We changed how copy_to is implemented in elastic#79922, which moved
the handling of dots in field names into a specialised parser. Unfortunately,
while doing this we added a bug whereby every time a copy_to directive
is processed for a nested field, the nested field's include_in_parent logic
would be run, meaning that the parent would end up with multiple copies
of the nested child's fields.

This commit fixes this by only running include_in_parent when the parser
is not in a copy_to context. It also fixes another bug that meant the parent
document would contain multiple copies of the ID field.

Fixes elastic#87036