diff --git a/Makefile b/Makefile
index cfbf4e79fd..6d9fb820ce 100644
--- a/Makefile
+++ b/Makefile
@@ -136,6 +136,8 @@ generated-sources benchmark $(FORMAT) $(LINT) $(TEST) doc: | build/.ran-cmake
 
 test: $(TEST)
 
+# The ignored header files should be synced with the `check_includes_ignore`
+# array in src/clint.py
 iwyu: build/.ran-cmake
 	cmake --preset iwyu
 	cmake --build build > build/iwyu.log
@@ -163,7 +165,6 @@ iwyu: build/.ran-cmake
 	|src/nvim/arglist_defs.h\
 	|src/nvim/ascii.h\
 	|src/nvim/assert.h\
-	|src/nvim/autocmd.c\
 	|src/nvim/autocmd.h\
 	|src/nvim/base64.h\
 	|src/nvim/buffer.h\
@@ -338,7 +339,8 @@ iwyu: build/.ran-cmake
 	|src/nvim/viml/parser/expressions.h\
 	|src/nvim/viml/parser/parser.h\
 	|src/nvim/window.h\
-	|src/nvim/winfloat.h)" --nosafe_headers < build/iwyu.log
+	|src/nvim/winfloat.h\
+	)" --nosafe_headers < build/iwyu.log
 	cmake -B build -U ENABLE_IWYU
 	cmake --build build
 
diff --git a/src/clint.py b/src/clint.py
index cda7c0e580..e302a10505 100755
--- a/src/clint.py
+++ b/src/clint.py
@@ -893,169 +893,207 @@ def CheckIncludes(filename, lines, error):
     }:
         return
 
+    # These should be synced with the ignored headers in the `iwyu` target in
+    # the Makefile.
     check_includes_ignore = [
-            "api/command.h",
-            "api/deprecated.h",
-            "api/extmark.h",
-            "api/keysets.h",
-            "api/options.h",
-            "api/private/converter.h",
-            "api/private/defs.h",
-            "api/private/dispatch.h",
-            "api/private/helpers.h",
-            "api/private/validate.h",
-            "api/tabpage.h",
-            "api/ui.h",
-            "api/vim.h",
-            "api/vimscript.h",
-            "api/win_config.h",
-            "arglist.h",
-            "arglist_defs.h",
-            "ascii.h",
-            "assert.h",
-            "autocmd.h",
-            "buffer.h",
-            "buffer_defs.h",
-            "buffer_updates.h",
-            "change.h",
-            "channel.h",
-            "charset.h",
-            "cmdexpand.h",
-            "cmdexpand_defs.h",
-            "cmdhist.h",
-            "context.h",
-            "cursor.h",
-            "cursor_shape.h",
-            "decoration.h",
-            "decoration_defs.h",
-            "decoration_provider.h",
-            "diff.h",
-            "digraph.h",
-            "drawline.h",
-            "drawscreen.h",
-            "edit.h",
-            "eval.h",
-            "eval/decode.h",
-            "eval/encode.h",
-            "eval/funcs.h",
-            "eval/typval.h",
-            "eval/typval_defs.h",
-            "eval/typval_encode.h",
-            "eval/userfunc.h",
-            "event/libuv_process.h",
-            "event/loop.h",
-            "event/multiqueue.h",
-            "event/process.h",
-            "event/rstream.h",
-            "event/signal.h",
-            "event/socket.h",
-            "event/stream.h",
-            "event/time.h",
-            "event/wstream.h",
-            "ex_cmds.h",
-            "ex_cmds_defs.h",
-            "ex_docmd.h",
-            "ex_eval_defs.h",
-            "ex_getln.h",
-            "extmark_defs.h",
-            "file_search.h",
-            "fileio.h",
-            "fold.h",
-            "fold_defs.h",
-            "garray.h",
-            "getchar.h",
-            "getchar_defs.h",
-            "globals.h",
-            "grid.h",
-            "grid_defs.h",
-            "hashtab.h",
-            "highlight.h",
-            "highlight_defs.h",
-            "highlight_group.h",
-            "iconv.h",
-            "indent.h",
-            "indent_c.h",
-            "input.h",
-            "insexpand.h",
-            "keycodes.h",
-            "linematch.h",
-            "log.h",
-            "lua/converter.h",
-            "lua/executor.h",
-            "lua/treesitter.h",
-            "macros.h",
-            "main.h",
-            "map.h",
-            "mapping.h",
-            "mapping_defs.h",
-            "mark.h",
-            "mark_defs.h",
-            "marktree.h",
-            "mbyte.h",
-            "mbyte_defs.h",
-            "memfile_defs.h",
-            "memline.h",
-            "memory.h",
-            "menu.h",
-            "message.h",
-            "mouse.h",
-            "move.h",
-            "msgpack_rpc/channel_defs.h",
-            "msgpack_rpc/helpers.h",
-            "msgpack_rpc/unpacker.h",
-            "normal.h",
-            "nvim/extmark.h",
-            "ops.h",
-            "option.h",
-            "option_defs.h",
-            "option_vars.h",
-            "os/fileio.h",
-            "os/fs.h",
-            "os/input.h",
-            "os/lang.h",
-            "os/os.h",
-            "os/process.h",
-            "os/pty_conpty_win.h",
-            "os/pty_process_unix.h",
-            "os/pty_process_win.h",
-            "os/shell.h",
-            "path.h",
-            "plines.h",
-            "popupmenu.h",
-            "profile.h",
-            "quickfix.h",
-            "regexp.h",
-            "regexp_defs.h",
-            "runtime.h",
-            "search.h",
-            "sha256.h",
-            "sign_defs.h",
-            "spell.h",
-            "spell_defs.h",
-            "spellfile.h",
-            "spellsuggest.h",
-            "statusline.h",
-            "statusline_defs.h",
-            "strings.h",
-            "syntax.h",
-            "tag.h",
-            "textformat.h",
-            "textobject.h",
-            "tui/input.h",
-            "tui/terminfo.h",
-            "tui/tui.h",
-            "ugrid.h",
-            "ui.h",
-            "ui_client.h",
-            "ui_compositor.h",
-            "undo_defs.h",
-            "usercmd.h",
-            "version.h",
-            "vim.h",
-            "viml/parser/expressions.h",
-            "viml/parser/parser.h",
-            "window.h",
-            "winfloat.h",
+            "src/nvim/api/autocmd.h",
+            "src/nvim/api/buffer.h",
+            "src/nvim/api/command.h",
+            "src/nvim/api/deprecated.h",
+            "src/nvim/api/extmark.h",
+            "src/nvim/api/keysets.h",
+            "src/nvim/api/options.h",
+            "src/nvim/api/private/converter.h",
+            "src/nvim/api/private/defs.h",
+            "src/nvim/api/private/dispatch.h",
+            "src/nvim/api/private/helpers.h",
+            "src/nvim/api/private/validate.h",
+            "src/nvim/api/tabpage.h",
+            "src/nvim/api/ui.h",
+            "src/nvim/api/vim.h",
+            "src/nvim/api/vimscript.h",
+            "src/nvim/api/win_config.h",
+            "src/nvim/api/window.h",
+            "src/nvim/arabic.h",
+            "src/nvim/arglist.h",
+            "src/nvim/arglist_defs.h",
+            "src/nvim/ascii.h",
+            "src/nvim/assert.h",
+            "src/nvim/autocmd.h",
+            "src/nvim/base64.h",
+            "src/nvim/buffer.h",
+            "src/nvim/buffer_defs.h",
+            "src/nvim/buffer_updates.h",
+            "src/nvim/bufwrite.h",
+            "src/nvim/change.h",
+            "src/nvim/channel.h",
+            "src/nvim/charset.h",
+            "src/nvim/cmdexpand.h",
+            "src/nvim/cmdexpand_defs.h",
+            "src/nvim/cmdhist.h",
+            "src/nvim/context.h",
+            "src/nvim/cursor.h",
+            "src/nvim/cursor_shape.h",
+            "src/nvim/debugger.h",
+            "src/nvim/decoration.h",
+            "src/nvim/decoration_defs.h",
+            "src/nvim/decoration_provider.h",
+            "src/nvim/diff.h",
+            "src/nvim/digraph.h",
+            "src/nvim/drawline.h",
+            "src/nvim/drawscreen.h",
+            "src/nvim/edit.h",
+            "src/nvim/eval.h",
+            "src/nvim/eval/buffer.h",
+            "src/nvim/eval/decode.h",
+            "src/nvim/eval/encode.h",
+            "src/nvim/eval/executor.h",
+            "src/nvim/eval/funcs.h",
+            "src/nvim/eval/gc.h",
+            "src/nvim/eval/typval.h",
+            "src/nvim/eval/typval_defs.h",
+            "src/nvim/eval/typval_encode.h",
+            "src/nvim/eval/userfunc.h",
+            "src/nvim/eval/vars.h",
+            "src/nvim/eval/window.h",
+            "src/nvim/event/libuv_process.h",
+            "src/nvim/event/loop.h",
+            "src/nvim/event/multiqueue.h",
+            "src/nvim/event/process.h",
+            "src/nvim/event/rstream.h",
+            "src/nvim/event/signal.h",
+            "src/nvim/event/socket.h",
+            "src/nvim/event/stream.h",
+            "src/nvim/event/time.h",
+            "src/nvim/event/wstream.h",
+            "src/nvim/ex_cmds.h",
+            "src/nvim/ex_cmds2.h",
+            "src/nvim/ex_cmds_defs.h",
+            "src/nvim/ex_docmd.h",
+            "src/nvim/ex_eval.h",
+            "src/nvim/ex_eval_defs.h",
+            "src/nvim/ex_getln.h",
+            "src/nvim/ex_session.h",
+            "src/nvim/extmark.h",
+            "src/nvim/extmark_defs.h",
+            "src/nvim/file_search.h",
+            "src/nvim/fileio.h",
+            "src/nvim/fold.h",
+            "src/nvim/fold_defs.h",
+            "src/nvim/garray.h",
+            "src/nvim/getchar.h",
+            "src/nvim/getchar_defs.h",
+            "src/nvim/globals.h",
+            "src/nvim/grid.h",
+            "src/nvim/grid_defs.h",
+            "src/nvim/hashtab.h",
+            "src/nvim/help.h",
+            "src/nvim/highlight.h",
+            "src/nvim/highlight_defs.h",
+            "src/nvim/highlight_group.h",
+            "src/nvim/iconv.h",
+            "src/nvim/indent.h",
+            "src/nvim/indent_c.h",
+            "src/nvim/input.h",
+            "src/nvim/insexpand.h",
+            "src/nvim/keycodes.h",
+            "src/nvim/linematch.h",
+            "src/nvim/log.h",
+            "src/nvim/lua/base64.h",
+            "src/nvim/lua/converter.h",
+            "src/nvim/lua/executor.h",
+            "src/nvim/lua/secure.h",
+            "src/nvim/lua/spell.h",
+            "src/nvim/lua/stdlib.h",
+            "src/nvim/lua/treesitter.h",
+            "src/nvim/lua/xdiff.h",
+            "src/nvim/macros.h",
+            "src/nvim/main.h",
+            "src/nvim/map.h",
+            "src/nvim/mapping.h",
+            "src/nvim/mapping_defs.h",
+            "src/nvim/mark.h",
+            "src/nvim/mark_defs.h",
+            "src/nvim/marktree.h",
+            "src/nvim/match.h",
+            "src/nvim/mbyte.h",
+            "src/nvim/mbyte_defs.h",
+            "src/nvim/memfile.h",
+            "src/nvim/memfile_defs.h",
+            "src/nvim/memline.h",
+            "src/nvim/memory.h",
+            "src/nvim/menu.h",
+            "src/nvim/message.h",
+            "src/nvim/mouse.h",
+            "src/nvim/move.h",
+            "src/nvim/msgpack_rpc/channel.h",
+            "src/nvim/msgpack_rpc/channel_defs.h",
+            "src/nvim/msgpack_rpc/helpers.h",
+            "src/nvim/msgpack_rpc/server.h",
+            "src/nvim/msgpack_rpc/unpacker.h",
+            "src/nvim/normal.h",
+            "src/nvim/nvim/extmark.h",
+            "src/nvim/ops.h",
+            "src/nvim/option.h",
+            "src/nvim/option_defs.h",
+            "src/nvim/option_vars.h",
+            "src/nvim/optionstr.h",
+            "src/nvim/os/dl.h",
+            "src/nvim/os/fileio.h",
+            "src/nvim/os/fs.h",
+            "src/nvim/os/input.h",
+            "src/nvim/os/lang.h",
+            "src/nvim/os/os.h",
+            "src/nvim/os/process.h",
+            "src/nvim/os/pty_conpty_win.h",
+            "src/nvim/os/pty_process_unix.h",
+            "src/nvim/os/pty_process_win.h",
+            "src/nvim/os/shell.h",
+            "src/nvim/os/time.h",
+            "src/nvim/os/tty.h",
+            "src/nvim/path.h",
+            "src/nvim/plines.h",
+            "src/nvim/popupmenu.h",
+            "src/nvim/profile.h",
+            "src/nvim/quickfix.h",
+            "src/nvim/regexp.h",
+            "src/nvim/regexp_defs.h",
+            "src/nvim/runtime.h",
+            "src/nvim/search.h",
+            "src/nvim/sha256.h",
+            "src/nvim/shada.h",
+            "src/nvim/sign.h",
+            "src/nvim/sign_defs.h",
+            "src/nvim/spell.h",
+            "src/nvim/spell_defs.h",
+            "src/nvim/spellfile.h",
+            "src/nvim/spellsuggest.h",
+            "src/nvim/state.h",
+            "src/nvim/statusline.h",
+            "src/nvim/statusline_defs.h",
+            "src/nvim/strings.h",
+            "src/nvim/syntax.h",
+            "src/nvim/tag.h",
+            "src/nvim/terminal.h",
+            "src/nvim/testing.h",
+            "src/nvim/textformat.h",
+            "src/nvim/textobject.h",
+            "src/nvim/tui/input.h",
+            "src/nvim/tui/terminfo.h",
+            "src/nvim/tui/tui.h",
+            "src/nvim/ugrid.h",
+            "src/nvim/ui.h",
+            "src/nvim/ui_client.h",
+            "src/nvim/ui_compositor.h",
+            "src/nvim/undo.h",
+            "src/nvim/undo_defs.h",
+            "src/nvim/usercmd.h",
+            "src/nvim/version.h",
+            "src/nvim/vim.h",
+            "src/nvim/viml/parser/expressions.h",
+            "src/nvim/viml/parser/parser.h",
+            "src/nvim/window.h",
+            "src/nvim/winfloat.h",
                              ]
 
     for i in check_includes_ignore:
diff --git a/src/nvim/autocmd.c b/src/nvim/autocmd.c
index 65e902ed4b..80c9ad9465 100644
--- a/src/nvim/autocmd.c
+++ b/src/nvim/autocmd.c
@@ -4,34 +4,36 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <time.h>
 
 #include "nvim/api/private/helpers.h"
 #include "nvim/ascii.h"
 #include "nvim/autocmd.h"
 #include "nvim/buffer.h"
 #include "nvim/charset.h"
+#include "nvim/cmdexpand_defs.h"
 #include "nvim/cursor.h"
 #include "nvim/eval.h"
 #include "nvim/eval/typval.h"
 #include "nvim/eval/userfunc.h"
 #include "nvim/eval/vars.h"
+#include "nvim/event/multiqueue.h"
 #include "nvim/ex_docmd.h"
 #include "nvim/ex_eval.h"
 #include "nvim/fileio.h"
-#include "nvim/garray.h"
 #include "nvim/getchar.h"
 #include "nvim/gettext.h"
+#include "nvim/globals.h"
 #include "nvim/grid.h"
 #include "nvim/hashtab.h"
 #include "nvim/highlight_defs.h"
 #include "nvim/insexpand.h"
 #include "nvim/lua/executor.h"
+#include "nvim/main.h"
 #include "nvim/map.h"
-#include "nvim/memline_defs.h"
 #include "nvim/memory.h"
 #include "nvim/message.h"
 #include "nvim/option.h"
+#include "nvim/option_vars.h"
 #include "nvim/optionstr.h"
 #include "nvim/os/input.h"
 #include "nvim/os/os.h"