chore: release v3.9.0

[github-actions]

Automated version bump to 3.9.0 and CHANGELOG update from publish workflow run #677.

[greptile-apps]

Greptile Summary

This is an automated release PR bumping @optave/codegraph from v3.8.1 to v3.9.0, generated by the publish.yml workflow. It updates package.json (version field and optional native binary deps pinned to 3.9.0), regenerates generated/DEPENDENCIES.json from CI, and updates package-lock.json. The CHANGELOG entry is comprehensive, covering engine parity fixes, cross-database queries, lazy WASM loading, and Windows ENOENT fixes.

• The regenerated generated/DEPENDENCIES.json records two extraneous packages (@emnapi/runtime@1.8.1 and tslib@2.8.1) in its problems array — these are napi-rs transitive deps hoisted to the top-level node_modules during the CI install, not a functional or security issue.

Confidence Score: 5/5

Safe to merge — standard automated release commit with no logic changes.

All three changed files are release artifacts (version bump, lockfile, dependency snapshot). No source code was modified. The only notable item is the two extraneous napi-rs transitive deps surfaced in the DEPENDENCIES.json snapshot, which is cosmetic and does not affect runtime behavior or consumers.

No files require special attention.

Important Files Changed

Filename	Overview
package.json	Version bumped to 3.9.0; optional native binary deps pinned to 3.9.0; @huggingface/transformers peer dep consistently set to ^4.0.1 matching devDeps — no issues.
generated/DEPENDENCIES.json	Regenerated from CI npm ls; records two extraneous packages (@emnapi/runtime, tslib) as napi-rs transitive hoisted deps — cosmetic noise in the snapshot, not a functional problem.
package-lock.json	Lockfile updated to reflect v3.9.0 and updated dependency tree; consistent with package.json declarations.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[publish.yml workflow_dispatch] --> B[commit-and-tag-version]
    B --> C[Bump version: 3.8.1 to 3.9.0]
    C --> D[Update package.json]
    C --> E[Update CHANGELOG.md]
    C --> F[Update package-lock.json]
    D --> G[Pin optional native deps to 3.9.0]
    G --> H[codegraph-darwin-arm64 3.9.0]
    G --> I[codegraph-linux-x64-gnu 3.9.0]
    G --> J[other platform binaries 3.9.0]
    B --> K[Regenerate DEPENDENCIES.json]
    K --> L[npm ls snapshot from CI]
    L --> M[extraneous: emnapi-runtime 1.8.1]
    L --> N[extraneous: tslib 2.8.1]

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