Align vers-fleets with Reef v2 provisioning model

[pranavpatilsce]

Summary

This PR aligns vers-fleets with the Reef v2 provisioning and runtime model.

At a product level, it makes image build and fleet provision behave correctly for the current Reef control plane, root authority model, and runtime boot expectations.

What changed

Provisioning / topology alignment

• aligned shared topology with the Reef v2 service set
• stopped provisioning root records through the old registry path
• provisioned scheduled checks on root
• kept the boot/runtime environment aligned with the vm-tree / logs / signals / scheduled model Reef now expects

Runtime boot behavior

• updated boot/runtime env generation to support the current Reef runtime expectations
• kept the normal runtime auth path centered on VERS_API_KEY and exchanged fleet credentials
• demoted wording that made secondary provider behavior sound like a user-facing setup path

Auth and operator guidance

• README and CLI continue to emphasize the supported build/provision auth flows:
  • shell auth via --email
  • or VERS_API_KEY
• local source overrides remain first-class:
  • --reef-path
  • --pi-vers-path

Why this matters

Reef v2 depends on the image/provisioning layer doing the right thing by default.

Without these changes, you can end up with:

• stale service topology in root or golden images
• old registry-era assumptions leaking into the runtime
• missing scheduled-check capability on root
• confusing operator guidance around credentials

This PR keeps vers-fleets as the correct substrate for the Reef v2 branch.

Validation

Local validation

• node --test test/topology.test.js
• node --test test/orchestrate.test.js

Integration validation

Used in repeated private reprovisions of the Reef v2 branch, including validations of:

• root/golden image boot behavior
• root task lifecycle
• logs browser
• scheduled checks
• active/history fleet views
• resource VM lifecycle behavior
• repo-oriented build benchmarks against live repos

Follow-ups / non-blocking notes

• the main supported operator path remains VERS_API_KEY or shell auth
• future work can make fleet/runtime auth surfaces even more explicit in operator tooling

Cross-repo context

This PR is part of a coordinated stack with:

• hdresearch/reef branch feat/reef-v2-orchestration
• hdresearch/pi-vers branch remote-bg-process-hardening