Set bin/regreph and bin/bench as binaries in composer.json

- Rename the binaries to remove the `.php` extensions.
  It could be confusing if you need to include them in your code or run them on the CLI.
- Make the files executable.
- Add a useful shebang to the top of the binary files.
- Add them to the `bin` section in `composer.json`.
  It is not only informative to the people reading `composer.json`, but Composer would
  move them to `vendor/bin/` when `regreph` is installed as a dependency.
  See https://github.com/sebastianbergmann/phpunit/blob/master/composer.json#L47
  See https://getcomposer.org/doc/articles/vendor-binaries.md
- Update examples in the readme.