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Same issue on a Bun monorepo..... The dependency graph lists catalog deps as catalog & ranges like ^4.8.2, with no transitive deps, so Dependabot showed 0 alerts while bun audit found 22 vulnerable packages.

dependabot version updates already support Bun catalogs (dependabot-core#16544), and dependabot-core has a Bun dependency grapher. Enabling Dependabot graph jobs for Bun, like Go and Python, would fix this.... for now we submit bun.lock through the dependency submission API.

I’ve also switched most of my projects to Bun, and it’s a bit disappointing that the Dependency Graph currently only shows the packages listed in package.json instead of the full resolved dependency tree from bun.lockb. https://geometrydasshapk.com/