Update README.md for improved installation instructions and clarity

[NaDa0Amr]

Update README.md for improved installation instructions and clarity for linux

[adamjohnwright]

Thank you — you were right that these instructions were wrong, and three separate people filing PRs against the same section is the clearest possible signal.

Fixed on main in #176, going further than the docs alone. The Quick Start had three defects, each verified:

• ./bin/embeddings_manager failed outright with /usr/bin/env: ‘python’: No such file or directory on any system providing only python3. Both bin/ scripts now use python3, and the documented commands use poetry run.
• PYTHONPATH was to be "verified" rather than set. Nothing sets it, so verifying only tells a new contributor that it is wrong.
• OPENAI_API_KEY was never mentioned, so the final step could not work even if everything before it did.

The underlying cause is the layout: src/ on PYTHONPATH instead of an installed package. Moving to a standard src-layout will make poetry install sufficient and delete this whole class of problem — but that should not have blocked fixing the instructions, and it did for too long.

Closing as resolved rather than stale.