fix: avoid duplicate table header when adding a key to an out-of-order table

Adding a plain key to an out-of-order table whose concrete `[x]` part is
declared after its sub-tables (the "defining a super-table afterward is ok"
spec form) wrote the value into the header-less super part, forcing it to
render a second `[x]` header next to the existing concrete one. The dumped
output then had a duplicate header and no longer parsed.

Route the value into the existing concrete (non-super) part instead, so the
header that already exists gains the key and no second header is emitted.

Author: sarathfrancis90

tests/test_toml_document.py

@@ -643,6 +643,20 @@ def test_valid_out_of_order_independent_tables() -> None:
     assert doc.as_string() == "[a]\nx=1\n[zz]\n[a.b]\nc=1\n"
 
 
+def test_set_value_on_out_of_order_table_with_empty_concrete_part() -> None:
+    # A super table defined after its sub-table (the "defining a super-table
+    # afterward is ok" spec example) leaves an empty concrete `[x]` part.
+    # Adding a plain value must land in that concrete part, not turn the
+    # header-less super part into a second `[x]` header -- which produced
+    # output with a duplicate header that no longer parsed.
+    doc = parse("[x.y.z.w]\n\n[x]\n")
+    doc["x"]["c"] = 3
+
+    assert doc["x"]["c"] == 3
+    assert doc.as_string() == "[x.y.z.w]\n\n[x]\nc = 3\n"
+    assert parse(doc.as_string()).unwrap() == {"x": {"y": {"z": {"w": {}}}, "c": 3}}
+
+
 def test_out_of_order_table_merges_aot_fragments() -> None:
     # https://github.com/python-poetry/tomlkit/issues/505
     content = """\

tomlkit/container.py

@@ -1168,7 +1168,18 @@ def _is_table_or_aot(it: Any) -> bool:
                         table[key] = value
                         break
                 else:
-                    self._tables[0][key] = value
+                    # No part holds a plain value yet, so the chosen part must
+                    # start rendering its own ``[key]`` header. Prefer a part
+                    # that is not a super table (it already renders that header):
+                    # turning a header-less super part concrete here would emit a
+                    # second, duplicate header next to an existing concrete part
+                    # and produce TOML that no longer parses.
+                    for table in self._tables:
+                        if not table.is_super_table():
+                            table[key] = value
+                            break
+                    else:
+                        self._tables[0][key] = value
             else:
                 self._tables[0][key] = value
         else: