chore: release v3.1.0

[github-actions]

Automated version bump to 3.1.0 and CHANGELOG update from publish workflow run #286.

[greptile-apps]

Greptile Summary

This is an automated release PR bumping @optave/codegraph from 3.0.4 to 3.1.0, updating all seven optional platform binary package pins in package.json and regenerating generated/DEPENDENCIES.json.

• package.json — All @optave/codegraph-* optional dependency versions cleanly updated from 3.0.4 → 3.1.0.
• generated/DEPENDENCIES.json — Contains a top-level "problems" array and a "error": {"code": "ELSPROBLEMS"} block, meaning this snapshot was taken while npm ls saw version mismatches. The two Linux x64 packages (@optave/codegraph-linux-x64-gnu and @optave/codegraph-linux-x64-musl) are still showing 3.0.4 in node_modules because npm install runs at the beginning of the publish workflow before those packages are published. A npm install --ignore-scripts step added after publishing would fix this for future releases.
• graphology — Incidentally updated from 0.25.4 → 0.26.0 in the lock/snapshot (matches the ^0.26.0 range already declared in package.json).

Confidence Score: 3/5

• Safe to merge for the version bump itself, but the committed DEPENDENCIES.json contains npm error state that should be cleaned up in the workflow before the next release.
• The package.json changes are correct and complete. The only issue is that generated/DEPENDENCIES.json was generated while npm reported ELSPROBLEMS for the two Linux x64 platform packages — the file itself is a generated artifact and doesn't affect runtime, but the error state is a signal that the publish workflow has a reproducible ordering bug that will recur on every release until the workflow is patched.
• generated/DEPENDENCIES.json — committed with embedded npm error state (ELSPROBLEMS); the root cause is in .github/workflows/publish.yml.

Important Files Changed

Filename	Overview
generated/DEPENDENCIES.json	Version bumped to 3.1.0, graphology updated to 0.26.0, but the file is committed in an error state — it contains a top-level "problems" array and "error": {"code": "ELSPROBLEMS"} block because npm ls was run before node_modules was refreshed with the newly-published 3.1.0 platform packages.
package.json	Clean version bump from 3.0.4 to 3.1.0 for all seven optional platform-specific binary packages. No other changes; looks correct.

Sequence Diagram

sequenceDiagram
    participant WF as publish.yml workflow
    participant NPM as npm registry
    participant GIT as git / PR

    WF->>NPM: npm install (3.0.4 platform pkgs installed — 3.1.0 not yet published)
    WF->>WF: npm version 3.1.0 (package.json now requires 3.1.0)
    WF->>NPM: Publish @optave/codegraph-linux-x64-gnu@3.1.0
    WF->>NPM: Publish @optave/codegraph-linux-x64-musl@3.1.0
    WF->>NPM: Publish @optave/codegraph@3.1.0
    Note over WF: node_modules still has 3.0.4 binaries
    WF->>WF: npm ls --json → ELSPROBLEMS (3.0.4 vs required 3.1.0)
    WF->>GIT: Commit DEPENDENCIES.json (with error state)
    GIT-->>GIT: PR opened (this PR)

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_{Last reviewed commit: 0c95b01}

[greptile-apps]

DEPENDENCIES.json committed with npm error state

The file contains a top-level "problems" array and a trailing "error": {"code": "ELSPROBLEMS"} block, indicating that npm ls exited non-zero when this snapshot was generated. Both @optave/codegraph-linux-x64-gnu and @optave/codegraph-linux-x64-musl are reported as "invalid" because their installed version (3.0.4) no longer satisfies the root project requirement (3.1.0).

The root cause is in .github/workflows/publish.yml line 495:

npm ls --json --all --omit=dev > generated/DEPENDENCIES.json 2>/dev/null || true

npm install runs at line 382 before the new 3.1.0 platform packages are published to npm, so node_modules is still populated with 3.0.4 binaries. After publishing, npm ls sees the version mismatch and embeds the error into stdout alongside the JSON.

The fix is to add a fresh npm install (or npm install --ignore-scripts) after the publish steps and before generating the snapshot:

- name: Refresh node_modules after publish
  run: npm install --ignore-scripts

- name: Generate DEPENDENCIES.json
  run: mkdir -p generated && npm ls --json --all --omit=dev > generated/DEPENDENCIES.json 2>/dev/null || true

Until then, any tooling that reads generated/DEPENDENCIES.json and checks for a top-level "error" key or "problems" array will see a spurious failure for the two Linux x64 packages.