When saving a file for the first time after opening Atom, the process takes much longer than normal. The issue goes away when opening Atom in safe mode or disabling the beautify package. After the first save, everything works as normal.
Here is a link to the debug.md Gist: https://gist.github.com/philippelesaux/34138a193b5762f47d170fc2c87d080f
Here is a screenshot of my profile as the issue happens:

And here is my saved cpu profile from the screenshot:
https://dl.dropboxusercontent.com/u/13874732/CPU-20160328T184112.cpuprofile
debug.md Gist to this issueI have experienced this, too, however I was not sure if it was Atom Beautify. Now that multiple users (including myself) have confirmed it, I deem this issue top priority.
I'm working on it now. Thank you for your patience!
Published to v0.29.0
Let me know if it is still slow! This should be a fairly dramatic performance improvement when the package activates. Still more improvements to go!
I'm not sure why I reopened this. Regardless, I will be looking to make performance improvements in future releases 馃槂 .
I also remember that your package took a lot of time to install on 5200 RPM HDD, maybe like ~15 minutes. I was surprised today that it took only a couple of seconds to install your package. Job well done! 馃槂
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I also remember that your package took a lot of time to install on 5200 RPM HDD, maybe like ~15 minutes. I was surprised today that it took only a couple of seconds to install your package. Job well done! 馃槂