fix(stock): cost a BOM-less secondary item out of the finished good

The legacy scrap checkbox deducted the scrap row's value from the
finished good, so a Manufacture entry balanced. Its replacement, the
Secondary Item Type dropdown, only balances when the row carries a BOM
Secondary Item link, because the cost allocation percentage lives there.
A row typed as Scrap in the UI has no such link, so its value was added
on top of a finished good that already absorbed the whole raw material
cost, and the entry closed with a non-zero difference.

Treat a secondary row with no BOM link the way the legacy scrap item was
treated: deduct its value from the finished good.

The finished good's rate is derived from the other incoming rows, so
those rows must be rated first. Previously the finished good was rated
in row order, ahead of the secondary rows, and picked up their amounts
only on a later validate pass. Rate the finished goods last so a single
pass is correct.

erpnext/stock/doctype/stock_entry/stock_entry.py

@@ -70,6 +70,15 @@ from erpnext.controllers.subcontracting_inward_controller import SubcontractingI
 form_grid_templates = {"items": "templates/form_grid/stock_entry_grid.html"}
 
 
+def is_costed_out_of_finished_item(row) -> bool:
+	"""Whether the row takes its value out of the finished good instead of adding to it.
+
+	A secondary item that is not linked to a BOM has no cost allocation of its own, so it is
+	valued the way the legacy scrap item was: its cost is deducted from the finished good.
+	"""
+	return bool(row.is_legacy_scrap_item or (row.secondary_item_type and not row.bom_secondary_item))
+
+
 class StockEntry(StockController, SubcontractingInwardController):
 	# begin: auto-generated types
 	# This code is auto-generated. Do not modify anything in this block.
@@ -564,7 +573,8 @@ class StockEntry(StockController, SubcontractingInwardController):
 		)
 
 		zero_valuation_items = []
-		for d in self.get("items"):
+		finished_items_last = sorted(self.get("items"), key=lambda row: cint(row.is_finished_item))
+		for d in finished_items_last:
 			if d.s_warehouse or d.set_basic_rate_manually:
 				continue
 
@@ -736,7 +746,9 @@ class StockEntry(StockController, SubcontractingInwardController):
 		self, finished_item_qty, outgoing_items_cost=0, has_consumption_basis=False
 	) -> float:
 		settings = frappe.get_single("Manufacturing Settings")
-		scrap_items_cost = sum([flt(d.basic_amount) for d in self.get("items") if d.is_legacy_scrap_item])
+		scrap_items_cost = sum(
+			[flt(d.basic_amount) for d in self.get("items") if is_costed_out_of_finished_item(d)]
+		)
 
 		if settings.material_consumption:
 			outgoing_items_cost = self._get_rm_cost_for_manufacture(