Deprecate environmentVariables, @secret references, and apify secrets #1577

With .env and apify env in place, the old local mechanisms are deprecated. Nothing stops working in this issue.

Scope

• Print a deprecation warning in apify run when actor.json has environmentVariables. Point to .env and apify env migrate.
• Print a deprecation warning in apify secrets add, ls, and rm, and mark the commands as deprecated in help and in the generated reference.
• Record in telemetry that a warning was shown, so the removal can be timed on real usage.
• Keep reading the values as before.

Done when

• A warning appears once per command run and goes to stderr, so --json output stays clean.

Depends on

• .env loading in apify run (Load .env in apify run #1569)
• apify env migrate (Add apify env migrate #1576)