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I kept re-doing the home base completely, because I wanted to make the most efficient thing that can have everything of practical use at once and be as immune to monsters as possible, and I stopped because I kind of did it. Flying monsters are stopped by any solid walls and you can make a ton of fun trap layouts that guarantee that walking enemies can't even have a chance to open the door, but wraiths/reapers screw up the system because they pass through ground and walls. The only way to to be immune to those too is by making a floating house. Then there's how during invasions and stuff, any monster can appear even inside covered houses, as long as it's not too close to where you currently are to see it appearing, so if the house is too big for the screen they will keep appearing on the part you're not on. Also, ground monsters can spawn above the roof, and besides eating up the spawn max before going away, this is a problem because if it's a wraith/reaper it immediately scales down to the inside even if you made sure they couldn't get in from below, and the only way to stop monsters from ever appearing above the house is by using construction blocks to build up the roof so far up that the top becomes "too far from player" to be a possible spawning point.
This is from an earlier save I had, taken with a ruler for counting blocks: http://images.akamai.steamusercontent.com/ugc/281846944705501070/A157A634AC0137D5CD1CE6C9B6590FE517F9B395/ I put the melee/ranged/magic/summon rows to make it easy to remember the equipment, and the transparent chests are the accessories. In the crafting room, the normal chest is pre-hardmode ore and the gold chest is post-hardmode ore. The lowered anvil still reaches up to work and the trash can is for storing general monster drops. The chest up-left of the alchemist table is for bottles/flowers/seeds and crafting water is right there. Near the middle, the blue chests are for inventory-accessories and mounts, the light brown chests are construction stuff like dirt and stone. Heal/buff items and boss triggers I leave with the piggy bank which you can spread in points of interest since they're all the same chest. Hellevator has fishing spots. You can make a small easy tree farm marked on the ground like that and you won't worry about wood again. The layout works great and I only wouldn't know how to make it prettier without changing function. All I know is that some construction blocks/walls give light and that's actually a bit convenient.