tomlkit dumps duplicate table

```python
#!/usr/bin/env python3

import tomlkit

doc = tomlkit.loads("[x.y]\n[x]\n")
doc["x"]["k"] = -7

output = tomlkit.dumps(doc)

print(output)
```
result
```
[x]
k = -7

[x.y]
[x]
```
which has too many `[x]`