Builtin optimize deletes files in root & node_modules

[rubas]

When I'm using the built in optimize & bundler, the command snowpack build deletes some files my project root (alias issue?) as well a lot in node_modules with the step Removing bundled source file.

ls node_modules/zod/lib/cjs/index.js
-> node_modules/zod/lib/cjs/index.js

snowpack build --verbose
[...]
[snowpack] Removing bundled source file: node_modules/zod/lib/cjs/index.js
[...]

ls node_modules/zod/lib/cjs/index.js
"node_modules/zod/lib/cjs/index.js": No such file or directory (os error 2)

---

snowpack.config.js

const path = require('path')
const root = 'theme/src/ts'

/** @type {import("snowpack").SnowpackUserConfig } */
module.exports = {
  root,
  alias: {
    '@app': path.resolve(root, 'app'),
    '@components': path.resolve(root, 'components'),
    '@config': path.resolve(root, 'config'),
    '@graphql': path.resolve(root, 'graphql'),
    '@hooks': path.resolve(root, 'hooks'),
    '@i18n': path.resolve(root, 'i18n'),
    '@provider': path.resolve(root, 'provider'),
    '@relay': path.resolve(root, 'relay'),
    '@utils': path.resolve(root, 'utils')
  },
  exclude: ['snowpack.crt', 'snowpack.key', 'aws-export.js'],
  mount: {
    [root]: { url: '/', resolve: false }
  },
  plugins: ['@snowpack/plugin-react-refresh', '@snowpack/plugin-dotenv'],
  // plugins: ['@snowpack/plugin-react-refresh', '@snowpack/plugin-dotenv', '@snowpack/plugin-typescript'],
  packageOptions: {},
  devOptions: {
    open: 'none',
    secure: true
  },
  buildOptions: {
    out: 'theme/dist/js'
  },
  optimize: {
    entrypoints: ['app/forms/contact/index.js', 'app/forms/jobs/index.js'],
    threeshake: true,
    bundle: true,
    minify: true,
    target: 'es2018'
  }
}

Using snowpack version 3.0.11.

[rubas]

Reason: src/build/optimise.ts#L505

if (options.bundle) {
    for (const bundledInput of Object.keys(manifest.inputs)) {
      if (!manifest.outputs![bundledInput]) {
        logger.debug(
          `Removing bundled source file: ${path.resolve(buildDirectoryLoc, bundledInput)}`,
        );
        await fs.unlink(path.resolve(buildDirectoryLoc, bundledInput));
      }
    }

The manifest shows relative paths for node_modules like "../../../node_modules/@material-ui/core/esm/NativeSelect/NativeSelectInput.js".