I also want to add my support to having project support in Atom. I would also like to request this incorporates a little useful feature that existed in Textmate 1 (and e-texteditor on Win). Sublime has a limitation where projects can only contain folders at top level and not files. And for a number of projects I have use folder from one location and then random files from another (a good example would be a “project” that I use to manage web server config, such as mysql.ini, php.ini and apache confs).
In TM1 this was possible (dont get me started on TM2), but in Sublime this was never possible and was a real bug bear of mine.