Change in output directory when upgrading from 2.3.0 to 3.1.1

[nstuyvesant]

Describe the bug

In a monorepo I am working on (@carbon/charts), there is a package called core. For that package, when I run yarn build:package with vite-plugin-dts@2.3.0, it runs vite and outputs the type declarations to dist with the correct paths (mirroring src).

When I bump vite-plugin-dts to 3.x (now 3..1.1) with no other configuration changes to tsconfig.json or vite.config.ts, the type declarations are being output to dist/dist/core/src instead of dist as they were previously.

Steps to reproduce:

git clone https://github.com/carbon-design-system/carbon-charts.git
cd carbon-charts
yarn install
cd packages/core
yarn build:package
# Now examine packages/core/dist - type declarations look good because we are on 2.3.0
# Modify packages/core/packages.json and change the version of `vite-plugin-dts` to `^3.1.1`
yarn build:package
# Examine dist and you'll see the type declarations in `dist/dist/core/src` instead of `dist`

Reproduction

See above

Steps to reproduce

See above

System Info

System:
    OS: macOS 13.4.1
    CPU: (10) arm64 Apple M1 Pro
    Memory: 7.32 GB / 32.00 GB
    Shell: 5.9 - /bin/zsh
  Binaries:
    Node: 18.16.1 - /opt/homebrew/bin/node
    Yarn: 3.5.1 - /opt/homebrew/bin/yarn
    npm: 9.8.0 - /opt/homebrew/bin/npm
  Browsers:
    Chrome: 114.0.5735.198
    Firefox: 114.0.2
    Safari: 16.5.1
  npmPackages:
    vite: ^4.4.2 => 4.4.2 
    vite-plugin-dts: ^3.1.1 => 3.1.1

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[nstuyvesant]

I suspect it is redefining the root as I have a file called packages/core/src/demo/utils/package-versions.ts that imports the package.json files from the other packages. This is technically a TypeScript compilation error because those package.json files are outside of my root directory - but it's also intentional because I don't need to type JSON files and I don't want type declaration generated for all packages.

[qmhc]

There are some incorrect when process public directory of entries.

Some limitations in v2 (led to some type errors) have gone in v3, the behavior most similar to tsc now. So you can specify entryRoot: 'src' (or override rootDir) to ensure result equivalents to use tsc (after the fix is released).