Found no fewer than three separate places that cause a pop-up prompt

for saving on a cell which is completely unmodified.  One of these
was due to the BPlane implementation, which forces an instance to be
deleted and re-placed on a bounding box recomputation, which should
not, in that case, be considered a modification.  Another always runs
DRC on a subcell upon reading rather than relying on any checkplane
entries in the file itself;  and the last one marking the timestamp
as modified stemming from an attempt to correct an O(N^2) check to
O(N).  All three cases have now been corrected.

database/DBcell.c

@@ -118,6 +118,7 @@ DBCellFindDup(use, parent)
  * ----------------------------------------------------------------------------
  *
  * DBPlaceCell --
+ * DBPlaceCellNoModify --
  *
  * Add a CellUse to the subcell tile plane of a CellDef.
  * Assumes prior check that the new CellUse is not an exact duplicate
@@ -162,11 +163,47 @@ DBPlaceCell (use, def)
     SigEnableInterrupts();
 }
 
+/* Like DBPlaceCell(), but don't change the flags of the parent cell.	*/
+/* This is needed by the bounding box recalculation routine, which may	*/
+/* cause the cell to be deleted and replaced for the purpose of		*/
+/* capturing the bounding box information in the BPlane structure, but	*/
+/* this does not mean that anything in the parent cell has changed.	*/
+
+void
+DBPlaceCellNoModify (use, def)
+    CellUse   * use;	/* new celluse to add to subcell tile plane */
+    CellDef   * def;    /* parent cell's definition */
+{
+    Rect             rect;    /* argument to DBSrCellPlaneArea(), placeCellFunc() */
+    BPlane          *bplane;  /* argument to DBSrCellPlaneArea(), placeCellFunc() */
+    struct searchArg arg;     /* argument to placeCellFunc() */
+
+    ASSERT(use != (CellUse *) NULL, "DBPlaceCell");
+    ASSERT(def, "DBPlaceCell");
+
+    /* To do:  Check non-duplicate placement, check non-duplicate ID */
+
+    use->cu_parent = def;
+
+    /* Be careful not to permit interrupts during this, or the
+     * database could be left in a trashed state.
+     */
+
+    SigDisableInterrupts();
+    BPAdd(def->cd_cellPlane, use);
+    if (UndoIsEnabled())
+	DBUndoCellUse(use, UNDO_CELL_PLACE);
+    SigEnableInterrupts();
+}
+
 /*
  * ----------------------------------------------------------------------------
  * DBDeleteCell --
  *
  * Remove a CellUse from the subcell tile plane of a CellDef.
+ * If "nomodify" is TRUE, then don't set the parent cell's CDMODIFIED flag.
+ * This is needed when recomputing the bounding box, which should not by
+ * itself change the modified state.
  *
  * Results:
  *	None.
@@ -197,3 +234,39 @@ DBDeleteCell (use)
     SigEnableInterrupts();
 }
 
+/*
+ * ----------------------------------------------------------------------------
+ * DBDeleteCellNoModify --
+ *
+ * Remove a CellUse from the subcell tile plane of a CellDef, as above,
+ * but don't set the parent cell's CDMODIFIED flag.  This is needed when
+ * recomputing the bounding box, which should not by itself change the
+ * modified state.
+ *
+ * Results:
+ *	None.
+ *
+ * Side effects:
+ *	Modifies the subcell tile plane of the CellDef, sets the
+ * 	parent pointer of the deleted CellUse to NULL.
+ * ----------------------------------------------------------------------------
+ */
+
+void
+DBDeleteCellNoModify (use)
+    CellUse * use;
+{
+    ASSERT(use != (CellUse *) NULL, "DBDeleteCell");
+
+    /* It's important that this code run with interrupts disabled,
+     * or else we could leave the subcell tile plane in a weird
+     * state.
+     */
+
+    SigDisableInterrupts();
+    dbInstanceUnplace(use);
+    if (UndoIsEnabled())
+	DBUndoCellUse(use, UNDO_CELL_DELETE);
+    use->cu_parent = (CellDef *) NULL;
+    SigEnableInterrupts();
+}

database/DBcellbox.c

@@ -723,7 +723,7 @@ dbReComputeBboxFunc(cellDef, boundProc, recurseProc)
 	     */
 
 	    parent = use->cu_parent;
-	    DBDeleteCell(use);
+	    DBDeleteCellNoModify(use);
 	    use->cu_parent = parent;
 	}
 
@@ -751,7 +751,7 @@ dbReComputeBboxFunc(cellDef, boundProc, recurseProc)
 	if ((parent = use->cu_parent) != (CellDef *) NULL)
 	{
 	    parent->cd_flags |= CDBOXESCHANGED;
-	    DBPlaceCell(use, parent);
+	    DBPlaceCellNoModify(use, parent);
 	    if (last != parent)
 	    {
 		if (last != NULL) (*recurseProc)(last);

database/DBio.c

@@ -411,7 +411,7 @@ dbCellReadDef(f, cellDef, name, ignoreTech, dereference)
     int cellStamp = 0, rectCount = 0, rectReport = 10000;
     char line[2048], tech[50], layername[50];
     PaintResultType *ptable;
-    bool result = TRUE, scaleLimit = FALSE;
+    bool result = TRUE, scaleLimit = FALSE, has_mismatch;
     Rect *rp;
     int c;
     TileType type, rtype, loctype;
@@ -844,6 +844,7 @@ done:
      * timestamp, then force the cell to be written out with a
      * correct timestamp.
      */
+    has_mismatch = FALSE;
     if ((cellDef->cd_timestamp != cellStamp) || (cellStamp == 0))
     {
 	CellUse *cu;
@@ -852,12 +853,13 @@ done:
 	    if (cu->cu_parent != NULL)
 	    {
 		DBStampMismatch(cellDef, &cellDef->cd_bbox);
+		has_mismatch = TRUE;
 		break;
 	    }
 	}
     }
     /* Update timestamp flags */
-    DBFlagMismatches(cellDef);
+    if (has_mismatch) DBFlagMismatches(cellDef);
 
     cellDef->cd_timestamp = cellStamp;
     if (cellStamp == 0)
@@ -869,7 +871,8 @@ done:
     }
 
     UndoEnable();
-    DRCCheckThis(cellDef, TT_CHECKPAINT, (Rect *) NULL);
+    /* Disabled 3/16/2021.  Let <<checkpaint>> in file force a DRC check */
+    /* DRCCheckThis(cellDef, TT_CHECKPAINT, (Rect *) NULL); */
     SigEnableInterrupts();
     return (result);
 

database/database.h.in

@@ -790,7 +790,9 @@ extern CellUse *DBFindUse();
 
     /* Insertion/deletion of cell uses into the cell tile plane of a parent */
 extern void DBPlaceCell();
+extern void DBPlaceCellNoModify();
 extern void DBDeleteCell();
+extern void DBDeleteCellNoModify();
 extern void DBClearCellPlane();
 
     /* Insertion/deletion of cell uses into the name space of a parent */