On the trail, comfort is relative. It's unlikely that you'll be as clean as you want or get as much sleep as you want. You should, however, aim to stay as dry as possible. Dry clothes and shoes help prevent blisters and keep you warm, and dry gear is lighter than wet gear.
So, how can you keep your backpack and all of its contents dry?
Even a waterproof backpack will not keep your equipment dry in a torrential downpour. There are a variety of waterproof covers you can choose from that will keep your backpack dry, but many people prefer to cover their backpacks with a garbage bag during the rain. In addition to covering your backpack, make sure that everything in the backpack is packed in a zip-top plastic bag or stuff sack as an additional layer of protection.
What if it's raining when you set up camp for the night? Or, what if you're camping in a wet area? Few materials, even those labeled waterproof, will remain so if left sitting in a puddle of water overnight. Provide your backpack with as much protection as possible -- cover it and hang it up, or at least elevate it somehow a few inches from the wet ground. Minimize the number of times you open your backpack in rainy weather. That way you don't allow moisture into the pack and then trap it there. When the weather dries out, empty your pack and let some sunshine in to prevent mold and mildew from growing inside.
If wet weather sets in for the day while you are backpacking, you have the choice to either hike through it or hunker down in camp for a zero day, or day of rest. If the weather is mild and the walking easy, hiking in the rain will keep you warm and pass the time. If the trail is rough, you're hiking off-trail, you must ford streams or rivers or the weather is cold, it makes sense to stay in camp for the day and wait for the weather to improve.
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