fix: make superblock checkpoints atomic

[bmuddha]

What changed

• Finalize a superblock boundary and enter its snapshot pause as one sequencer message.
• Keep transactions queued after the checkpoint out of the sealed snapshot until the pacemaker releases execution.
• Preserve ordinary block handling, standalone barriers, and simulation pacing.

Closes #81

Impact

Prevents concurrent transaction submission from producing leader and follower seals over different state prefixes. Adds an internal SequencerMessage::Checkpoint variant without changing replication, ledger, or persistence formats.

Reviewer notes

The execution-channel position of Checkpoint is the cutoff: earlier transactions are finalized into the block and snapshot, while later transactions remain queued until snapshot creation and seal append complete.

[coderabbitai]

Warning

Review limit reached

@bmuddha, you've reached your PR review limit, so we couldn't start this review.

Next review available in: 11 minutes

Limit details: You’ve used the included review currently available.

You've used all free OSS reviews for now. Wait for the free limit to reset to keep reviewing this public repository.

How can I continue?

Wait for the limit to reset, then comment @coderabbitai review or push new commits to the PR.

An organization admin can change what happens after included review limits in Billing.

How do review limits work?

CodeRabbit enforces per-developer PR review limits within each organization.

For paid Pro and Pro+ reviews, CodeRabbit uses a developer's included PR review attempts over the past 7 days to set the current hourly allowance. At typical activity levels, the full plan allowance applies. Higher sustained activity can lower the allowance until earlier attempts leave the 7-day window.

Please refer docs for additional details.

Review details

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: 5251b961-f2ad-4d65-9382-f1d84518b8e7

📥 Commits

Reviewing files that changed from the base of the PR and between 22d9e8d and c761005.

📒 Files selected for processing (5)

• engine/src/pacemaker.rs
• nucleus/README.md
• nucleus/src/runtime.rs
• processor/README.md
• processor/src/sequencer/mod.rs

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}