Vite can use the wrong module if local or linked modules include their own `node_modules`, breaking Vue

### Describe the bug

I am building a UI library package and a Vue app at the same time. Both projects are following best practices from Vite. The UI package and the Vue app both rely on Headless UI.

If the UI package is linked or added as a local file, the `node_modules` folder comes along with the `dist` folder. When this happens, Vite will analyse the `node_modules` folder within the UI package first to resolve Headless UI, which I think grabs a separate instance of Vue and results in errors like `provide() can only be used inside setup()`.

Evidence from the logs below:

```
vite:deps Scan completed in 123.33ms: {
  vue: 'E:/Work/vite-module-bug/website/node_modules/vue/dist/vue.runtime.esm-bundler.js',
  '@headlessui/vue': 'E:/Work/vite-module-bug/ui-library/node_modules/@headlessui/vue/dist/headlessui.esm.js'
}
```

Ideally `@headlessui/vue` should resolve to the one in in `/website` instead of `/ui-library`.

### Reproduction

https://github.com/JeffSchofield/vite-module-bug

### System Info

```shell
System:
    OS: Windows 10 10.0.19044
    CPU: (8) x64 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
    Memory: 3.24 GB / 31.94 GB
  Binaries:
    Node: 16.14.0 - C:\Program Files\nodejs\node.EXE
    Yarn: 1.22.17 - ~\AppData\Roaming\npm\yarn.CMD
    npm: 8.3.1 - C:\Program Files\nodejs\npm.CMD
  Browsers:
    Edge: Spartan (44.19041.1266.0), Chromium (99.0.1150.46)
    Internet Explorer: 11.0.19041.1566
  npmPackages:
    @vitejs/plugin-vue: ^2.2.4 => 2.2.4
    vite: ^2.8.6 => 2.8.6
```


### Used Package Manager

npm

### Logs

```shell
vite:config bundled config file loaded in 104.92ms +0ms
  vite:config using resolved config: {
  vite:config   plugins: [
  vite:config     'vite:pre-alias',
  vite:config     'alias',
  vite:config     'vite:modulepreload-polyfill',
  vite:config     'vite:resolve',
  vite:config     'vite:html-inline-proxy',     
  vite:config     'vite:css',
  vite:config     'vite:esbuild',
  vite:config     'vite:json',
  vite:config     'vite:wasm',
  vite:config     'vite:worker',
  vite:config     'vite:worker-import-meta-url',
  vite:config     'vite:asset',
  vite:config     'vite:vue',
  vite:config     'vite:define',
  vite:config     'vite:css-post',
  vite:config     'vite:client-inject',
  vite:config     'vite:import-analysis'        
  vite:config   ],
  vite:config   server: {
  vite:config     preTransformRequests: true,
  vite:config     force: true,
  vite:config     fs: { strict: true, allow: [Array], deny: [Array] }
  vite:config   },
  vite:config   define: { __VUE_OPTIONS_API__: true, __VUE_PROD_DEVTOOLS__: false },
  vite:config   ssr: { external: [ 'vue', '@vue/server-renderer' ] },
  vite:config   configFile: 'E:/Work/vite-module-bug/website/vite.config.ts',
  vite:config   configFileDependencies: [ 'vite.config.ts' ],
  vite:config   inlineConfig: {
  vite:config     root: undefined,
  vite:config     base: undefined,
  vite:config     mode: undefined,
  vite:config     configFile: undefined,
  vite:config     logLevel: undefined,
  vite:config     clearScreen: undefined,
  vite:config     server: { force: true }
  vite:config   },
  vite:config   root: 'E:/Work/vite-module-bug/website',
  vite:config   base: '/',
  vite:config   resolve: { dedupe: undefined, alias: [ [Object], [Object] ] },
  vite:config   publicDir: 'E:\\Work\\vite-module-bug\\website\\public',
  vite:config   cacheDir: 'E:\\Work\\vite-module-bug\\website\\node_modules\\.vite',
  vite:config   command: 'serve',
  vite:config   mode: 'development',
  vite:config   isProduction: false,
  vite:config   build: {
  vite:config     target: [ 'es2019', 'edge88', 'firefox78', 'chrome87', 'safari13.1' ],
  vite:config     polyfillModulePreload: true,
  vite:config     outDir: 'dist',
  vite:config     assetsDir: 'assets',
  vite:config     assetsInlineLimit: 4096,
  vite:config     cssCodeSplit: true,
  vite:config     cssTarget: [ 'es2019', 'edge88', 'firefox78', 'chrome87', 'safari13.1' ],
  vite:config     sourcemap: false,
  vite:config     rollupOptions: {},
  vite:config     minify: 'esbuild',
  vite:config     terserOptions: {},
  vite:config     write: true,
  vite:config     emptyOutDir: null,
  vite:config     manifest: false,
  vite:config     lib: false,
  vite:config     ssr: false,
  vite:config     ssrManifest: false,
  vite:config     reportCompressedSize: true,
  vite:config     chunkSizeWarningLimit: 500,
  vite:config     watch: null,
  vite:config     commonjsOptions: { include: [Array], extensions: [Array] },
  vite:config     dynamicImportVarsOptions: { warnOnError: true, exclude: [Array] }
  vite:config   },
  vite:config   preview: {
  vite:config     port: undefined,
  vite:config     strictPort: undefined,
  vite:config     host: undefined,
  vite:config     https: undefined,
  vite:config     open: undefined,
  vite:config     proxy: undefined,
  vite:config     cors: undefined,
  vite:config     headers: undefined
  vite:config   },
  vite:config   env: { BASE_URL: '/', MODE: 'development', DEV: true, PROD: false },
  vite:config   assetsInclude: [Function: assetsInclude],
  vite:config   logger: {
  vite:config     hasWarned: false,
  vite:config     info: [Function: info],
  vite:config     warn: [Function: warn],
  vite:config     warnOnce: [Function: warnOnce],
  vite:config     error: [Function: error],
  vite:config     clearScreen: [Function: clearScreen],
  vite:config     hasErrorLogged: [Function: hasErrorLogged]
  vite:config   },
  vite:config   packageCache: Map(0) {},
  vite:config   createResolver: [Function: createResolver],
  vite:config   optimizeDeps: {
  vite:config     esbuildOptions: { keepNames: undefined, preserveSymlinks: undefined }
  vite:config   },
  vite:config   worker: {
  vite:config     format: 'iife',
  vite:config     plugins: [
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object],
  vite:config       [Object], [Object]
  vite:config     ],
  vite:config     rollupOptions: {}
  vite:config   }
  vite:config } +8ms
  vite:deps Crawling dependencies using entries:
  vite:deps   E:/Work/vite-module-bug/website/index.html +0ms
  vite:resolve 1.20ms /src/entry-client.ts -> E:/Work/vite-module-bug/website/src/entry-client.ts +0ms
  vite:resolve 5.07ms ./main -> E:/Work/vite-module-bug/website/src/main.ts +12ms
  vite:resolve 19.97ms vue -> E:/Work/vite-module-bug/website/node_modules/vue/dist/vue.runtime.esm-bundler.js +28ms
  vite:resolve 2.29ms ./App.vue -> E:/Work/vite-module-bug/website/src/App.vue +8ms
  vite:resolve 4.97ms ui-library -> E:/Work/vite-module-bug/ui-library/dist/index.es.js +17ms
  vite:resolve 7.23ms @headlessui/vue -> E:/Work/vite-module-bug/ui-library/node_modules/@headlessui/vue/dist/headlessui.esm.js +20ms
  vite:deps Scan completed in 123.33ms: {
  vue: 'E:/Work/vite-module-bug/website/node_modules/vue/dist/vue.runtime.esm-bundler.js',
  '@headlessui/vue': 'E:/Work/vite-module-bug/ui-library/node_modules/@headlessui/vue/dist/headlessui.esm.js'
} +112ms
Pre-bundling dependencies:
  vue
  @headlessui/vue
(this will be run only when your dependencies or config have changed)
  vite:resolve 3.16ms @vue/runtime-dom -> E:/Work/vite-module-bug/website/node_modules/@vue/runtime-dom/dist/runtime-dom.esm-bundler.js +0ms
  vite:resolve 5.77ms @vue/runtime-core -> E:/Work/vite-module-bug/website/node_modules/@vue/runtime-core/dist/runtime-core.esm-bundler.js +20ms
  vite:resolve 5.99ms vue -> E:/Work/vite-module-bug/ui-library/node_modules/vue/dist/vue.runtime.esm-bundler.js +9ms
  vite:resolve 6.31ms @vue/shared -> E:/Work/vite-module-bug/website/node_modules/@vue/shared/dist/shared.esm-bundler.js +7ms
  vite:resolve 6.34ms @vue/runtime-dom -> E:/Work/vite-module-bug/ui-library/node_modules/@vue/runtime-dom/dist/runtime-dom.esm-bundler.js +9ms
  vite:resolve 3.79ms @vue/runtime-core -> E:/Work/vite-module-bug/ui-library/node_modules/@vue/runtime-core/dist/runtime-core.esm-bundler.js +26ms
  vite:resolve 3.44ms @vue/shared -> E:/Work/vite-module-bug/ui-library/node_modules/@vue/shared/dist/shared.esm-bundler.js +5ms
  vite:resolve 5.76ms @vue/reactivity -> E:/Work/vite-module-bug/website/node_modules/@vue/reactivity/dist/reactivity.esm-bundler.js +55ms
  vite:resolve 4.60ms @vue/reactivity -> E:/Work/vite-module-bug/ui-library/node_modules/@vue/reactivity/dist/reactivity.esm-bundler.js +31ms
  vite:deps deps bundled in 294.85ms +0ms

  vite v2.8.6 dev server running at:

  > Local: http://localhost:3000/
  > Network: use `--host` to expose

  ready in 1137ms.

  vite:time 0.59ms / +0ms
  vite:spa-fallback Rewriting GET / to /index.html +0ms
  vite:time 30.37ms /index.html +62ms
  vite:resolve 1.30ms E:\Work\vite-module-bug\website\node_modules\vite\dist\client\client.mjs -> E:/Work/vite-module-bug/website/node_modules/vite/dist/client/client.mjs +0ms
  vite:resolve 2.64ms /@vite/client -> E:/Work/vite-module-bug/website/node_modules/vite/dist/client/client.mjs +1ms
  vite:load 3.73ms [fs] /@vite/client +0ms
  vite:resolve 1.20ms E:\Work\vite-module-bug\website\node_modules\vite\dist\client\env.mjs -> E:/Work/vite-module-bug/website/node_modules/vite/dist/client/env.mjs +18ms
  vite:resolve 3.43ms @vite/env -> E:/Work/vite-module-bug/website/node_modules/vite/dist/client/env.mjs +2ms
  vite:resolve 1.05ms /node_modules/vite/dist/client/env.mjs -> E:/Work/vite-module-bug/website/node_modules/vite/dist/client/env.mjs +1ms
  vite:import-analysis 9.72ms [1 imports rewritten] node_modules\vite\dist\client\client.mjs +0ms
  vite:transform 14.59ms /@vite/client +0ms
  vite:time 33.94ms /@vite/client +63ms    
  vite:resolve 1.27ms /src/main.css?direct -> E:/Work/vite-module-bug/website/src/main.css?direct +20ms
  vite:load 11.60ms [fs] /node_modules/vite/dist/client/env.mjs +39ms
  vite:import-analysis 0.25ms [no imports] node_modules\vite\dist\client\env.mjs +24ms
  vite:transform 1.39ms /node_modules/vite/dist/client/env.mjs +24ms
  vite:load 6.43ms [fs] /src/main.css?direct +4ms
  vite:import-analysis [skipped] src\main.css?direct +15ms
  vite:transform 12.67ms /src/main.css?direct +15ms
  vite:time 25.31ms /src/main.css +35ms
  vite:resolve 0.90ms /src/entry-client.ts -> E:/Work/vite-module-bug/website/src/entry-client.ts +26ms
  vite:load 0.81ms [fs] /src/entry-client.ts +20ms
  vite:resolve 1.80ms ./main -> E:/Work/vite-module-bug/website/src/main.ts +20ms
  vite:resolve 1.01ms /src/main.ts -> E:/Work/vite-module-bug/website/src/main.ts +2ms
  vite:import-analysis 6.50ms [1 imports rewritten] src\entry-client.ts +29ms
  vite:transform 22.49ms /src/entry-client.ts +30ms
  vite:time 29.72ms /src/entry-client.ts +32ms
  vite:load 1.74ms [fs] /src/main.ts +30ms
  vite:resolve 0.22ms vue -> E:/Work/vite-module-bug/website/node_modules/.vite/vue.js?v=a40dd0ad +22ms
  vite:resolve 1.34ms /node_modules/.vite/vue.js?v=a40dd0ad -> E:/Work/vite-module-bug/website/node_modules/.vite/vue.js?v=a40dd0ad +2ms
  vite:resolve 1.01ms ./App.vue -> E:/Work/vite-module-bug/website/src/App.vue +2ms
  vite:resolve 0.97ms /src/App.vue -> E:/Work/vite-module-bug/website/src/App.vue +2ms
  vite:import-analysis 10.60ms [2 imports rewritten] src\main.ts +29ms
  vite:transform 20.52ms /src/main.ts +28ms
  vite:load 1.34ms [fs] /src/App.vue +29ms
  vite:load 50.32ms [fs] /node_modules/.vite/vue.js?v=a40dd0ad +48ms
  vite:resolve 2.36ms ./chunk-AWPMEBIP.js -> E:/Work/vite-module-bug/website/node_modules/.vite/chunk-AWPMEBIP.js +106ms
  vite:resolve 2.95ms /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad -> E:/Work/vite-module-bug/website/node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +5ms
  vite:import-analysis 40.26ms [1 imports rewritten] node_modules\.vite\vue.js?v=a40dd0ad +132ms
  vite:transform 43.98ms /node_modules/.vite/vue.js?v=a40dd0ad +132ms
  vite:cache [memory] /node_modules/vite/dist/client/env.mjs +0ms
  vite:time 2.02ms /node_modules/vite/dist/client/env.mjs +163ms
  vite:cache [memory] /src/main.ts +4ms
  vite:time 5.23ms /src/main.ts +7ms
  vite:resolve 0.41ms ui-library -> E:/Work/vite-module-bug/ui-library/dist/index.es.js +55ms
  vite:resolve 0.84ms /@id/plugin-vue:export-helper -> null +7ms
  vite:hmr [self-accepts] src\App.vue +0ms
  vite:import-analysis 19.48ms [3 imports rewritten] src\App.vue +47ms
  vite:transform 173.13ms /src/App.vue +48ms
  vite:cache [memory] /node_modules/.vite/vue.js?v=a40dd0ad +48ms
  vite:load 0.09ms [plugin] plugin-vue:export-helper +142ms
  vite:import-analysis 0.04ms [no imports] plugin-vue:export-helper +23ms
  vite:transform 3.50ms plugin-vue:export-helper +24ms
  vite:cache [memory] /node_modules/.vite/vue.js?v=a40dd0ad +39ms
  vite:time 29.60ms /node_modules/.vite/vue.js?v=a40dd0ad +112ms
  vite:load 134.25ms [fs] /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +73ms
  vite:import-analysis 0.07ms [no imports] node_modules\.vite\chunk-AWPMEBIP.js?v=a40dd0ad +75ms
  vite:transform 5.30ms /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +74ms
  vite:load 86.44ms [fs] ..\ui-library\dist\index.es.js +10ms
  vite:resolve 0.13ms @headlessui/vue -> E:/Work/vite-module-bug/website/node_modules/.vite/@headlessui_vue.js?v=a40dd0ad +119ms
  vite:resolve 4.95ms /node_modules/.vite/@headlessui_vue.js?v=a40dd0ad -> E:/Work/vite-module-bug/website/node_modules/.vite/@headlessui_vue.js?v=a40dd0ad +11ms
  vite:import-analysis 29.07ms [2 imports rewritten] E:/Work/vite-module-bug/ui-library/dist/index.es.js +36ms
  vite:transform 31.96ms ..\ui-library\dist\index.es.js +37ms
  vite:cache [memory] /node_modules/.vite/vue.js?v=a40dd0ad +91ms
  vite:time 57.90ms /src/App.vue +69ms
  vite:cache [memory] /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +15ms
  vite:time 9.98ms /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +16ms
  vite:cache [memory] ..\ui-library\dist\index.es.js +12ms
  vite:time 9.68ms ..\ui-library\dist\index.es.js +13ms
  vite:cache [memory] plugin-vue:export-helper +12ms
  vite:time 3.13ms /@id/plugin-vue:export-helper +5ms
  vite:load 45.59ms [fs] /node_modules/.vite/@headlessui_vue.js?v=a40dd0ad +90ms
  vite:import-analysis 12.85ms [1 imports rewritten] node_modules\.vite\@headlessui_vue.js?v=a40dd0ad +82ms
  vite:transform 14.68ms /node_modules/.vite/@headlessui_vue.js?v=a40dd0ad +80ms
  vite:time 56.30ms /node_modules/.vite/@headlessui_vue.js?v=a40dd0ad +65ms
  vite:cache [memory] /node_modules/.vite/chunk-AWPMEBIP.js?v=a40dd0ad +89ms
  vite:resolve 1.80ms /node_modules/.vite/chunk-AWPMEBIP.js -> E:/Work/vite-module-bug/website/node_modules/.vite/chunk-AWPMEBIP.js +332ms
  vite:time 17.43ms /node_modules/.vite/chunk-AWPMEBIP.js.map +221ms
```


### Validations

- [X] Follow our [Code of Conduct](https://github.com/vitejs/vite/blob/main/CODE_OF_CONDUCT.md)
- [X] Read the [Contributing Guidelines](https://github.com/vitejs/vite/blob/main/CONTRIBUTING.md).
- [X] Read the [docs](https://vitejs.dev/guide).
- [X] Check that there isn't [already an issue](https://github.com/vitejs/vite/issues) that reports the same bug to avoid creating a duplicate.
- [X] Make sure this is a Vite issue and not a framework-specific issue. For example, if it's a Vue SFC related bug, it should likely be reported to https://github.com/vuejs/core instead.
- [X] Check that this is a concrete bug. For Q&A open a [GitHub Discussion](https://github.com/vitejs/vite/discussions) or join our [Discord Chat Server](https://chat.vitejs.dev/).
- [X] The provided reproduction is a [minimal reproducible example](https://stackoverflow.com/help/minimal-reproducible-example) of the bug.

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Uh oh!

Vite can use the wrong module if local or linked modules include their own `node_modules`, breaking Vue #7454

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Uh oh!

Vite can use the wrong module if local or linked modules include their own node_modules, breaking Vue #7454

Description

Describe the bug

Reproduction

System Info

Used Package Manager

Logs

Validations

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions

Vite can use the wrong module if local or linked modules include their own `node_modules`, breaking Vue #7454