Stop cyclic dependency between `SDK code that uses user code` and `user code that uses SDK code`.

[FranjoMindek]

Part of #2247
This issue addresses point 3. from the following comment: #2247 (comment)
Blocked by: #3517

We should:

1. Research the best way to stop the cyclic dependency between:

   • SDK code that uses user code
   • user code that uses SDK code

   Filip already proposed a solution on the original issue: Always use the user's tsconfig.json when processing their code #2247 (comment)

2. Refine the issue with information above.

3. Stop the cyclic dependency.

4. Make the user code (src dir) be a separate tsconfig project rather than part of SDK code that depends on user code project.
   (this will maybe be a separate PR)

Estimate: todo