Fix bugs of upstream tomlkit

[frostming]

• Comment not parsed when value is boolean python-poetry/tomlkit#119
• Critical data loss python-poetry/tomlkit#113
• Empty table name after a non-empty one results in: UnboundLocalError: local variable 'table_name' referenced before assignment python-poetry/tomlkit#117
• Dotted keys values go missing python-poetry/tomlkit#105
• Not having an empty newline at the end makes the file corrupt itself after dumping python-poetry/tomlkit#97
• Comment before table causes next entry to be in table python-poetry/tomlkit#98
• Indenting error in updating variables python-poetry/tomlkit#106
• document.pop(key) doesn't actually remove the item from the document python-poetry/tomlkit#66