fix(sqlite-native): keep truncate cache coherent

[NathanFlurry]

Description

Please include a summary of the changes and the related issue. Please also include relevant motivation and context.

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[NathanFlurry]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
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• chore(engine): publish engine bases in ci #4649
• chore: lockfile lefthook #4647
• fix(rivetkit): surface native sqlite kv errors to callers #4645
• fix(rivetkit): prevent sleep races during disconnect and db work #4644
• fix(rivetkit): isolate engine envoys and propagate startup failures #4643
• test(rivetkit): remove wasm sqlite-only fixtures and coverage #4642
• chore(sqlite-vfs): remove wasm sqlite packages and workspace wiring #4641
• chore(rivetkit): remove wasm sqlite runtime #4614
• fix(sqlite-native): restore native startup kv preload #4639
• fix(sqlite-native): delete metadata before chunk range #4638
• fix(sqlite-native): keep truncate cache coherent #4637 👈 (View in Graphite)
• fix(sqlite-vfs): use delete range for truncate cleanup #4636
• fix(sqlite-native): restore kv error hook #4635
• perf(sqlite-native): avoid cloning cached read chunks #4634
• perf(sqlite-native): gate kv operation labels #4633
• perf(sqlite-native): reuse read cache for partial writes #4632
• perf(sqlite-native): remove delete file existence probe #4631
• fix(sqlite-native): gate native read cache behind env var #4630
• fix(pegboard): isolate runner config dc lookup failures #4625 : 1 other dependent PR (#4626 )
• docs(pegboard): note runner config upsert split write risk #4624
• fix(pegboard): unpack global runner config keys correctly #4623
• fix(pegboard-gateway): enforce tunnel message state #4622
• fix(pegboard-runner): clear terminal tunnel routes #4621
• fix(pegboard): skip protocol version keys in runner pool backfill #4620
• fix(pegboard): create missing normal runner configs #4619
• fix(epoxy): reuse cached optimistic value #4618
• main

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[claude]

PR Review: fix(sqlite-native): keep truncate cache coherent

Both bugs fixed here are real and the fixes are correct.

Fix 1 — off-by-one in cache eviction boundary

The old formula:

let truncate_from_chunk = if size == 0 { 0u32 } else { (size as u32 / kv::CHUNK_SIZE as u32) + 1 };
// kept chunks with: chunk_idx < truncate_from_chunk

was off-by-one on chunk-aligned truncations. Truncating to exactly CHUNK_SIZE bytes gave truncate_from_chunk = 2, retaining chunk 1 in the cache even though chunk 1 now lies beyond the new file end.

The new formula uses (size - 1) / CHUNK_SIZE with chunk_idx as i64 <= last_chunk_to_keep, which correctly matches the KV-level delete boundary.

Fix 2 — stale cache after partial-chunk truncation

The old code wrote the shortened slice to KV via kv_put but never updated the read cache, causing subsequent reads to return stale (longer) cached data for the last chunk. The new code inserts the truncated chunk into the read cache after a successful kv_put, keeping both stores coherent.

Variable reordering

Moving last_chunk_to_keep / last_existing_chunk before the read_cache.retain block is necessary to use the correct boundary in Fix 1 and is a clean structural improvement.

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Concerns

WASM VFS parity (required per CLAUDE.md)

The repo requires the native Rust VFS and the WASM TypeScript VFS to match 1:1. The WASM truncate path in rivetkit-typescript/packages/sqlite-wasm/src/vfs.ts should be audited for the same two bugs (off-by-one cache eviction and stale cache after partial-chunk write). No corresponding WASM change is included here.

Test coverage

No tests were added. Suggested cases to cover:

• Truncate to a chunk-aligned boundary (exercises Fix 1)
• Truncate to a non-aligned size (exercises Fix 2)
• Truncate to zero

Minor: cache eviction before metadata write

The read cache is evicted before the metadata is written. If the metadata write fails, evicted entries are gone from the cache but the KV store is unchanged, forcing unnecessary round-trips on subsequent reads. This is a performance issue on error paths only, not a correctness issue.

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Summary

The two correctness fixes are well-reasoned and the math is sound. The main outstanding item is WASM VFS parity, which is a hard requirement per the project's conventions.