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]

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ℹ️ Recent review info

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Run ID: 429587fc-060e-4480-bd35-be95003cf482

📥 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

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📝 Walkthrough

Walkthrough

The pacemaker now sends simulation messages before sequencer messages. Non-superblock slots use the existing block message. Superblock slots use a guarded checkpoint message. The runtime message contract carries the block and barrier guard. The sequencer finalizes the block, pauses scheduling, acknowledges the barrier, and resumes after release. Documentation describes the atomic checkpoint behavior.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes address issue #81 by combining block finalization and snapshot pause while preserving ordinary pacing and formats.
Out of Scope Changes check	✅ Passed	The code and documentation changes support the linked issue and do not show unrelated scope.
Docstring Coverage	✅ Passed	Docstring check was indeterminate for this PR — some files could not be analyzed in time. Not blocking.
Title check	✅ Passed	The title clearly and concisely describes the main change: making superblock checkpoints atomic.
Description check	✅ Passed	The description directly explains the atomic checkpoint change, transaction cutoff, preserved behavior, and impact.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/atomic-superblock-checkpoints

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[bmuddha]

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