[tooling] Small fixes for fresh installs

[the-glu]

Fix a small hicuups I ran into with a fresh project:

• Add reminder about submodules
• Don't install useless packages in dockerfile
• Add an empty .cache and output folder. If not present, docker will create with root owner, but we use -u to run the tool with current user privilege. With the fix, git is going to create then, probably with current user rights.
• Exclude schema from ruff