I am documenting the steps to migrate from v3 to v7, so it will help others:

First I have copied the data from v3 server to new server in /var/lib/sqlpad, here's the details:

root@sqlpad:/var/lib/sqlpad# ls
cache  cache.db  connections.db  queries.db  sessions  users.db
root@sqlpad:/var/lib/sqlpad#

After that remove these files/directories from that data:

root@sqlpad:/var/lib/sqlpad#rm -rf cache* connection*

Then spinup the sqlpad verion 4 using docker:

docker run --name sqlpad -p 8080:3000 --volume /var/lib/sqlpad:/var/lib/sqlpad --detach sqlpad/sqlpad:4.0.0

It will run all the necessary migrations.

NOTE: I have been facing the connections migration issue during this migration, that's why I have deleted the connections.db from the above data. But you can first try to keep it, as it might work for you.

After that, you just need to stop your previous container(v4) and run the v5:

docker stop sqlpad && docker rm sqlpad
docker run --name sqlpad -p 8080:3000 --volume /var/lib/sqlpad:/var/lib/sqlpad --detach sqlpad/sqlpad:5.0

If everything went well, you can stop it and then run the v6:

docker stop sqlpad && docker rm sqlpad
docker run --name sqlpad -p 8080:3000 --volume /var/lib/sqlpad:/var/lib/sqlpad --detach sqlpad/sqlpad:6.0

Again, if it works for you, then upgrade to latest(v7 at the writing of this comment):

docker stop sqlpad && docker rm sqlpad
docker run --name sqlpad -p 8080:3000 --volume /var/lib/sqlpad:/var/lib/sqlpad --detach sqlpad/sqlpad:latest