Add configurable and atomic checkpoint controls

[Toti330]

Summary

Adds explicit checkpoint frequency and overwrite controls, safer atomic checkpoint replacement, and validation for resume data.

Why this is useful

Checkpoint behavior was previously implicit and the main-loop sleep converted 0.1 seconds to 0 ms, causing continuous checkpoint writes. This PR makes checkpoint I/O deliberate, tunable, and safe to disable during measurement.

Implementation

• Adds CHECKPOINT_FREQUENCY=none|very_low|low|medium|high|xhigh|atomic.
• Uses exact cadences: disabled, 60s, 30s, 10s default, 1s, 250ms, and 100ms.
• Adds CHECKPOINT_OVERWRITE=1 to discard an existing resume file intentionally.
• Replaces files via temporary file plus rename so readers see a complete old or complete new checkpoint.
• Stores absolute per-worker seed positions, limits rewind to the existing 2-seed policy, and validates entry count plus each worker range.
• Fixes the scheduler sleep to Duration::from_secs_f32(0.1).

Independence

This PR is based directly on main and has no feature-branch dependency. It can be merged independently of timing, diagnostics, tuning, preflight, and progress logging.

Verification

• cargo test --all-targets: 5 checkpoint tests passed.
• Benchmark smoke run completed with CHECKPOINT_FREQUENCY=none.

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Generated by GPT-5.6 Terra & Sol. Ideas from the author; implementation by AI.

[SuperB3333]

Implemented in 58c5e39