Rewrite the CLI env var guide #1578

docs/vars.md describes environmentVariables, @secret references, and push overriding Console values.

Scope

• Rewrite docs/vars.md around .env, the apify env commands, and the deprecations. Include a pre-commit hook example for apify env diff.
• Update the env var mentions in README.md.
• Update skills/apify/SKILL.md, so agents use apify env and .env.

Depends on

• apify push stops uploading env vars (Stop uploading environmentVariables in apify push #1575)
• The CLI deprecation (Deprecate environmentVariables, @secret references, and apify secrets #1577)
• apify env diff (Add apify env diff to check that .env and the platform are in sync #1574)