Relay-compiler will delete any file in a hidden directory!!

Running relay-compiler (tested v16-18) will remove files from `__generated__` in any hidden directory such as `.wtf/__generated__`

For example, when running relay-compiler, all files in `.nodevenv/lib/node_modules/npm/node_modules/@sigstore/protobuf-specs/dist/__generated__/` are nuked.

This happens even if I've set the exclude paths in relay.config.js

```
excludes: [
'.nodeenv/**',
'**/node_modules/**',
'**/__mocks__/**',
'**/__generated__/**',
],
```

It breaks my npm installation.

Start by reproducing the deletion with relay-compiler and the relay.config.js excludes shown in the report, using a hidden directory containing __generated__ files. Trace the compiler's exclude-path handling and verify that files under hidden directories and node_modules are preserved when the issue's exclude patterns are configured.

Written by the indexing model from the issue text.