Any idea why the pkg process in OS X Yosemite (10.10.2) would replace the Markup.appex plug-in Preview?
Markup.appex is a new extension that was added in Yosemite. It delivers the Markup feature shown on Apple's Yosemite page:


  Mark up attachments right in Mail. It happens often. Someone sends you
  an attachment that requires quick feedback. It could be a form you
  need to fill out and sign or an image you need to comment on. Markup
  lets you respond quickly to these requests without opening the file in
  another app. Just click Reply and add your notations right in your
  response. Add shapes, text, and callouts to images by drawing on the
  Multi‑Touch trackpad. Fill out forms and PDFs, and add your signature
  by signing with your finger on the trackpad or capturing it with the
  camera on your Mac


Is it possible you installed the 10.10.2 update lately?