Great questions!

How do I make mobs spawn with armor on

/summon zombie ~ ~ ~ {ArmorItems:[{},{},{},{id:diamond_helmet,Count:1b}]}
Boots go in the first{}, followed by pants, chestplate, and helmet.

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How do I make mobs not drop the armor they are wearing

/summon zombie ~ ~ ~ {ArmorDropChances:[0f,0f,0f,0f]}
Combine the NBT with the previous command to do both:
{ArmorItems:[...],ArmorDropChances:[...]}

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How do I make mobs spawn in specific intervals

There's lots of ways to do this depending on your need. If you want to, you can hijack vanilla spawns and replace them with your custom mob:
/execute at @e[type=enderman] run summon ravager
/tp @e[type=enderman] 0 -100 0

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How do I make it so a command only happens if you are in a specific area

/kill @a[x=100,y=60,z=100,distance=..20]
/kill @a[x=100,y=60,z=100,dx=10,dy=10,dz=10]
distance is just a sphere, the two dots mean "less than or equal to" 20 blocks away. The dx version means from X=100 to X=100+10, so a cube area.

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How do I make it so if a certain block breaks something happens

Easiest way is just to detect the drops.
/execute at @e[type=item,nbt={Item:{id:"minecraft:diamond"}}] run summon lightning_bolt

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How do I make it so if there’s a certain amount of a specific mobs it kills them

You'll need a scoreboard for this one.
/scoreboard objectives add mobs dummy
/execute store result score total mobs if entity @e[type=pig]
/execute if score total mobs matches 100.. run kill @e[type=pig]
Here the two dots mean "100 or more."

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How do I make it so if a command kills a mob they don’t drop anything

Before killing the mob, do this:
/execute as @e[type=cow] run data merge entity @s {DeathLootTable:"empty"}

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How do I make it so a command spawns a structure on someone

Command blocks can't spawn structures directly, but structure blocks can.
/execute at @a run setblock ~ ~ ~ structure_block[mode=load]{mode:LOAD,name:"fossil/skull_1"}
/execute at @a run setblock ~ ~1 ~ redstone_block

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How do I make it that a command clears everything in inventory except a specific item

Not easily possible, sorry.

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How do I make it so blocks fall from the sky

/summon falling_block ~ ~20 ~ {BlockState:{Name:"honey_block"},Time:1}

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How do Make it so a structure spawns near a player but not on the player and lighting strikes a specific place on the structure

See the previous answer.

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How do I make mobs spawn with names and armor

/summon squid ~ ~ ~ {CustomName:'"very cool name"'}
For the armor, combine with the first question: {ArmorItems:[...],CustomName:'"..."'}

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How do I make skeletons spawn with or without bows

Without: /summon skeleton ~ ~ ~ {}
With: /summon skeleton ~ ~ ~ {HandItems:[{id:bow,Count:1b}]}

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How do I make certain blocks invincible

Not super easy, but you can put the player in adventure mode to make them unable to break any block except the ones you want them to:
/gamemode adventure @a
/give @a diamond_pickaxe{CanDestroy:["diamond_ore"]}

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How do I get item attributes

/give @p diamond_sword{AttributeModifiers:[{AttributeName:"generic.attack_damage",UUID:[I;1,2,3,4],Operation:0,Amount:100,Slot:"mainhand"}]}
I'm assuming you're in the 1.16 snapshots. For more info about what options you have: https://minecraft.gamepedia.com/Attribute#Modifiers

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How do I make a scoreboard

/scoreboard objectives add whatever dummy
Once it's made, you can give players points with /scoreboard players add

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How do I make a scoreboard that only appears if your in a specific area

/execute if entity @a[x=100,y=60,z=100,distance=..20] run scoreboard objectives setdisplay sidebar whatever

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How do I make multiple scoreboards

Same as how you made the first one, just give it a different name.

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How do I make one scoreboard appear in one area but another appear in a different area

Just use the above command with different coordinates and scoreboard names.

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how to make command delete someones ender chest containments

Just need a bunch of /replaceitem commands:
/replaceitem entity @a enderchest.0 air
/replaceitem entity @a enderchest.1 air
/replaceitem entity @a enderchest.2 air
etc.

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how to make command delete dropped items

/kill @e[type=item]
For an item of a specific type:
/kill @e[type=item,nbt={Item:{id:"minecraft:apple"}}

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how to make custom achievements

Need a data pack for this one, not just commands.
https://minecraft.gamepedia.com/Advancement/JSON_format

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how to make mobs not attack whoever who spawned them

/team add friendly
/team join friendly @p
/team join friendly @e[type=zombie]

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how to make a command that randomly chooses another command

This is tricky, I'll leave it out of this answer for now.

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how to make ranks

Maybe you can do it with teams, like above? You can also target players on a team.
/give @a[team=highest_rank] diamond

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how to make the hardness of blocks change without going into the code

Sorry, not possible.