True, you must read the perldocs to truly grasp the power of the command line switches. Perl is a beast when it comes to text file molesting.
Basically your one-liner there is doing an inline edit on a file (inline means it makes a backup of the original file, and then creates a new file in it's place, the new file's content being the output from the one-liner, which in this case will print out every line of the original file MINUS the lines that match the regex. The regex will match lines containing "<built-in>" or "<command line>".
The one-liner is expecting to molest two separate files: 'makefile', and 'x2p/makefile'.
And if I may advise: You don't need the 'l', it adds newlines to the end of print statements, which you should already be present since you are iterating over each line via the 'n' switch.
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