V6 regression: dependency optimizer pre-bundler did not re-run after lock file change

[smeng9]

Describe the bug

I manually adjusted the package versions in package.json file and then run $ yarn to install the latest packages with bug fix.

Then I started $ yarn dev, however I am still using an older package with bug. The optimize dependency is not working, and this caused some confusion in our team.

Reproduction

https://stackblitz.com/edit/vitejs-vite-swnnga3g?file=index.html&terminal=dev

Steps to reproduce

Install the dependency, then open and close vite dev server.

Next upgrade or downgrade the react version 18->19 in package.json

Install the dependency, then open and close vite dev server again.

Check the folder content in node_modules/.vite/deps and it did not change despite the version is updated.

Additional info: we configured the installStatePath in yarn to be a non-default one so the dependency info can be automatically collected by our logging system which monitors dependency confusion attacks.

Work around: use --force flag

Regression seems get introduced in #18560

System Info

System:
    OS: macOS 14.5
    CPU: (8) arm64 Apple M2
    Memory: 82.11 MB / 16.00 GB
    Shell: 5.9 - /bin/zsh
  Binaries:
    Node: 20.10.0 - /usr/local/bin/node
    Yarn: 1.22.21 - /usr/local/bin/yarn
    npm: 10.2.3 - /usr/local/bin/npm
    pnpm: 8.12.0 - /usr/local/bin/pnpm
  Browsers:
    Safari: 17.5

Used Package Manager

yarn

Logs

No response

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