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Drupal contains many, many template files. For a front-end developer, these are one of your greatest tools in taking over a Drupal theme and turning it into exactly what you need it to be. However, with power comes responsibility. Because working with template files is so easy, it's also an area where you can get in trouble quickly.
Most front-end developers experience some frustration working with Drupal's markup. Because it's relatively easy to go in and make changes, doing exactly that is often a first reflex. Resist it. While you'll definitely feel the power and control you have over things, changing too many template files is often the wrong approach. Just because you can change things doesn't always mean you should.