Npm audit may skip some dependencies

[yahavi]

• All tests passed. If this feature is not already covered by the tests, I added new tests.
• All static analysis checks passed.
• This pull request is on the dev branch.
• I used gofmt for formatting the code before submitting the pull request.

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When auditing npm projects with jf audit, bundled and peer dependencies may be skipped if they do not appear in the local cache.

To replicate the issue, follow these steps:

1. Clone the repository https://github.com/npm/cli.
2. Execute the command jf audit.
3. Observe that instead of scanning 399 dependencies, only 2 are being scanned.

[github-actions]

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