diff --git a/lib/compiler/Driver.ml b/lib/compiler/Driver.ml
index 1e1121d..17d41d5 100644
--- a/lib/compiler/Driver.ml
+++ b/lib/compiler/Driver.ml
@@ -45,8 +45,9 @@ let update ?(bail = true) ?(progress = Phases.no_progress) (action : Action.t)
     | Some code ->
       let result, errors = Phases.expand forest code in
       forest.={uri} <- Tree result;
+      Diagnostics_store.replace forest.diagnostics uri Expand errors;
       (report ~errors ~and_then:(Eval uri), forest)
-  end
+    end
   | Render uri ->
     let errors = Phases.render uri in
     (report ~errors ~and_then:Done, forest)
diff --git a/lib/compiler/Phases.ml b/lib/compiler/Phases.ml
index 35d7e41..258d988 100644
--- a/lib/compiler/Phases.ml
+++ b/lib/compiler/Phases.ml
@@ -90,7 +90,7 @@ let parse (forest : State.t) uri =
          match Parse.parse_document tree with
          | Ok code ->
            forest.={uri} <- Tree code;
-           Diagnostics_store.set forest.diagnostics uri [];
+           Diagnostics_store.clear_phase forest.diagnostics uri Parse;
            Expand uri
          | Error parse_error ->
            let errors = [Error.parse_error parse_error] in
@@ -98,11 +98,15 @@ let parse (forest : State.t) uri =
            report ~errors ~and_then:Done
        end
        ~none:begin match State.get_document ~forest uri with
-       | Some doc -> begin
-         match Parse.parse_document doc with
-         | Error e -> report ~errors:[Error.parse_error e] ~and_then:Done
+       | Some doc ->
+         begin match Parse.parse_document doc with
+         | Error e ->
+           let errors = [Error.parse_error e] in
+           Diagnostics_store.set forest.diagnostics uri errors;
+           report ~errors ~and_then:Done
          | Ok code ->
            forest.={uri} <- Tree code;
+           Diagnostics_store.clear_phase forest.diagnostics uri Parse;
            Expand uri
        end
        | None -> assert false
@@ -119,7 +123,7 @@ let parse_all (forest : State.t) ~progress =
     match Parse.parse_document document with
     | Ok tree -> begin
       forest.={uri} <- Tree tree;
-      Diagnostics_store.clear forest.diagnostics uri;
+      Diagnostics_store.clear_phase forest.diagnostics uri Parse;
       None
     end
     | Error error ->
@@ -135,8 +139,11 @@ let reparse (doc : Lsp.Text_document.t) (forest : State.t) =
     URI.of_lsp_uri ~base:forest.config.url @@ Lsp.Text_document.documentUri doc
   in
   begin match Parse.parse_document doc with
-  | Ok code -> forest.={uri} <- Tree code
-  | Error d -> Diagnostics_store.set forest.diagnostics uri [Error.parse_error d]
+  | Ok code ->
+    forest.={uri} <- Tree code;
+    Diagnostics_store.clear_phase forest.diagnostics uri Parse
+  | Error d ->
+    Diagnostics_store.set forest.diagnostics uri [Error.parse_error d]
   end
 
 let build_import_graph ~(forest : State.t) : Error.t list * Forest_graph.t =
@@ -161,7 +168,7 @@ let expand_all (forest : State.t) ~progress =
           let expanded, errors = Expand.expand_tree ~forest tree in
           diagnostics := errors @ !diagnostics;
           forest.={uri} <- Tree expanded;
-          Diagnostics_store.set forest.diagnostics uri errors
+          Diagnostics_store.replace forest.diagnostics uri Expand errors
         | None ->
           forest.log.err ~src:Log.Src.compiler (fun m ->
               m "expanding: no source code for %a" URI.pp uri);
@@ -194,20 +201,46 @@ let run_jobs (forest : State.t) jobs ~progress =
     result
   in
   begin
-    (* It is probably not save to plant the articles in parallel, so this is
+    (* It is probably not safe to plant the articles in parallel, so this is
        done sequentially! *)
     let@ result = List.iter @~ resources_to_plant in
     match result with
     | Ok resource -> State.plant_resource ~forest resource
-    | Error tex_error -> begin
-      match guess_uri (Error.tex_range tex_error) with
+    | Error tex_error ->
+      begin match guess_uri (Error.tex_range tex_error) with
       | None -> assert false
       | Some uri ->
         let uri = URI.of_lsp_uri ~base:forest.config.url uri in
-        Diagnostics_store.set forest.diagnostics uri [Error.of_tex_error tex_error]
-    end
+        Diagnostics_store.set forest.diagnostics uri
+          [Error.of_tex_error tex_error]
+      end
   end
 
+let subtree_uris (articles : T.content T.article list) =
+  let@ article = List.filter_map @~ articles in
+  Option.bind article.frontmatter.designated_parent
+    (Fun.const article.frontmatter.uri)
+
+let flag_duplicate_subtrees ~(forest : State.t) ?owner
+    (articles : T.content T.article list) =
+  let subtrees = subtree_uris articles in
+  let counts = URI.Tbl.create 8 in
+  let count_uri uri =
+    let n = 1 + Option.value ~default:0 (URI.Tbl.find_opt counts uri) in
+    URI.Tbl.replace counts uri n
+  in
+  List.iter count_uri subtrees;
+  begin
+    let@ owner = Option.iter @~ owner in
+    State.set_owned_subtrees ~forest ~owner subtrees
+  end;
+  URI.Tbl.iter
+    (fun uri n ->
+      if n > 1 then
+        Diagnostics_store.set forest.diagnostics uri [Error.duplicate_tree ~uri]
+      else Diagnostics_store.clear_phase forest.diagnostics uri Duplicate)
+    counts
+
 let organize results =
   let open List in
   Pair.map_fst (split >>> Pair.map concat concat)
@@ -227,14 +260,20 @@ let eval (forest : State.t) ~progress =
     organize
     @@
     let@ uri, tree = List.map @~ expanded in
-    let result = Eval.(eval_tree ~config ~uri tree) in
+    let value, errors = Eval.(eval_tree ~config ~uri tree) in
+    begin
+      let@ {articles; _} = Option.iter @~ value in
+      State.set_owned_subtrees ~forest ~owner:uri (subtree_uris articles)
+    end;
     tick ();
-    result
+    (value, errors)
   in
+  flag_duplicate_subtrees ~forest articles;
   let () =
     let@ article = List.iter @~ articles in
     State.plant_resource ~forest T.(Article article)
   in
+  State.set_duplicate_diagnostics forest;
   (jobs, errors)
 
 let eval_only (uri : URI.t) (forest : State.t) =
@@ -246,14 +285,19 @@ let eval_only (uri : URI.t) (forest : State.t) =
     | Loaded | Parsed | Evaluated -> assert false
     | Expanded -> begin
       let result, errors = Eval.eval_tree ~config ~uri t in
-      Diagnostics_store.set forest.diagnostics uri errors;
+      Diagnostics_store.replace forest.diagnostics uri Eval errors;
       match result with
-      | None -> (errors, [])
+      | None ->
+        State.set_owned_subtrees ~forest ~owner:uri [];
+        State.set_duplicate_diagnostics forest;
+        (errors, [])
       | Some {articles; jobs} ->
+        flag_duplicate_subtrees ~forest ~owner:uri articles;
         let () =
           let@ article = List.iter @~ articles in
           State.plant_resource ~forest (Article article)
         in
+        State.set_duplicate_diagnostics forest;
         (errors, jobs)
     end
   end
diff --git a/lib/compiler/State.ml b/lib/compiler/State.ml
index 74ba039..f899c41 100644
--- a/lib/compiler/State.ml
+++ b/lib/compiler/State.ml
@@ -19,6 +19,9 @@ type t = {
   dev: bool;
   config: Config.t;
   index: Tree.t URI.Tbl.t;
+  paths: string URI.Tbl.t;
+  mutable duplicate_uris: URI.Set.t;
+  subtree_owners: URI.t list URI.Tbl.t;
   last_good_articles: T.content T.article URI.Tbl.t;
   diagnostics: Diagnostics_store.t;
   mutable broken_links: URI.Set.t;
@@ -43,6 +46,42 @@ let config forest = forest.config
 let env forest = forest.env
 let base forest = forest.config.url
 let iter_diagnostics f forest = Diagnostics_store.iter forest.diagnostics f
+
+let set_duplicate_diagnostics forest =
+  let origin_exists uri =
+    match URI.Tbl.find_opt forest.paths uri with
+    | Some path -> Result.is_ok (Eio_util.path_of_file ~env:forest.env path)
+    | None -> false
+  in
+  let live, gone = URI.Set.partition origin_exists forest.duplicate_uris in
+  forest.duplicate_uris <- live;
+  begin
+    let@ uri = URI.Set.iter @~ gone in
+    URI.Tbl.remove forest.paths uri;
+    Diagnostics_store.clear_phase forest.diagnostics uri Duplicate
+  end;
+  let@ uri = URI.Set.iter @~ live in
+  Diagnostics_store.set forest.diagnostics uri [Error.duplicate_tree ~uri]
+
+let set_owned_subtrees ~forest ~owner uris =
+  URI.Tbl.replace forest.subtree_owners owner (List.sort_uniq URI.compare uris)
+
+let owned_subtrees forest owner =
+  Option.value (URI.Tbl.find_opt forest.subtree_owners owner) ~default:[]
+
+let check_and_register_origin state uri origin =
+  match URI.Tbl.find_opt state.paths uri with
+  | Some existing when existing <> origin ->
+    state.duplicate_uris <- URI.Set.add uri state.duplicate_uris
+  | _ -> URI.Tbl.replace state.paths uri origin
+
+let register_path state uri tree =
+  match tree with
+  | Tree {phase = Loaded; document = Some doc; _} ->
+    check_and_register_origin state uri
+      (Lsp.Uri.to_path (Lsp.Text_document.documentUri doc))
+  | _ -> ()
+
 let imports forest = forest.import_graph
 
 let make ~(env : Eio_unix.Stdenv.base) ~(config : Config.t) ~(dev : bool)
@@ -59,6 +98,9 @@ let make ~(env : Eio_unix.Stdenv.base) ~(config : Config.t) ~(dev : bool)
     dev;
     config;
     index;
+    paths = URI.Tbl.create 1000;
+    duplicate_uris = URI.Set.empty;
+    subtree_owners = URI.Tbl.create 1000;
     last_good_articles = URI.Tbl.create 1000;
     diagnostics;
     import_graph;
@@ -82,20 +124,12 @@ module Syntax = struct
   let ( .={} ) state uri = URI.Tbl.find_opt state.index uri
 
   let ( .={}<- ) state uri tree =
+    register_path state uri tree;
     let wrote =
       match state.={uri} with
-      | None ->
-        URI.Tbl.replace state.index uri tree;
-        true
       | Some existing when Tree.is_asset tree && Tree.is_asset existing -> false
-      | Some existing ->
-        if Tree.same_revision tree existing && Tree.equal_phases tree existing
-        then begin
-          Diagnostics_store.set state.diagnostics uri
-            [Error.duplicate_tree ~uri];
-          URI.Tbl.replace state.index uri tree
-        end
-        else URI.Tbl.replace state.index uri tree;
+      | _ ->
+        URI.Tbl.replace state.index uri tree;
         true
     in
     if wrote then begin
@@ -337,6 +371,14 @@ let plant_resource :
   let uri = URI.canonicalise uri in
   (* Seems dodgy if this isn't already canonical! *)
   Graphs.register_uri uri;
+  begin match resource with
+  | T.Article {frontmatter = {designated_parent = Some parent_uri; _}; _} ->
+    let root_uri = parent_file_uri ~forest parent_uri in
+    Option.iter
+      (check_and_register_origin forest uri)
+      (URI.Tbl.find_opt forest.paths root_uri)
+  | _ -> ()
+  end;
   begin
     let@ host = Option.iter @~ URI.host uri in
     let base = URI.make ?scheme:(URI.scheme uri) ~host () in
diff --git a/lib/core/Tree.ml b/lib/core/Tree.ml
index a858de6..0034e20 100644
--- a/lib/core/Tree.ml
+++ b/lib/core/Tree.ml
@@ -138,16 +138,7 @@ let phase : type a. a tree -> phase = function
     | Parsed -> Phase Parsed
     | Expanded -> Phase Expanded
     | Evaluated -> Phase Evaluated
-  end
-
-let equal_phases =
- fun (Tree {phase = phase1; _}) (Tree {phase = phase2; _}) ->
-  match (phase1, phase2) with
-  | Loaded, Loaded -> true
-  | Parsed, Parsed -> true
-  | Expanded, Expanded -> true
-  | Evaluated, Evaluated -> true
-  | _ -> false
+    end
 
 let document : t -> document option = function
   | Tree {document; _} as t -> document
@@ -157,15 +148,6 @@ let of_doc : Lsp.Text_document.t -> t =
   let uri = Lsp.Text_document.documentUri document in
   Tree {phase = Loaded; tree = (); document = Some document}
 
-let same_revision (t1 : t) (t2 : t) : bool =
-  match (document t1, document t2) with
-  | Some d1, Some d2 ->
-    Lsp.Uri.equal
-      (Lsp.Text_document.documentUri d1)
-      (Lsp.Text_document.documentUri d2)
-    && Lsp.Text_document.version d1 = Lsp.Text_document.version d2
-  | _ -> compare (source t1) (source t2) = 0
-
 let syn = function {tree; _} -> tree.nodes
 
 let get_syn = function
diff --git a/lib/language_server/Diagnostics.ml b/lib/language_server/Diagnostics.ml
index 06d87b6..3b2be78 100644
--- a/lib/language_server/Diagnostics.ml
+++ b/lib/language_server/Diagnostics.ml
@@ -38,7 +38,6 @@ let render_diagnostics (forest : State.t) (uri : URI.t) :
   match State.get_article ~forest uri with
   | None -> []
   | Some article ->
-    let pipeline_errors = Diagnostics_store.get forest.diagnostics uri in
     let errors = Link_checker.verify_links ~forest article in
     let own = ref [] in
     let foreign : (Lsp.Uri.t option * Error.t list ref) URI.Tbl.t =
@@ -54,11 +53,12 @@ let render_diagnostics (forest : State.t) (uri : URI.t) :
         | None -> URI.Tbl.add foreign owner (lsp_uri_of_error error, ref [error])
         end
     end;
-    Diagnostics_store.set forest.diagnostics uri
-      (pipeline_errors @ List.rev !own);
+    Diagnostics_store.replace forest.diagnostics uri Link_check
+      (List.rev !own);
     URI.Tbl.fold
       (fun owner (lsp_uri, errs) acc ->
-        Diagnostics_store.set forest.diagnostics owner (List.rev !errs);
+        Diagnostics_store.replace forest.diagnostics owner Link_check
+          (List.rev !errs);
         match lsp_uri with
         | Some lsp_uri -> (owner, lsp_uri) :: acc
         | None -> acc)
@@ -98,13 +98,10 @@ let store_errors_by_owner (store : Diagnostics_store.t) ~default errors =
       | Some errs -> errs := error :: !errs
       | None -> URI.Tbl.add subtrees owner (ref [error])
   end;
-  Diagnostics_store.set store default
-    (Diagnostics_store.get store default @ List.rev !own);
+  Diagnostics_store.replace store default Link_check (List.rev !own);
   URI.Tbl.fold
     (fun owner errs acc ->
-      (* A subtree won't produce compilation errors of its own, so we 
-         overwrite the diagnostics.*)
-      Diagnostics_store.set store owner (List.rev !errs);
+      Diagnostics_store.replace store owner Link_check (List.rev !errs);
       owner :: acc)
     subtrees []
 
@@ -115,8 +112,13 @@ let compute (document : Lsp.Text_document.t) =
   let uri = URI.of_lsp_uri ~base:forest.config.url lsp_uri in
   let foreign_targets = render_diagnostics forest uri in
   let by_lsp_uri : (Lsp.Uri.t, Error.t list) Hashtbl.t = Hashtbl.create 4 in
+  let owned_diagnostics =
+    List.concat_map
+      (Diagnostics_store.get forest.diagnostics)
+      (State.owned_subtrees forest uri)
+  in
   Hashtbl.replace by_lsp_uri lsp_uri
-    (Diagnostics_store.get forest.diagnostics uri);
+    (Diagnostics_store.get forest.diagnostics uri @ owned_diagnostics);
   begin
     let@ owner, owner_lsp_uri = List.iter @~ foreign_targets in
     let existing =
diff --git a/test/duplicate-tree-dispersed.t b/test/duplicate-tree-dispersed.t
new file mode 100644
index 0000000..89cbd6a
--- /dev/null
+++ b/test/duplicate-tree-dispersed.t
@@ -0,0 +1,12 @@
+  $ forester init > /dev/null
+
+  $ cat > trees/one.tree << EOF
+  > \subtree[dupaddr]{}
+  > EOF
+
+  $ cat > trees/two.tree << EOF
+  > \subtree[parent]{\subtree[dupaddr]{}}
+  > EOF
+
+  $ forester build 2>&1 | grep duplicate_tree
+  error[duplicate_tree]: duplicate tree https://www.my-great-forest.net/dupaddr/
diff --git a/test/duplicate-tree-distinct-paths.t b/test/duplicate-tree-distinct-paths.t
new file mode 100644
index 0000000..2043dc2
--- /dev/null
+++ b/test/duplicate-tree-distinct-paths.t
@@ -0,0 +1,19 @@
+  $ mkdir a b
+  $ cat > forest.toml << EOF
+  > [forest]
+  > trees = ["a", "b"]
+  > assets = []
+  > home = "dup"
+  > url = "https://www.my-great-forest.net/"
+  > EOF
+
+  $ cat > a/dup.tree << EOF
+  > \title{From a}
+  > EOF
+
+  $ cat > b/dup.tree << EOF
+  > \title{From b}
+  > EOF
+
+  $ forester build 2>&1 | grep duplicate_tree
+  error[duplicate_tree]: duplicate tree https://www.my-great-forest.net/dup/
diff --git a/test/duplicate-tree-same-file.t b/test/duplicate-tree-same-file.t
new file mode 100644
index 0000000..7928379
--- /dev/null
+++ b/test/duplicate-tree-same-file.t
@@ -0,0 +1,9 @@
+  $ forester init > /dev/null
+
+  $ cat > trees/index.tree << EOF
+  > \subtree[dupaddr]{\title{First}}
+  > \subtree[dupaddr]{\title{Second}}
+  > EOF
+
+  $ forester build 2>&1 | grep duplicate_tree
+  error[duplicate_tree]: duplicate tree https://www.my-great-forest.net/dupaddr/