I am using sublime as the latex editor of choice, and I like it. You can learn more about it here. The only problem with the current workflow is that it creates all the output files and auxiliary files in the root directory. These additional files make a mess. I desire to keep things clean and minimal.

Today I found a solution for my problem. We need to set the aux_directory and the output_directory keys in the .sublime-project file. Sublime will then create all the additional folders and files in that directory. If you need to clean your LaTeX project, you only need to delete the cache folder.

{
   "folders":[
      {
         "file_exclude_patterns":[
            "*.cls",
            "*.md",
            "*.gitignore",
            "*.sublime-project"
         ],
         "path":"."
      }
   ],
   "settings":{
      "TEXroot":"thesis.tex",
      "ensure_newline_at_eof_on_save":true,
      "spell_check":true,
      "trim_trailing_white_space_on_save":true,
      "word_wrap":true,
      "wrap_width":100,
      "aux_directory":"cache",
      "output_directory":"cache"
   }
}

This procedure only works with TexLive in windows. On MAC, it works with MacTex. Unfortunately, it does not work with MikeTex.