Strip only trailing whitespace, not newlines. Also, strip *all* trailing whitespace, not just the first.

spec/app/extensions/strip-trailing-whitespace-spec.coffee

@@ -7,7 +7,7 @@ describe "StripTrailingWhitespace", ->
 
   beforeEach ->
     rootView = new RootView
-    StripTrailingWhitespace.initialize(rootView)
+    StripTrailingWhitespace.activate(rootView)
     rootView.focus()
     editor = rootView.activeEditor()
 
@@ -15,9 +15,9 @@ describe "StripTrailingWhitespace", ->
     spyOn(fs, 'write')
 
     # works for buffers that are already open when extension is initialized
-    editor.insertText("foo   ")
+    editor.insertText("foo   \nbar\t   \n\nbaz")
     editor.buffer.saveAs("/tmp/test")
-    expect(editor.buffer.getText()).toBe "foo"
+    expect(editor.buffer.getText()).toBe "foo\nbar\n\nbaz"
 
     # works for buffers that are opened after extension is initialized
     rootView.open(require.resolve('fixtures/sample.txt'))
@@ -25,4 +25,4 @@ describe "StripTrailingWhitespace", ->
     editor.insertText("           ")
 
     editor.buffer.save()
-    expect(editor.buffer.getText()).toBe 'Some text.'
+    expect(editor.buffer.getText()).toBe 'Some text.\n'

src/app/extensions/strip-trailing-whitespace.coffee

@@ -1,5 +1,5 @@
 module.exports =
-  initialize: (rootView) ->
+  activate: (rootView) ->
     for buffer in rootView.project.buffers
       @stripTrailingWhitespaceBeforeSave(buffer)
 
@@ -8,5 +8,5 @@ module.exports =
 
   stripTrailingWhitespaceBeforeSave: (buffer) ->
     buffer.on 'before-save', ->
-      buffer.scan /\s+$/, (match, range, { replace }) ->
+      buffer.scan /[ \t]+$/g, (match, range, { replace }) ->
         replace('')