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

[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 : 3 dependent PRs (#4650 , #4652 , #4666 )
• 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

Overview

A minimal 4-line swap in rivetkit-typescript/packages/sqlite-native/src/vfs.rs that reverses the deletion order in delete_file: the metadata key is now deleted before the chunk range, not after.

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Correctness: The Fix Is Right

The new ordering is safer for crash/error recovery:

• Old order (chunks first, then metadata): If kv_delete_range succeeds but the subsequent kv_delete on the metadata key fails, SQLite finds a metadata key pointing to a file with no chunks. On next open it reads a non-zero size but gets empty pages, which can silently corrupt the database.
• New order (metadata first, then chunks): If kv_delete succeeds but kv_delete_range fails, orphaned chunks remain in KV with no reachable metadata key. SQLite treats the file as non-existent. The orphaned chunks are a storage leak but not a correctness issue.

Metadata-first deletion is the standard "delete the pointer before the data" pattern for crash-consistent KV-backed filesystems.

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Parity Violation with WASM VFS

Per CLAUDE.md, the Rust native VFS and the TypeScript WASM VFS must match 1:1, and the delete/truncate strategy is explicitly called out. However, the WASM VFS (packages/sqlite-vfs/src/vfs.ts, lines 1402-1407) still uses the old order: chunks are deleted before metadata. This PR fixes the Rust side but leaves the TypeScript side with the unsafe ordering.

Recommendation: Either include the WASM fix (deleteBatch([metaKey]) before deleteRange) in this PR, or track it as an explicit follow-up.

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Other Notes

• The PR description is empty (template checkboxes unchecked, no motivation or test plan). A short explanation of the bug and its impact would help future readers.
• The change itself is clean and appropriately minimal.

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Summary

Fix correctness	Correct: metadata-first is the right crash-safe order
Parity with WASM VFS	Missing - packages/sqlite-vfs/src/vfs.ts still deletes chunks before metadata
Code quality	Clean, no style issues
Tests	No new test added

The core fix is sound. The main ask is to also update the WASM VFS for parity.