What type of punctuation signals the reader that words from the direct quote have been changed but the writer?

That would have to be an ellipsis. When you say something like, "There was only one catch, and that was Catch-22, which specified that a concern for one's own safety in the face of dangers that were real and immediate was the process of a rational mind. Orr was crazy and could be grounded (blah blah) " (Joseph Heller 46).

OR

,"There was only one catch, and that was Catch-22, ... Orr was crazy and could be grounded (blah blah) " (Joseph Heller 46).