Fix errors when running the project the first time

[Janpot]

• Avoid crashing on first start because of missing queries file
• Initialize project only once when the dev command runs
• More fine grained initialization where we decide when and how to generate initial project files. Also run it in the application process for now colocated with the other project code. We'll see for the future how we can share this functionality between cli process and next.js process

Closes #1763