diff --git a/hosts/ocaml/bin/mcp_tree.ml b/hosts/ocaml/bin/mcp_tree.ml
index 2ec947b6..663ad2ba 100644
--- a/hosts/ocaml/bin/mcp_tree.ml
+++ b/hosts/ocaml/bin/mcp_tree.ml
@@ -322,6 +322,18 @@ type comment_map = {
   trailing : value list;                  (* comments after last expression *)
 }
 
+(* Recursively strip Comment nodes from inside lists — tree-tools
+   must not see them or index-based paths break. *)
+let rec strip_interior_comments v =
+  match v with
+  | List items ->
+    let clean = List.filter (function Comment _ -> false | _ -> true) items in
+    List (List.map strip_interior_comments clean)
+  | ListRef { contents = items } ->
+    let clean = List.filter (function Comment _ -> false | _ -> true) items in
+    List (List.map strip_interior_comments clean)
+  | _ -> v
+
 let separate_comments items =
   let before = Hashtbl.create 16 in
   let exprs = ref [] in
@@ -334,7 +346,8 @@ let separate_comments items =
       if !pending <> [] then
         Hashtbl.replace before !idx (List.rev !pending);
       pending := [];
-      exprs := item :: !exprs;
+      (* Strip interior comments from the expression before passing to tree-tools *)
+      exprs := strip_interior_comments item :: !exprs;
       incr idx
   ) items;
   let trailing = List.rev !pending in
@@ -351,6 +364,29 @@ let reinterleave exprs cmap =
   List.iter (fun c -> result := c :: !result) cmap.trailing;
   List.rev !result
 
+(* Extract leading comments from fragment source and attach to a position
+   in the comment map.  Returns the clean source (comments stripped). *)
+let extract_fragment_comments src cmap target_idx =
+  let items = Sx_parser.parse_all ~comments:true src in
+  let cmt_nodes = ref [] in
+  let expr_nodes = ref [] in
+  List.iter (fun item ->
+    match item with
+    | Comment _ -> cmt_nodes := item :: !cmt_nodes
+    | _ -> expr_nodes := item :: !expr_nodes
+  ) items;
+  let cmts = List.rev !cmt_nodes in
+  if cmts <> [] then begin
+    let existing = match Hashtbl.find_opt cmap.before target_idx with
+      | Some cs -> cs | None -> [] in
+    Hashtbl.replace cmap.before target_idx (existing @ cmts)
+  end;
+  (* Reconstruct source without comments *)
+  if cmts = [] then src
+  else
+    let clean = List.rev !expr_nodes in
+    String.concat " " (List.map inspect clean)
+
 let parse_path_str s =
   (* Parse SX path string: "(0 3 2)" or "(0,3,2)" or "0 3 2" → SX list of numbers.
      Commas are unquote in SX, so strip them before parsing. *)
@@ -434,13 +470,24 @@ let rec est_width = function
     2 + List.fold_left (fun acc x -> acc + est_width x + 1) 0 items
   | _ -> 10
 
+let rec has_interior_comments = function
+  | List items | ListRef { contents = items } ->
+    List.exists (fun item -> match item with
+      | Comment _ -> true
+      | List _ | ListRef _ -> has_interior_comments item
+      | _ -> false
+    ) items
+  | _ -> false
+
 let pretty_print_value ?(max_width=80) v =
   let buf = Buffer.create 4096 in
   let rec pp indent v =
     match v with
+    | Comment text ->
+      Buffer.add_string buf text
     | List items | ListRef { contents = items } when items <> [] ->
-      if est_width v <= max_width - indent then
-        (* Fits on one line *)
+      if est_width v <= max_width - indent && not (has_interior_comments v) then
+        (* Fits on one line and has no comments *)
         Buffer.add_string buf (pp_atom v)
       else begin
         (* Multi-line *)
@@ -449,9 +496,14 @@ let pretty_print_value ?(max_width=80) v =
         Buffer.add_string buf (pp_atom head);
         let child_indent = indent + 2 in
         let rest = List.tl items in
-        (* Special case: keyword args stay on same line as their value *)
         let rec emit = function
           | [] -> ()
+          | Comment text :: rest ->
+            (* Interior comment: indented, on its own line *)
+            Buffer.add_char buf '\n';
+            Buffer.add_string buf (String.make child_indent ' ');
+            Buffer.add_string buf text;
+            emit rest
           | Keyword k :: v :: rest ->
             Buffer.add_char buf '\n';
             Buffer.add_string buf (String.make child_indent ' ');
@@ -626,9 +678,15 @@ let handle_tool name args =
     text_result (String.concat "\n" lines)
 
   | "sx_get_siblings" ->
-    let tree = parse_file (args |> member "file" |> to_string) in
+    let file = args |> member "file" |> to_string in
+    let tree, cmap = parse_file_with_comments file in
     let path = resolve_path tree (args |> member "path" |> to_string) in
-    text_result (value_to_string (call_sx "get-siblings" [tree; path]))
+    let output = value_to_string (call_sx "get-siblings" [tree; path]) in
+    (* Inject comments for top-level siblings *)
+    let is_top_level = match path with
+      | List [Number _] | List [Number _; Number _] -> true
+      | _ -> false in
+    text_result (if is_top_level then inject_comments output cmap else output)
 
   | "sx_validate" ->
     let tree = parse_file (args |> member "file" |> to_string) in
@@ -638,7 +696,12 @@ let handle_tool name args =
     let file = args |> member "file" |> to_string in
     let tree, cmap = parse_file_with_comments file in
     let path = resolve_path tree (args |> member "path" |> to_string) in
-    let src = args |> member "new_source" |> to_string in
+    let raw_src = args |> member "new_source" |> to_string in
+    (* Extract leading comments from fragment, attach to target position *)
+    let top_idx = match path with List (Number n :: _) -> Some (int_of_float n) | _ -> None in
+    let src = match top_idx with
+      | Some idx -> extract_fragment_comments raw_src cmap idx
+      | None -> raw_src in
     write_edit_with_comments file cmap (call_sx "replace-node" [tree; path; String src])
 
   | "sx_insert_child" ->
@@ -960,16 +1023,36 @@ let handle_tool name args =
   | "sx_doc_gen" ->
     let dir = args |> member "dir" |> to_string in
     let files = glob_sx_files dir in
+    let strip_comment_prefix text =
+      let lines = String.split_on_char '\n' text in
+      let cleaned = List.map (fun line ->
+        let s = String.trim line in
+        if String.length s >= 3 && s.[0] = ';' && s.[1] = ';' && s.[2] = ' ' then
+          String.sub s 3 (String.length s - 3)
+        else if String.length s >= 2 && s.[0] = ';' && s.[1] = ';' then
+          String.sub s 2 (String.length s - 2)
+        else s
+      ) lines in
+      (* Filter out section divider lines (═══, ---) *)
+      let non_dividers = List.filter (fun s ->
+        not (String.length s > 3 && (s.[0] = '=' || s.[0] = '-' || s.[0] = '#'))
+      ) cleaned in
+      let trimmed = List.filter (fun s -> String.trim s <> "") non_dividers in
+      String.concat "\n" trimmed
+    in
     let all_docs = List.concat_map (fun path ->
       let rel = relative_path ~base:dir path in
       try
-        let exprs = Sx_parser.parse_all (In_channel.with_open_text path In_channel.input_all) in
-        List.filter_map (fun expr ->
-          match expr with
-          | List (Symbol head :: Symbol name :: rest) | ListRef { contents = Symbol head :: Symbol name :: rest } ->
-            (match head with
+        let exprs = Sx_parser.parse_all ~comments:true (In_channel.with_open_text path In_channel.input_all) in
+        (* Walk list tracking preceding comment *)
+        let rec collect prev_comment = function
+          | [] -> []
+          | Comment text :: rest -> collect (Some text) rest
+          | (List (Symbol head :: Symbol name :: params_rest) as _expr) :: rest
+          | (ListRef { contents = Symbol head :: Symbol name :: params_rest } as _expr) :: rest ->
+            let doc = match head with
              | "defcomp" | "defisland" ->
-               let params_str = match rest with
+               let params_str = match params_rest with
                  | List ps :: _ | ListRef { contents = ps } :: _ ->
                    let keys = List.filter_map (fun p -> match p with
                      | Symbol s when s <> "&key" && s <> "&rest" && not (String.length s > 0 && s.[0] = '&') -> Some s
@@ -982,12 +1065,27 @@ let handle_tool name args =
                    key_str ^ rest_str
                  | _ -> ""
                in
-               Some (Printf.sprintf "## %s `%s`\nDefined in: %s\nType: %s\n%s" head name rel head params_str)
+               let comment_str = match prev_comment with
+                 | Some text ->
+                   let cleaned = strip_comment_prefix text in
+                   if cleaned = "" then "" else "  " ^ cleaned ^ "\n"
+                 | None -> ""
+               in
+               Some (Printf.sprintf "## %s `%s`\nDefined in: %s\nType: %s\n%s%s" head name rel head comment_str params_str)
              | "defmacro" ->
-               Some (Printf.sprintf "## %s `%s`\nDefined in: %s\nType: macro\n" head name rel)
-             | _ -> None)
-          | _ -> None
-        ) exprs
+               let comment_str = match prev_comment with
+                 | Some text ->
+                   let cleaned = strip_comment_prefix text in
+                   if cleaned = "" then "" else "  " ^ cleaned ^ "\n"
+                 | None -> ""
+               in
+               Some (Printf.sprintf "## %s `%s`\nDefined in: %s\nType: macro\n%s" head name rel comment_str)
+             | _ -> None
+            in
+            (match doc with Some d -> d :: collect None rest | None -> collect None rest)
+          | _ :: rest -> collect None rest
+        in
+        collect None exprs
       with _ -> []
     ) files in
     if all_docs = [] then text_result "(no components found)"
@@ -1523,7 +1621,19 @@ let handle_tool name args =
     let tree, cmap = parse_file_with_comments file in
     let pattern = args |> member "pattern" |> to_string in
     let position = args |> member "position" |> to_string_option |> Option.value ~default:"after" in
-    let src = args |> member "new_source" |> to_string in
+    let raw_src = args |> member "new_source" |> to_string in
+    (* Find the match index so we can attach fragment comments *)
+    let match_result = call_sx "find-all" [tree; String pattern] in
+    let target_idx = match match_result with
+      | List (List (List (Number n :: _) :: _) :: _) -> Some (int_of_float n)
+      | List (List (Number n :: _) :: _) -> Some (int_of_float n)
+      | _ -> None in
+    let insert_idx = match target_idx with
+      | Some n -> Some (if position = "before" then n else n + 1)
+      | None -> None in
+    let src = match insert_idx with
+      | Some idx -> extract_fragment_comments raw_src cmap idx
+      | None -> raw_src in
     write_edit_with_comments file cmap (call_sx "insert-near-pattern" [tree; String pattern; String position; String src])
 
   | "sx_rename_across" ->
diff --git a/hosts/ocaml/lib/sx_parser.ml b/hosts/ocaml/lib/sx_parser.ml
index f71d1364..9be3f71d 100644
--- a/hosts/ocaml/lib/sx_parser.ml
+++ b/hosts/ocaml/lib/sx_parser.ml
@@ -110,7 +110,35 @@ let try_number str =
   | Some n -> Some (Number n)
   | None -> None
 
+(* Module-level flag — when true, comments are captured as Comment nodes.
+   Set by parse_all ~comments:true, reset after. *)
+let _preserve_comments = ref false
+
+(* Collect consecutive comment lines into a Comment node *)
+let collect_comment_node s =
+  let lines = ref [] in
+  let rec go () =
+    skip_whitespace s;
+    if not (at_end s) && s.src.[s.pos] = ';' then begin
+      lines := read_comment s :: !lines;
+      go ()
+    end
+  in
+  go ();
+  Comment (String.concat "\n" (List.rev !lines))
+
 let rec read_value s : value =
+  (* In comment-preserving mode, check for comments first *)
+  if !_preserve_comments then begin
+    skip_whitespace s;
+    if not (at_end s) && s.src.[s.pos] = ';' then
+      collect_comment_node s
+    else
+      read_value_core s
+  end else
+    read_value_core s
+
+and read_value_core s : value =
   skip_whitespace_and_comments s;
   if at_end s then begin
     let line = ref 1 in
@@ -184,14 +212,29 @@ and read_list s close_char =
   advance s; (* skip opening paren/bracket *)
   let items = ref [] in
   let rec go () =
-    skip_whitespace_and_comments s;
-    if at_end s then raise (Parse_error "Unterminated list");
-    if s.src.[s.pos] = close_char then begin
-      advance s;
-      List (List.rev !items)
+    if !_preserve_comments then begin
+      skip_whitespace s;
+      if at_end s then raise (Parse_error "Unterminated list");
+      if s.src.[s.pos] = close_char then begin
+        advance s;
+        List (List.rev !items)
+      end else if s.src.[s.pos] = ';' then begin
+        items := collect_comment_node s :: !items;
+        go ()
+      end else begin
+        items := read_value_core s :: !items;
+        go ()
+      end
     end else begin
-      items := read_value s :: !items;
-      go ()
+      skip_whitespace_and_comments s;
+      if at_end s then raise (Parse_error "Unterminated list");
+      if s.src.[s.pos] = close_char then begin
+        advance s;
+        List (List.rev !items)
+      end else begin
+        items := read_value s :: !items;
+        go ()
+      end
     end
   in go ()
 
@@ -220,42 +263,25 @@ and read_dict s =
 
 
 (** Parse a string into a list of SX values.
-    When [~comments:true], top-level ;; comments are preserved as [Comment]
-    nodes in the result list.  Default is [false] (strip comments). *)
+    When [~comments:true], comments are preserved as [Comment] nodes —
+    both at top level and inside lists.  Default is [false] (strip). *)
 let parse_all ?(comments=false) src =
+  _preserve_comments := comments;
   let s = make_state src in
   let results = ref [] in
   let rec go () =
-    if comments then begin
-      skip_whitespace s;
-      if at_end s then List.rev !results
-      else if s.src.[s.pos] = ';' then begin
-        (* Collect consecutive comment lines into one Comment node *)
-        let lines = ref [] in
-        let rec collect () =
-          skip_whitespace s;
-          if not (at_end s) && s.src.[s.pos] = ';' then begin
-            lines := read_comment s :: !lines;
-            collect ()
-          end
-        in
-        collect ();
-        let text = String.concat "\n" (List.rev !lines) in
-        results := Comment text :: !results;
-        go ()
-      end else begin
-        results := read_value s :: !results;
-        go ()
-      end
-    end else begin
-      skip_whitespace_and_comments s;
-      if at_end s then List.rev !results
-      else begin
-        results := read_value s :: !results;
-        go ()
-      end
+    if !_preserve_comments then skip_whitespace s
+    else skip_whitespace_and_comments s;
+    if at_end s then (
+      _preserve_comments := false;
+      List.rev !results
+    ) else begin
+      results := read_value s :: !results;
+      go ()
     end
-  in go ()
+  in
+  try go ()
+  with e -> _preserve_comments := false; raise e
 
 (** Parse a file into a list of SX values. *)
 let parse_file ?(comments=false) path =