Git init не в том каталоге? Как восстановить? (теоретическая ситуация)

Вы не можете и не должны. Kali — это специфический дистрибутив, предназначенный для пентестинга, и настраивать его как медиацентр не имеет смысла.

Из официальной документации Kali:

Kali Linux is specifically geared to meet the requirements of professional penetration testing and security auditing. To achieve this, several core changes have been implemented in Kali Linux which reflect these needs:

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A minimal and trusted set of repositories: given the aims and goals of Kali Linux, maintaining the integrity of the system as a whole is absolutely key. With that goal in mind, the set of upstream software sources which Kali uses is kept to an absolute minimum. Many new Kali users are tempted to add additional repositories to their sources.list, but doing so runs a very serious risk of breaking your Kali Linux installation.