The #{MRUBY_ROOT}/build and {MRUBY_ROOT}/bin directories, which are now hardcoded by this PR, can still be replaced.

• Alternatives to the #{MRUBY_ROOT}/build directory can be specified with the MRuby::Build#build_dir= accessor.
• The {MRUBY_ROOT}/bin directory can be replaced by the INSTALL_DIR environment variable.
  NOTE: There is no documentation for the INSTALL_DIR environment variable, so I believe it is a hidden feature.

Also, #{MRUBY_ROOT}/build/repos/#{MRuby::Build#name} contains a git clone of the third party mrbgems.
The git repository is also removed by rake clean with this PR, so people who are in the middle of modifying other people's code may have trouble with rake clean.
NOTE: The MRuby::Build#gem_clone_dir= accessor allows you to specify an alternative, but I believe it is a hidden feature that is not documented.

Therefore, I will create a PR to revert to.

In my opinion, if the content of this PR is needed, it would be better to define it as a different task than rake clean or rake deep_clean.