Description

Prior to #1687 and #1995, Biome traversed all directories regardless of include and ignore.
Glob patterns of include and ignore were only tested on regular files.

Users were not able to prevent Biome from traversing a directory. This resulted in a performance penalty (when a large hierarchy was traversed for nothing) and reporting errors (broken symlinks and files with higher permissions).

#1687 fixed this by skipping folders that match at least one ignore pattern and folders that don't match all include patterns.
Unfortunately, this introduced a regression because it is likely that a folder don't match any include pattern.

Let's take an example:

❯ tree
.
├── biome.json
├── src
│   └── file.js

❯ cat biome.json
{
  "files": {
    "include": ["./**/*.js"]
  }
}

❯ biome format src
internalError/io ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

  ✖ No files were processed in the specified paths.

Here src/file.js is not processed because src doesn't match ./**/*.js.
This is an unexpected result.

To avoid this issue, #1995 doesn't match folders (including symlinks that target a folder) against include.

This fixed the regression. However, this partially reverts #1687 by not ignoring the folders in which all its files don't match all patterns of include.
For instance, the following configuration should prevent Biome from traversing the test folder.

❯ tree
.
├── biome.json
├── src
│   └── file.js
├── test
│   └── ...

❯ cat biome.json
{
  "files": {
    "include": ["./src/**/*.js"]
  }
}

To prevent Biome from visiting test, we should adopt a dedicated strategy for matching directories within include:
If a folder is not a prefix of at least one pattern of include, it should be ignored.
Here test/ is not a prefix of ./src/**/*.js. test/ is a valid prefix of ./**/*.js or ./test/**/*.js.

See #1995 for more context.