Validate and document .env loading for Docker/CLI start

[RonaldRonnie]

Description:

Backend containers may not have access to .env (e.g. when started via CLI or from a different working directory). All I see is that "Environment variables will be loaded from .env only" but the container can still start without those vars, leading to failed analyses and unclear errors.

Tasks:

• Document in README/SETUP_GUIDE: where to place .env and how Docker Compose and the CLI pass it into the backend container (e.g. env_file: .env in compose, and that compose is run from project root).
• Optionally: add a startup check in the container that logs clearly if required vars are missing (and, if combined with issue Fail application startup when required env vars are missing in production #85 , exit in production).

Acceptance criteria:

• Docs state explicitly that .env must be in the project root and that docker compose / BioAnalyzer start are run from that root so the backend receives the file.
• One sentence or bullet on "if analyses fail with auth errors, check that the container has API keys" with a link to env/docs.