refactor: remove checkpoint persistence and pending replacement flow

[rlippmann]

What changed

• Removed checkpoint persistence as a supported runtime workflow.
• Updated persistence guidance and runtime behavior to use export_json() / import_json() as the authoritative state persistence contract.
• Removed checkpoint-related public runtime APIs and migrated preview, regression, fixture, and test workflows away from checkpoint artifacts.
• Updated conformance fixtures and regression coverage to validate authoritative state restoration instead of checkpoint serialization.
• Changed missing-source replacement semantics so use <new> instead of <old> applies deterministically when <old> is absent and there is no semantic conflict.
• Removed the obsolete pending/clarification flow for missing-source replacement while preserving clarification for actual semantic conflicts.
• Updated examples, demos, README guidance, and AGENTS expectations to reflect the simplified persistence and clarification model, including renaming the state-restore example.

Why

• Checkpointing was introduced to support pending continuation, but the remaining supported semantics no longer require persisted continuation state.
• export_json() / import_json() already provide the necessary authoritative state persistence boundary.
• Missing-source replacement does not require user clarification because the intended resulting state is deterministic; clarification should remain reserved for genuine semantic conflicts.
• This keeps the core engine authoritative and avoids duplicating hidden runtime behavior in consumers such as directive drafters.

Closes #187