fix(highlight): prevent duplicate extmarks from two-pass rendering

Problem: the deferred pass (pass 2) cleared the hunk range and called
`highlight_hunk` with full opts, reapplying line backgrounds, intra-line
diffs, prefix DiffsClear, and per-char prefix highlights that pass 1
already set. This doubled extmark counts on affected lines.

Solution: add `syntax_only` flag to `diffs.HunkOpts`. When set,
`highlight_hunk` skips non-syntax extmarks (line backgrounds, intra-line,
prefix DiffsClear, per-char prefix fg, hide_prefix overlay, conflict
markers). The deferred pass uses `syntax_only = true` and no longer
clears the namespace range, so pass 1's extmarks persist while pass 2
layers treesitter and content DiffsClear on top.

lua/diffs/highlight.lua

@@ -65,6 +65,7 @@ end
 ---@field hide_prefix boolean
 ---@field highlights diffs.Highlights
 ---@field defer_vim_syntax? boolean
+---@field syntax_only? boolean
 
 ---@param bufnr integer
 ---@param ns integer
@@ -398,7 +399,13 @@ function M.highlight_hunk(bufnr, ns, hunk, opts)
   ---@type diffs.IntraChanges?
   local intra = nil
   local intra_cfg = opts.highlights.intra
-  if intra_cfg and intra_cfg.enabled and pw == 1 and #hunk.lines <= intra_cfg.max_lines then
+  if
+    not opts.syntax_only
+    and intra_cfg
+    and intra_cfg.enabled
+    and pw == 1
+    and #hunk.lines <= intra_cfg.max_lines
+  then
     dbg('computing intra for hunk %s:%d (%d lines)', hunk.filename, hunk.start_line, #hunk.lines)
     intra = diff.compute_intra_hunks(hunk.lines, intra_cfg.algorithm)
     if intra then
@@ -513,6 +520,7 @@ function M.highlight_hunk(bufnr, ns, hunk, opts)
         or content:match('^|||||||')
     end
 
+    if not opts.syntax_only then
       if opts.hide_prefix then
         local virt_hl = (opts.highlights.background and line_hl) or nil
         pcall(vim.api.nvim_buf_set_extmark, bufnr, ns, buf_line, 0, {
@@ -548,14 +556,6 @@ function M.highlight_hunk(bufnr, ns, hunk, opts)
         end
       end
 
-    if line_len > pw and covered_lines[buf_line] then
-      pcall(vim.api.nvim_buf_set_extmark, bufnr, ns, buf_line, pw + qw, {
-        end_col = line_len + qw,
-        hl_group = 'DiffsClear',
-        priority = p.clear,
-      })
-    end
-
       if opts.highlights.background and is_diff_line then
         pcall(vim.api.nvim_buf_set_extmark, bufnr, ns, buf_line, 0, {
           line_hl_group = line_hl,
@@ -598,6 +598,15 @@ function M.highlight_hunk(bufnr, ns, hunk, opts)
       end
     end
 
+    if line_len > pw and covered_lines[buf_line] then
+      pcall(vim.api.nvim_buf_set_extmark, bufnr, ns, buf_line, pw + qw, {
+        end_col = line_len + qw,
+        hl_group = 'DiffsClear',
+        priority = p.clear,
+      })
+    end
+  end
+
   dbg('hunk %s:%d applied %d extmarks', hunk.filename, hunk.start_line, extmark_count)
 end
 

lua/diffs/init.lua

@@ -797,18 +797,13 @@ local function init()
             return
           end
           local t1 = config.debug and vim.uv.hrtime() or nil
-          local full_opts = {
+          local syntax_opts = {
             hide_prefix = config.hide_prefix,
             highlights = config.highlights,
+            syntax_only = true,
           }
           for _, hunk in ipairs(deferred_syntax) do
-            local start_row = hunk.start_line - 1
+            highlight.highlight_hunk(bufnr, ns, hunk, syntax_opts)
-            local end_row = hunk.start_line + #hunk.lines
-            if hunk.header_start_line then
-              start_row = hunk.header_start_line - 1
-            end
-            vim.api.nvim_buf_clear_namespace(bufnr, ns, start_row, end_row)
-            highlight.highlight_hunk(bufnr, ns, hunk, full_opts)
           end
           if t1 then
             dbg('deferred pass: %d hunks in %.2fms', #deferred_syntax, (vim.uv.hrtime() - t1) / 1e6)

spec/highlight_spec.lua

@@ -1251,6 +1251,123 @@ describe('highlight', function()
       end
       delete_buffer(bufnr)
     end)
+
+    it('two-pass rendering produces no duplicate extmarks', function()
+      vim.api.nvim_set_hl(0, 'DiffsAddText', { bg = 0x00FF00 })
+      vim.api.nvim_set_hl(0, 'DiffsDeleteText', { bg = 0xFF0000 })
+      vim.api.nvim_set_hl(0, 'DiffsAddNr', { fg = 0x80c080, bg = 0x2e4a3a })
+      vim.api.nvim_set_hl(0, 'DiffsDeleteNr', { fg = 0xc08080, bg = 0x4a2e3a })
+
+      local bufnr = create_buffer({
+        '@@ -1,2 +1,2 @@',
+        '-local x = 1',
+        '+local x = 2',
+      })
+
+      local hunk = {
+        filename = 'test.lua',
+        lang = 'lua',
+        start_line = 1,
+        lines = { '-local x = 1', '+local x = 2' },
+      }
+
+      local fast = default_opts({
+        highlights = {
+          treesitter = { enabled = false },
+          background = true,
+          gutter = true,
+          intra = { enabled = true, algorithm = 'default', max_lines = 500 },
+        },
+      })
+
+      local syntax = default_opts({
+        highlights = {
+          treesitter = { enabled = true },
+          background = true,
+          gutter = true,
+          intra = { enabled = true, algorithm = 'default', max_lines = 500 },
+        },
+      })
+      syntax.syntax_only = true
+
+      highlight.highlight_hunk(bufnr, ns, hunk, fast)
+      highlight.highlight_hunk(bufnr, ns, hunk, syntax)
+
+      local extmarks = get_extmarks(bufnr)
+      for row = 1, 2 do
+        local line_hl_count = 0
+        local number_hl_count = 0
+        local intra_count = 0
+        for _, mark in ipairs(extmarks) do
+          if mark[2] == row then
+            local d = mark[4]
+            if d.line_hl_group then
+              line_hl_count = line_hl_count + 1
+            end
+            if d.number_hl_group then
+              number_hl_count = number_hl_count + 1
+            end
+            if d.hl_group == 'DiffsAddText' or d.hl_group == 'DiffsDeleteText' then
+              intra_count = intra_count + 1
+            end
+          end
+        end
+        assert.are.equal(1, line_hl_count, 'row ' .. row .. ' has duplicate line_hl_group')
+        assert.are.equal(1, number_hl_count, 'row ' .. row .. ' has duplicate number_hl_group')
+        assert.is_true(intra_count <= 1, 'row ' .. row .. ' has duplicate intra extmarks')
+      end
+      delete_buffer(bufnr)
+    end)
+
+    it('syntax_only pass adds treesitter without duplicating backgrounds', function()
+      local bufnr = create_buffer({
+        '@@ -1,2 +1,3 @@',
+        ' local x = 1',
+        '+local y = 2',
+        ' return x',
+      })
+
+      local hunk = {
+        filename = 'test.lua',
+        lang = 'lua',
+        start_line = 1,
+        lines = { ' local x = 1', '+local y = 2', ' return x' },
+      }
+
+      local fast = default_opts({
+        highlights = {
+          treesitter = { enabled = false },
+          background = true,
+        },
+      })
+
+      local syntax = default_opts({
+        highlights = {
+          treesitter = { enabled = true },
+          background = true,
+        },
+      })
+      syntax.syntax_only = true
+
+      highlight.highlight_hunk(bufnr, ns, hunk, fast)
+      highlight.highlight_hunk(bufnr, ns, hunk, syntax)
+
+      local extmarks = get_extmarks(bufnr)
+      local has_ts = false
+      local line_hl_count = 0
+      for _, mark in ipairs(extmarks) do
+        local d = mark[4]
+        if d and d.hl_group and d.hl_group:match('^@.*%.lua$') then
+          has_ts = true
+        end
+        if d and d.line_hl_group then
+          line_hl_count = line_hl_count + 1
+        end
+      end
+      assert.is_true(has_ts)
+      assert.are.equal(1, line_hl_count)
+      delete_buffer(bufnr)
+    end)
   end)
 
   describe('diff header highlighting', function()