Vite 6 config's source map file reference is off

[hi-ogawa]

Describe the bug

I would assume users haven't done this often, but I just realized it's possible to enable node's source map for Vite's config import. When it's enabled, file reference is off since we moved bundle file to node_modules/.vite-temp #18509 but source map sources entries are still relative from cwd.

On Vite 5

$ NODE_OPTIONS=--enable-source-maps npx vite
Trace: test
    at f2 (/my/cwd/vite.config.ts:10:11)
    at f1 (/my/cwd/vite.config.ts:6:3)
    at <anonymous> (/my/cwd/vite.config.ts:13:1)

On Vite 6

$ NODE_OPTIONS=--enable-source-maps npx vite
Trace: test
    at f2 (/my/cwd/node_modules/.vite-temp/vite.config.ts:10:11) 
    at f1 (/my/cwd/node_modules/.vite-temp/vite.config.ts:6:3)
    at <anonymous> (/my/cwd/node_modules/.vite-temp/vite.config.ts:13:1)

Reproduction

https://github.com/hi-ogawa/reproductions/tree/main/vite-config-bundle-source-map

Steps to reproduce

Cannot reproduce on stackblitz but you can test locally by downloading https://stackblitz.com/github/hi-ogawa/reproductions/tree/main/vite-config-bundle-source-map?file=README.md

System Info

System:
    OS: Linux 6.11 Arch Linux
    CPU: (16) x64 12th Gen Intel(R) Core(TM) i7-12650H
    Memory: 15.93 GB / 31.05 GB
    Container: Yes
    Shell: 5.2.37 - /usr/bin/bash
  Binaries:
    Node: 20.18.1 - ~/.volta/tools/image/node/20.18.1/bin/node
    npm: 10.8.2 - ~/.volta/tools/image/node/20.18.1/bin/npm
    pnpm: 9.14.2 - ~/.volta/bin/pnpm
    bun: 1.1.29 - ~/.volta/bin/bun
  Browsers:
    Chromium: 131.0.6778.85
  npmPackages:
    vite: ^6 => 6.0.1

Used Package Manager

pnpm

Logs

No response

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