One of the best way to learn music theory (much of which is harmony) is to play jazz, or jazz-inspired styles of music – you'll get the most exposure to the most diverse array of concepts in the least amount of time (not saying it will be a short amount of time – just compared to, say, being a classical musician). The emphasis on improvisation requires players to have comprehensive understanding of the underlying harmonic concepts – you can play jazz completely by ear, but this is not the norm by any means.

As a couple of commenters have said, your HTML analogy just doesn't seem to fit here, music theory is descriptive, not prescriptive. The best way to learn it is through playing music, a lot, and then using concepts from music theory to go back and gain more insight into why certain things sound the way they do, why certain progressions work well, why an F natural sounds ethereal and sublime on top of a B∆9 chord while an E natural sounds awful, and so on.

Again, I believe the optimal way to learn music concepts is to play (not study) music.

If jazz doesn't interest you, I would ask you what your musical goals are, and what genres do interest you, and just encourage you to play, and then play some more. Ideally, play with musicians who are better than you - you'll learn more, faster, just like anything else. It takes thousands of hours to get good at this stuff.