Write Atom.desktop file directly from template

Previously running `sudo script/grunt install` followed by `script/grunt mkdeb` would result in an error since the file created at `resources/linux/Atom.desktop` would be owned by root.

Now this file is directly written to the install location instead of written into the source tree and the copied over.

Refs #2129
This diff was because I installed temp in a commit, then reverted and used the build folder instead. Newer versions of npm sort this list which explains the remaining diff.

I think I'm going to leave this diff in so it will be sorted going forwards.