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Preserve custom message timestamps across persistence and compaction #76

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@rynfar

Pylon PrimeIntellect-ai#552's isolated compaction fixture exposed a native history mismatch: the first live harness digest timestamp was 1789432878875, while its persisted custom-message entry timestamp was 1789432878921. Rebuilding the context from the session tree changes the message fingerprint without changing its content.

appendCustomMessageEntry mints a second timestamp instead of preserving the custom message's timestamp. The same path is used for background, refinement and command records. Current upstream f585916 still does this.

Preserve the original timestamp at every native custom-message persistence boundary, including rollback-backed writes. Keep default behavior for callers that do not supply an existing message identity. Add real faux-provider compaction/reload coverage and targeted command/refinement/background regressions. No retrospective rewriting of existing session data or relaxed Pylon fingerprint comparisons.

Tracking: pylon-code/pylon#552 and PrimeIntellect-ai#557. Maintainer authorized implementation, review, green-check merge and managed delivery in the Pylon task conversation.

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