:%02d:%02d %04d" (weekday date) (month date)
+             date.tm_mday date.tm_hour date.tm_min date.tm_sec
+             (date.tm_year + 1900)
+         in
+         let repo = S.repo t in
+         let skip = ref (Option.value ~default:0 skip) in
+         let num = Option.value ~default:0 num in
+         let num_count = ref 0 in
+         let commit formatter key =
+           if num > 0 && !num_count >= num then raise Return
+           else if !skip > 0 then
+             let () = decr skip in
+             Lwt.return_unit
+           else
+             let+ commit = S.Commit.of_key repo key >|= Option.get in
+             let hash = S.Backend.Commit.Key.to_hash key in
+             let info = S.Commit.info commit in
+             let date = S.Info.date info in
+             let author = S.Info.author info in
+             let message = S.Info.message info in
+             let date = Unix.localtime (Int64.to_float date) in
+             let () =
+               Fmt.pf formatter "commit %a\nAuthor: %s\nDate: %a\n\n%s\n\n%!"
+                 (Irmin.Type.pp S.hash_t) hash author fmt date message
+             in
+             incr num_count
+         in
+         let* max = S.Head.get t >|= fun x -> [ `Commit (S.Commit.key x) ] in
+         let iter ~commit ~max repo =
+           Lwt.catch
+             (fun () ->
+               if reverse then S.Repo.iter ~commit ~min:[] ~max repo
+               else S.Repo.breadth_first_traversal ~commit ~max repo)
+             (function Return -> Lwt.return_unit | exn -> raise exn)
+         in
+         if plain then
+           let commit = commit Format.std_formatter in
+           iter ~commit ~max repo
+         else
+           Lwt.catch
+             (fun () ->
+               let out = Unix.open_process_out pager in
+               let commit = commit (Format.formatter_of_out_channel out) in
+               let+ () = iter ~commit ~max repo in
+               let _ = Unix.close_process_out out in
+               ())
+             (function
+               | Sys_error s when String.equal s "Broken pipe" ->
+                   Lwt.return_unit
+               | exn -> raise exn)
        in
        Term.(mk commits $ store () $ plain $ pager $ num $ skip $ reverse));
   }
diff --git a/src/irmin-cli/resolver.ml b/src/irmin-cli/resolver.ml
index 07591bdeac..f96435e27d 100644
--- a/src/irmin-cli/resolver.ml
+++ b/src/irmin-cli/resolver.ml
@@ -446,8 +446,6 @@ let rec json_of_yaml : Yaml.value -> Yojson.Basic.t = function
 
 let parse_config ?root y spec =
   let config = Conf.empty spec in
-  (* Initialise root for the examples in README to pass. *)
-  let config = Conf.add config (Conf.root spec) "." in
   let config =
     List.fold_left
       (fun config k ->
diff --git a/src/irmin-git/conf.ml b/src/irmin-git/conf.ml
index ad95ba6f01..d62f98dbf2 100644
--- a/src/irmin-git/conf.ml
+++ b/src/irmin-git/conf.ml
@@ -49,15 +49,14 @@ module Key = struct
       "dot-git"
       Irmin.Type.(option string)
       None
+
+  let root = root spec
 end
 
 let init ?head ?bare ?level ?dot_git ?buffers root =
   let module C = Irmin.Backend.Conf in
   let config = C.empty spec in
-  (* Initialise an fresh root_key, otherwise [C.add config root_key root] has no
-     effect on current config. *)
-  let root_key = C.root spec in
-  let config = C.add config root_key root in
+  let config = C.add config Key.root root in
   let config =
     match bare with
     | None -> C.add config Key.bare (C.default Key.bare)
diff --git a/src/irmin-test/common.ml b/src/irmin-test/common.ml
index 01436177bb..b6f59d37b9 100644
--- a/src/irmin-test/common.ml
+++ b/src/irmin-test/common.ml
@@ -219,14 +219,20 @@ module Make_helpers (S : Generic_key) = struct
       (fun () ->
         let module Conf = Irmin.Backend.Conf in
         let generate_random_root config =
-          let id = Random.int 100 |> string_of_int in
-          let root_value =
-            match Conf.find_root config with
-            | None -> "test_" ^ id
-            | Some v -> v ^ "_" ^ id
-          in
-          let root_key = Conf.(root (spec config)) in
-          Conf.add config root_key root_value
+          let sp = Conf.spec config in
+          match Conf.Spec.find_key sp "root" with
+          | None -> config
+          | Some (K k) ->
+              let id = Random.int 100 |> string_of_int in
+              let root_value =
+                match Conf.find_root config with
+                | None -> "test_" ^ id
+                | Some v -> v ^ "_" ^ id
+              in
+              let v =
+                Irmin.Type.of_string (Conf.ty k) root_value |> Result.get_ok
+              in
+              Conf.add config k v
         in
         let config = generate_random_root x.config in
         config_ptr := Some config;
diff --git a/src/irmin/conf.ml b/src/irmin/conf.ml
index 6411c92629..0788380ce0 100644
--- a/src/irmin/conf.ml
+++ b/src/irmin/conf.ml
@@ -87,7 +87,7 @@ type t = Spec.t * Univ.t M.t
 
 let spec = fst
 
-let key ?docs ?docv ?doc ?(allow_duplicate = false) ~spec name ty default =
+let key ?docs ?docv ?doc ~spec name ty default =
   let () =
     String.iter
       (function
@@ -96,8 +96,7 @@ let key ?docs ?docv ?doc ?(allow_duplicate = false) ~spec name ty default =
       name
   in
   match Spec.find_key spec name with
-  | Some _ when allow_duplicate = false ->
-      Fmt.invalid_arg "duplicate key: %s" name
+  | Some _ -> Fmt.invalid_arg "duplicate key: %s" name
   | _ ->
       let to_univ, of_univ = Univ.create () in
       let k = { name; ty; default; to_univ; of_univ; doc; docv; docs } in
@@ -166,9 +165,8 @@ let equal t1 t2 =
 
 (* ~root *)
 let root spec =
-  key ~allow_duplicate:true ~spec ~docv:"ROOT"
-    ~doc:"The location of the Irmin store on disk." ~docs:"COMMON OPTIONS"
-    "root"
+  key ~spec ~docv:"ROOT" ~doc:"The location of the Irmin store on disk."
+    ~docs:"COMMON OPTIONS" "root"
     Type.(string)
     "."
 
diff --git a/src/irmin/conf.mli b/src/irmin/conf.mli
index 6be4167c70..e850a49d2a 100644
--- a/src/irmin/conf.mli
+++ b/src/irmin/conf.mli
@@ -59,7 +59,6 @@ val key :
   ?docs:string ->
   ?docv:string ->
   ?doc:string ->
-  ?allow_duplicate:bool ->
   spec:Spec.t ->
   string ->
   'a Type.t ->
diff --git a/test/irmin/test_conf.ml b/test/irmin/test_conf.ml
index 140cc146d0..b05d6cfbcc 100644
--- a/test/irmin/test_conf.ml
+++ b/test/irmin/test_conf.ml
@@ -50,9 +50,33 @@ let test_duplicate_key_names () =
   Alcotest.check_raises "Duplicate key" (Invalid_argument "duplicate key: name")
     (fun () -> ignore (key ~spec name Irmin.Type.bool false))
 
+let test_subsequent_root_paths () =
+  let spec = Spec.v "roots1" in
+  let module K = struct
+    let root = root spec
+  end in
+  let r1 = "_build/test-roots-1" in
+  let r2 = "_build/test-roots-2" in
+  let c1 = add (empty spec) K.root r1 in
+  let c2 = add (empty spec) K.root r2 in
+  Alcotest.(check string) "same string" (find_root c1 |> Option.get) r1;
+  Alcotest.(check string) "same string" (find_root c2 |> Option.get) r2
+
+let test_subsequent_root_paths_duplicate () =
+  let spec = Spec.v "roots2" in
+  let r1 = "_build/test-roots-duplicate-1" in
+  let root_key = root spec in
+  let _ = add (empty spec) root_key r1 in
+  Alcotest.check_raises "Duplicate key" (Invalid_argument "duplicate key: root")
+    (fun () -> ignore (root spec))
+
 let suite =
   [
     Alcotest_lwt.test_case_sync "conf" `Quick test_conf;
     Alcotest_lwt.test_case_sync "duplicate key names" `Quick
       test_duplicate_key_names;
+    Alcotest_lwt.test_case_sync "subsequent root paths" `Quick
+      test_subsequent_root_paths;
+    Alcotest_lwt.test_case_sync "subsequent root paths duplicate" `Quick
+      test_subsequent_root_paths_duplicate;
   ]