It has a loong-loong history.
Line numbering actually comes from Dartmouth BASIC, which was the original version of the BASIC programming language and was the integral part of a so called Dartmouth Time Sharing System. That DTSS had a rudimentary IDE, which was nothing more than an interactive command line.
So every line typed inside this "IDE", and beginning with a line number, was added to the program, replacing any previously stored line with the same number; anything else was assumed to be a DTSS command and immediately executed.
