The project pane is nice, unless you're trying to edit a single file and it takes up too much space. Originally an Atom bug/feature, Pulsar's init is now in Javascript.
File > Init script
(function() { atom.workspace.onDidOpen(function(arg) { var dock, item, itemName; item = arg.item; itemName = item.constructor.name; if (itemName !== 'TreeView') { dock = atom.workspace.paneContainerForURI('atom://tree-view'); if (dock && dock.isVisible()) { return dock.hide(); } } }); }).call(this);