diff --git a/CLAUDE.md b/CLAUDE.md
index aa0a0f6..a3d9836 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -52,7 +52,7 @@ and their args are documented in `local/track-source-annotate.md` and
 - `init` — creates session, returns session path on stdout. Accepts
   `--base-uri` and `--base-ref` for VCS anchoring.
 - `step` — records an edit. Accepts `--source` (JSON vcsSource). Async in
-  normal flow, sync during gap replay.
+  normal flow, sync during gap replay (on scratch buffer).
 - `visit` — caches content for undo/redo navigation. No `--source`.
 - `note` — sets intent on head step. Still works, not deprecated.
 - `annotate` — generalized note. Can target any step, set intent, source, refs.
@@ -72,10 +72,17 @@ and `--source` JSON. This keeps the CLI editor-agnostic and VCS-agnostic.
 `ShellCmdPost` trigger cache refresh. Never run git commands in the
 `on_text_changed` hot path.
 
+**Never modify buffer contents.** The plugin is a passive observer — it reads
+buffer text via `nvim_buf_get_lines` but must never use `vim.cmd("undo")`,
+`nvim_buf_set_lines`, or any other API that mutates a tracked buffer. Gap
+replay uses a hidden scratch buffer with `wundo`/`rundo` to clone the undo
+tree. This prevents interference with the user's editing, LSP, and other
+plugins.
+
 **Async for step/visit, sync for everything else.** The `on_text_changed`
 handler enqueues step and visit calls on a per-buffer serial queue using
 `vim.system()` callbacks. Gap replay (intermediate undo entries) is sync
-because it moves the buffer through undo states. `init`, `close`, `note`,
+because it replays on a scratch buffer. `init`, `close`, `note`,
 `annotate`, and `export` are sync.
 
 **Stop order matters.** `M.stop()` must: (1) delete the augroup first to
diff --git a/lua/toolpath/init.lua b/lua/toolpath/init.lua
index c835d63..461e83e 100644
--- a/lua/toolpath/init.lua
+++ b/lua/toolpath/init.lua
@@ -5,7 +5,7 @@
 
 local M = {}
 
-M.version = "0.2.0"
+M.version = "0.3.0"
 
 -- Per-buffer state: { session_path, last_seq, async_queue, step_count, ... }
 local buf_state = {}
@@ -272,7 +272,6 @@ end
 local function on_text_changed(bufnr)
   local state = buf_state[bufnr]
   if not state then return end
-  if state.replaying then return end
 
   local tree = vim.fn.undotree()
   local cur_seq = tree.seq_cur or 0
@@ -293,28 +292,46 @@ local function on_text_changed(bufnr)
     -- Check for intermediate undo entries (TextChanged batched > 1 entry)
     local gap = cur_seq - prev_seq
     if gap > 1 then
-      state.replaying = true
       local parent_map = build_parent_map(tree.entries)
-      for seq = prev_seq + 1, cur_seq - 1 do
-        vim.cmd("silent! undo " .. seq)
-        local content = get_buffer_text(bufnr)
-        local step_args = {
-          "step",
-          "--session", state.session_path,
-          "--seq", tostring(seq),
-          "--parent-seq", tostring(parent_map[seq] or prev_seq),
-        }
-        if source_json then
-          table.insert(step_args, "--source")
-          table.insert(step_args, source_json)
+      -- Clone undo tree to hidden scratch buffer to avoid modifying tracked buffer
+      local undo_tmp = vim.fn.tempname()
+      local ok_wundo = pcall(vim.cmd, "wundo! " .. vim.fn.fnameescape(undo_tmp))
+      if ok_wundo then
+        local orig_lines = vim.api.nvim_buf_get_lines(bufnr, 0, -1, false)
+        local scratch = vim.api.nvim_create_buf(false, true)
+        vim.api.nvim_buf_set_lines(scratch, 0, -1, false, orig_lines)
+        local ok_rundo = pcall(function()
+          vim.api.nvim_buf_call(scratch, function()
+            vim.cmd("silent rundo " .. vim.fn.fnameescape(undo_tmp))
+          end)
+        end)
+        if ok_rundo then
+          local saved_ei = vim.o.eventignore
+          vim.o.eventignore = "all"
+          for seq = prev_seq + 1, cur_seq - 1 do
+            vim.api.nvim_buf_call(scratch, function()
+              vim.cmd("silent! undo " .. seq)
+            end)
+            local content = get_buffer_text(scratch)
+            local step_args = {
+              "step",
+              "--session", state.session_path,
+              "--seq", tostring(seq),
+              "--parent-seq", tostring(parent_map[seq] or prev_seq),
+            }
+            if source_json then
+              table.insert(step_args, "--source")
+              table.insert(step_args, source_json)
+            end
+            run_cmd(step_args, content)
+            state.step_seqs[seq] = true
+            state.step_count = state.step_count + 1
+          end
+          vim.o.eventignore = saved_ei
         end
-        run_cmd(step_args, content)
-        state.step_seqs[seq] = true
-        state.step_count = state.step_count + 1
+        vim.api.nvim_buf_delete(scratch, { force = true })
       end
-      -- Restore to current seq
-      vim.cmd("silent! undo " .. cur_seq)
-      state.replaying = false
+      os.remove(undo_tmp)
     end
 
     -- Record the current edit (async)
@@ -415,13 +432,15 @@ function M.start(actor_override, quiet)
     repo_root = repo_root,    -- nil if file is not in a git repo
     last_seq = tree.seq_cur or 0,
     last_seq_last = tree.seq_last or 0,
-    step_seqs = {},     -- seqs that have recorded steps (for ancestor lookup)
+    step_seqs = {},     -- seqs with recorded steps; seq 0 pending CLI root-step support
     step_count = 0,     -- total steps recorded in this session
-    replaying = false,  -- guard against re-entrancy during gap replay
     async_queue = {},   -- serial queue for async CLI calls
     queue_running = false,
   }
 
+  -- TODO(cli): Once `init` creates a root step at seq 0, enable:
+  -- buf_state[bufnr].step_seqs[0] = true
+
   set_buf_vars(bufnr, buf_state[bufnr])
 
   -- Set up autocommands for this buffer
diff --git a/test/test_internals.lua b/test/test_internals.lua
index d314a4f..8610012 100644
--- a/test/test_internals.lua
+++ b/test/test_internals.lua
@@ -87,4 +87,23 @@ T.test("find_step_ancestor: target seq is 0 (initial state)", function()
   T.eq(I.find_step_ancestor(parent_map, 1, step_seqs), 0)
 end)
 
+T.test("find_step_ancestor: second branch from seq 0 returns 0 (orphan)", function()
+  -- Undo tree: 0 → 1 → 2, 0 → 3 (two branches from initial state)
+  local parent_map = { [1] = 0, [2] = 1, [3] = 0 }
+  local step_seqs = { [1] = true }  -- step at seq 1, none at seq 0
+  -- Seq 3 walks up: parent=0, step_seqs[0]=nil, parent==0 → returns 0
+  -- This creates an orphan in the Path document. Fixed when CLI creates
+  -- a root step at seq 0 on init (step_seqs[0] = true).
+  T.eq(I.find_step_ancestor(parent_map, 3, step_seqs), 0)
+end)
+
+T.test("find_step_ancestor: root step at seq 0 connects second branch", function()
+  -- Same undo tree, but with CLI root-step support (step_seqs[0] = true).
+  -- Return value is the same (0), but the CLI will map seq 0 to step-000
+  -- instead of "" — the step has a real parent and the graph is connected.
+  local parent_map = { [1] = 0, [2] = 1, [3] = 0 }
+  local step_seqs = { [0] = true, [1] = true }
+  T.eq(I.find_step_ancestor(parent_map, 3, step_seqs), 0)
+end)
+
 os.exit(T.run())