readme: command reference, npm -- separator, instance ids

[mnkprs]

Why

Readers saw commands like npm run screen -- --swebench django__django-11099 with no explanation of the double --, of what django__django-11099 is (a dataset instance id, not something to download), or of which flags each script accepts.

What changed

• Quick start: comments explain that the screen command fetches the task and clones the repository itself, that -- is npm's argument separator, and that the id is <owner>__<repo>-<PR number>.
• New §2c "Command reference": every npm script grouped by purpose (screening, evaluation, running the pipeline, data, checks) with what it does and every flag it accepts; the list of committed run ids and variants.
• "Where to go" table links to it.