In src/moduleutils/PhutilBootloader.php:

if (empty($_SERVER['PHUTIL_DISABLE_RUNTIME_EXTENSIONS'])) {
      $extdir = $path.DIRECTORY_SEPARATOR.'extensions';
      if (Filesystem::pathExists($extdir)) {
        $extensions = id(new FileFinder($extdir))
          ->withSuffix('php')
          ->withType('f')
          ->withFollowSymlinks(true)
          ->setForceMode('php')
          ->find();

        foreach ($extensions as $extension) {
          $this->loadExtension(
            $name,
            $path,
            $extdir.DIRECTORY_SEPARATOR.$extension);
        }
      }
    }

the code selects all regular files whose filename ends with .php. While debugging custom extensions' problems (after ugprading Phabricator to latest), users got arcanist errors

Usage Exception: Failed to connect to server (https://our.phab.domain/api/): [HTTP/500] Internal Server Error
[Core Exception/PhutilBootloaderException] Include of extension file '/usr/local/lib/php/phabricator/src/extensions/.#OurCustomField.php' failed!

and that's because the admin was live-editing the extension file with the editor "joe" which saves backup files .#thefilename. Vim is a bit nicer by changing the file extension (appends .swp or ~).

Therefore: Hidden files, i.e. the ones starting with a dot, should most probably be excluded from the search.