diff --git a/mercurial/cext/parsers.c b/mercurial/cext/parsers.c
--- a/mercurial/cext/parsers.c
+++ b/mercurial/cext/parsers.c
@@ -492,6 +492,21 @@
 	}
 }
 
+/* See docstring of the python implementation for details */
+static PyObject *dirstate_item_set_clean(dirstateItemObject *self,
+                                         PyObject *args)
+{
+	int size, mode, mtime;
+	if (!PyArg_ParseTuple(args, "iii", &mode, &size, &mtime)) {
+		return NULL;
+	}
+	self->flags = dirstate_flag_wc_tracked | dirstate_flag_p1_tracked;
+	self->mode = mode;
+	self->size = size;
+	self->mtime = mtime;
+	Py_RETURN_NONE;
+}
+
 static PyObject *dirstate_item_set_untracked(dirstateItemObject *self)
 {
 	self->flags &= ~dirstate_flag_wc_tracked;
@@ -531,6 +546,8 @@
      "constructor to help legacy API to build a new \"normal\" item"},
     {"set_possibly_dirty", (PyCFunction)dirstate_item_set_possibly_dirty,
      METH_NOARGS, "mark a file as \"possibly dirty\""},
+    {"set_clean", (PyCFunction)dirstate_item_set_clean, METH_VARARGS,
+     "mark a file as \"clean\""},
     {"set_untracked", (PyCFunction)dirstate_item_set_untracked, METH_NOARGS,
      "mark a file as \"untracked\""},
     {NULL} /* Sentinel */
diff --git a/mercurial/dirstate.py b/mercurial/dirstate.py
--- a/mercurial/dirstate.py
+++ b/mercurial/dirstate.py
@@ -508,10 +508,9 @@
             (mode, size, mtime) = parentfiledata
         else:
             (mode, size, mtime) = self._get_filedata(filename)
-        self._addpath(filename, mode=mode, size=size, mtime=mtime)
-        self._map.copymap.pop(filename, None)
-        if filename in self._map.nonnormalset:
-            self._map.nonnormalset.remove(filename)
+        if not self._map[filename].tracked:
+            self._check_new_tracked_filename(filename)
+        self._map.set_clean(filename, mode, size, mtime)
         if mtime > self._lastnormaltime:
             # Remember the most recent modification timeslot for status(),
             # to make sure we won't miss future size-preserving file content
diff --git a/mercurial/dirstatemap.py b/mercurial/dirstatemap.py
--- a/mercurial/dirstatemap.py
+++ b/mercurial/dirstatemap.py
@@ -162,6 +162,15 @@
         """record that the current state of the file on disk is unknown"""
         self[filename].set_possibly_dirty()
 
+    def set_clean(self, filename, mode, size, mtime):
+        """mark a file as back to a clean state"""
+        entry = self[filename]
+        mtime = mtime & rangemask
+        size = size & rangemask
+        entry.set_clean(mode, size, mtime)
+        self.copymap.pop(filename, None)
+        self.nonnormalset.discard(filename)
+
     def addfile(
         self,
         f,
@@ -924,6 +933,15 @@
             entry.set_possibly_dirty()
             self._rustmap.set_v1(filename, entry)
 
+        def set_clean(self, filename, mode, size, mtime):
+            """mark a file as back to a clean state"""
+            entry = self[filename]
+            mtime = mtime & rangemask
+            size = size & rangemask
+            entry.set_clean(mode, size, mtime)
+            self._rustmap.set_v1(filename, entry)
+            self._rustmap.copymap().pop(filename, None)
+
         def __setitem__(self, key, value):
             assert isinstance(value, DirstateItem)
             self._rustmap.set_v1(key, value)
diff --git a/mercurial/pure/parsers.py b/mercurial/pure/parsers.py
--- a/mercurial/pure/parsers.py
+++ b/mercurial/pure/parsers.py
@@ -222,6 +222,24 @@
         """
         self._possibly_dirty = True
 
+    def set_clean(self, mode, size, mtime):
+        """mark a file as "clean" cancelling potential "possibly dirty call"
+
+        Note: this function is a descendant of `dirstate.normal` and is
+        currently expected to be call on "normal" entry only. There are not
+        reason for this to not change in the future as long as the ccode is
+        updated to preserve the proper state of the non-normal files.
+        """
+        self._wc_tracked = True
+        self._p1_tracked = True
+        self._p2_tracked = False  # this might be wrong
+        self._merged = False
+        self._clean_p2 = False
+        self._possibly_dirty = False
+        self._mode = mode
+        self._size = size
+        self._mtime = mtime
+
     def set_untracked(self):
         """mark a file as untracked in the working copy
 
diff --git a/rust/Cargo.lock b/rust/Cargo.lock
--- a/rust/Cargo.lock
+++ b/rust/Cargo.lock
@@ -1,7 +1,5 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
-
 [[package]]
 name = "adler"
 version = "0.2.3"