The default misskey docker install guide will place misskey code and your instance data in the same directory. Is something goes wrong on a later time, you may accidentally trash your datas (docker volumes mounted for the postgres database, redis cache...).
Separate the misskey code (git clone...) from you container's volumes, something like this should do:
```
/usr/local/misskey/code
/usr/local/misskey/data
```
You will need a custom yaml file for docker-compose, but it's worth it (see sample yaml file).
Manage your misskey instance containers with docker-compose and the right path for code and datas: