fix(sqlite-native): delete metadata before chunk range

[NathanFlurry]

Description

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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

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• I have added tests that prove my fix is effective or that my feature works
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[NathanFlurry]

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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 👈 (View in Graphite)
• fix(sqlite-native): keep truncate cache coherent #4637
• 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): delete metadata before chunk range

The fix is directionally correct. Deleting metadata before chunks is the crash-safe ordering: if the process is killed between the two operations, you end up with orphaned chunks (wasted space) rather than live metadata pointing at missing chunks (potential read-time corruption).

Inconsistency with the WASM VFS

The CLAUDE.md requirement says: "The native Rust VFS and the WASM TypeScript VFS must match 1:1." This PR only updates the native Rust VFS, leaving the WASM VFS out of sync.

In rivetkit-typescript/packages/sqlite-vfs/src/vfs.ts (lines 1402-1407), the #delete method still deletes chunks before metadata:

// Delete all chunks via range delete and the metadata key.
await options.deleteRange(
    getChunkKey(fileTag, 0),
    getChunkKeyRangeEnd(fileTag),
);
await options.deleteBatch([metaKey]);   // metadata last — still wrong

The WASM VFS is also internally inconsistent: xTruncate (~line 1293) carries a comment explicitly motivating metadata-first order ("Update metadata first so a crash leaves orphaned chunks rather than metadata pointing at missing chunks (corruption)") but #delete does the opposite.

Suggested fix for the WASM VFS #delete method

// Delete metadata first so a crash leaves orphaned chunks (wasted
// space) rather than metadata pointing at missing chunks (corruption).
await options.deleteBatch([metaKey]);
await options.deleteRange(
    getChunkKey(fileTag, 0),
    getChunkKeyRangeEnd(fileTag),
);

Summary

	Native Rust VFS (after this PR)	WASM VFS (unchanged)
xDelete order	metadata then chunks ✅	chunks then metadata ❌
xTruncate order	metadata then chunks ✅	metadata then chunks ✅

The native fix is correct — please also update packages/sqlite-vfs/src/vfs.ts in the same change to keep both implementations in sync and fix the internal inconsistency in the WASM VFS.