a dep import in absolute path (with alias) isn't scanned in optimize process at first in Vite 6

[Jinjiang]

Describe the bug

For special reasons, I have to import some packages in absolute path, like:

import '/Users/xxx/my-project/node_modules/foo/x.js'

with config:

{
  resolve: {
    alias: [{
      find: '/Users/xxx/my-project/node_modules/foo',
      replacement: 'foo',
    }]
  }
}

In both Vite 5 and Vite 6 they work as expected, however, in Vite 6, it will cause a warning message like:

5:50:59 PM [vite] (client) ✨ new dependencies optimized: foo/x.js

I understand the optimize process didn't well reorganize the absolute path import as a package one at first but somehow did it later.

Repro: https://github.com/Jinjiang/reproductions/tree/vite-deps-alias-20250507-2

Even in some cases, there will be some other "file not exist" warnings like:

5:44:27 PM [vite] (client) ✨ new dependencies optimized: foo/foo1.mjs, foo/foo-a.cjs, foo/foo-b.cjs, foo/foo-c.mjs, @mdx-js/react, bar
5:44:27 PM [vite] (client) ✨ optimized dependencies changed. reloading
The file does not exist at "/<project-root>/node_modules/.vite/deps/chunk-E6KUT42S.js?v=05fb22f8" which is in the optimize deps directory. The dependency might be incompatible with the dep optimizer. Try adding it to `optimizeDeps.exclude`.

Repro: https://github.com/Jinjiang/reproductions/tree/vite-deps-alias-20250507 (sorry I can't simplify it further to keep the whole warnings on)

I'd like to understand what the difference is between Vite 5 and Vite 6, and how to avoid or skip the warning messages being printed if it's not a bug.

Thanks.

Reproduction

https://github.com/Jinjiang/reproductions/tree/vite-deps-alias-20250507-2

Steps to reproduce

How to reproduce:

pnpm install
pnpm dev

run it in VIte 5

pnpm dev:5

System Info

System:
    OS: Linux 5.15 Ubuntu 22.04.3 LTS 22.04.3 LTS (Jammy Jellyfish)
    CPU: (10) arm64 unknown
    Memory: 5.82 GB / 7.64 GB
    Container: Yes
    Shell: 5.1.16 - /bin/bash
  Binaries:
    Node: 22.14.0 - ~/.volta/tools/image/node/22.14.0/bin/node
    npm: 10.9.2 - ~/.volta/tools/image/node/22.14.0/bin/npm
    pnpm: 10.9.0 - ~/.volta/bin/pnpm
  Browsers:
    Chromium: 135.0.7049.114
  npmPackages:
    @vitejs/plugin-react: ^4.4.1 => 4.4.1

Used Package Manager

pnpm

Logs

5:50:59 PM [vite] (client) ✨ new dependencies optimized: foo/foo.mjs

or:

5:44:27 PM [vite] (client) ✨ new dependencies optimized: foo/foo1.mjs, foo/foo-a.cjs, foo/foo-b.cjs, foo/foo-c.mjs, @mdx-js/react, bar
5:44:27 PM [vite] (client) ✨ optimized dependencies changed. reloading
The file does not exist at "/<project-root>/node_modules/.vite/deps/chunk-E6KUT42S.js?v=05fb22f8" which is in the optimize deps directory. The dependency might be incompatible with the dep optimizer. Try adding it to `optimizeDeps.exclude`.

Validations

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• The provided reproduction is a minimal reproducible example of the bug.