Dogfood Program Intake end to end

[yvette-carlisle]

Summary

• Promote decodex intake issues ... --apply as the issue-batch persistence mode while keeping --persist as a legacy alias.
• Treat mapped terminal issues as completed in Execution Program readiness so issue-batch DAGs unlock downstream nodes after upstream completion.
• Add controlled Program Intake dogfood E2E coverage for issue-batch apply/reconcile/status readback and goal-intake latent rejection/apply/reconcile/status readback.
• Update README and specs to align the CLI surface and queue-label ownership boundaries.

Verification

• npm ci in site/
• cargo test -p decodex program_intake_dogfood -- --nocapture
• cargo test -p decodex intake_issues -- --nocapture
• cargo vstyle curate --language rust --workspace --all-features
• cargo make check
• git diff --check
• Semantic drift audit: pass by manual review; docs claims match CLI/parser, intake persistence behavior, reconciler behavior, and E2E readback tests.