fix(checkpoints): publish durable refs and preserve captured state

[rynfar]

Checkpoint publication can leave incomplete Git objects/refs after an unclean restart, and a late missing placeholder can overwrite a ready checkpoint in SQL. Flush each capture's object/ref writes before publishing, and preserve ready/error projection state against a later missing placeholder.

Adopts upstream 8130a9f13a1ef506f4393423ded21d71f3c9b5e4 (#10944) and d42a3bd2ae3e698141b26f6426aa28d8886e1754 (#8432), with source attribution preserved. Adapted the fsync arguments to Pylon's current temporary-index capture path; no unrelated sparse-index optimization imported. Pylon identity, running/interrupted turn handling, exact rollback and workspace leases remain intact. This prevents future damage; it does not repair existing corrupt refs. Older Git versions may ignore unsupported fsync settings.

Validation: 57 focused tests across GitVcsDriver, real CheckpointStore captures/restores, and ProjectionPipeline pass. Scoped server typecheck and lint pass. No wire migration or UI change; all providers and clients using the shared checkpoint path benefit.

Part of #585. Frozen upstream head 6d1d549441be84f19696ab59ed7e2fbf305280d4; review cursor unchanged. No release or installation.

Implemented with GPT-6 in Codex.

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Thread transfer impact

✅ Thread transfer remains within every enforced ceiling.

Provider	Metric	Main baseline	This PR	Impact	PR ceiling
Codex	Total thread wire	13.9 KiB	14.0 KiB	+54 B (+0.4%)	15.1 KiB	✅
Codex	Thread snapshot wire	7.2 KiB	7.2 KiB	−6 B (−0.1%)	7.3 KiB	✅
Codex	Live turn WebSocket wire	6.7 KiB	6.8 KiB	+60 B (+0.9%)	7.8 KiB	✅
Codex	Live turn WebSocket decoded	58.0 KiB	58.0 KiB	+44 B (+0.1%)	66.4 KiB	✅
Codex	Live turn messages	8	9	+1 (+12.5%)	21	✅
Claude	Total thread wire	13.9 KiB	13.9 KiB	+16 B (+0.1%)	15.1 KiB	✅
Claude	Thread snapshot wire	7.2 KiB	7.2 KiB	+7 B (+0.1%)	7.3 KiB	✅
Claude	Live turn WebSocket wire	6.7 KiB	6.7 KiB	+9 B (+0.1%)	7.8 KiB	✅
Claude	Live turn WebSocket decoded	58.8 KiB	58.8 KiB	0 B (0.0%)	66.4 KiB	✅
Claude	Live turn messages	8	8	0 (0.0%)	21	✅

Baseline: 5dad0b0 · PR result: 4415aa2 · Source CI: success

Scenario and decoded snapshot size

10 historical turns, 5 command tools per turn, 878.9 KiB retained MCP result per historical turn, and a 1.05 MiB retained result in the measured turn.

• Codex decoded thread snapshot: 115.6 KiB
• Claude decoded thread snapshot: 116.3 KiB

Updated in place by a trusted workflow. PR artifacts are strictly validated and never executed.