Server settings are set with three files: bukkit.yml containing bukkit specific settings, spigot.yml for the spigot settings, paper for paper settings, and server.properties for minecraft settings.

This complete cluster***k of settings is because of the history of development of the server API.
In the beginning there was Bukkit API, which introduced settings specific to Bukkit. Spigot is a performance-based fork on the now defunct Bukkit API, which also added additional settings. Paper is an even more performant and configurable fork of Spigot and also adds extra settings.

I personally don't think there's a single dev anymore who knows what settings takes precedence to another, but these are the default files that are generated on a fresh install.


[CODE lang="yaml" title="bukkit.yml"]# This is the main configuration file for Bukkit.
# As you can see, there's actually not that much to configure without any plugins.
# For a reference for any variable inside this file, check out the Bukkit Wiki at
# https://www.spigotmc.org/go/bukkit-yml
#
# If you need help on this file, feel free to join us on irc or leave a message
# on the forums asking for advice.
#
# IRC: #spigot @ irc.spi.gt
# (If this means nothing to you, just go to https://www.spigotmc.org/go/irc )
# Forums: https://www.spigotmc.org/
# Bug tracker: https://www.spigotmc.org/go/bugs


settings:
allow-end: true
warn-on-overload: true
permissions-file: permissions.yml
update-folder: update
plugin-profiling: false
connection-throttle: 4000
query-plugins: true
deprecated-verbose: default
shutdown-message: Server closed
minimum-api: none
spawn-limits:
monsters: 70
animals: 10
water-animals: 15
ambient: 15
chunk-gc:
period-in-ticks: 600
ticks-per:
animal-spawns: 400
monster-spawns: 1
water-spawns: 1
ambient-spawns: 1
autosave: 6000
aliases: now-in-Commands.yml[/CODE]

Taken from the official BukkitWiki

[CODE lang="yaml" title="paper.yml"]# This is the main configuration file for Paper.
# As you can see, there's tons to configure. Some options may impact gameplay, so use
# with caution, and make sure you know what each option does before configuring.
#
# If you need help with the configuration or have any questions related to Paper,
# join us in our Discord or IRC channel.
#
# Discord: https://paperdiscord.emc.gs
# IRC: #paper @ irc.spi.gt ( http://irc.spi.gt/iris/?channels=paper )
# Website: https://papermc.io/
# Docs: https://paper.readthedocs.org/

verbose: false
config-version: 20
settings:
load-permissions-yml-before-plugins: true
bungee-online-mode: true
region-file-cache-size: 256
incoming-packet-spam-threshold: 300
use-alternative-luck-formula: false
save-player-data: true
suggest-player-names-when-null-tab-completions: true
enable-player-collisions: true
chunk-tasks-per-tick: 1000
save-empty-scoreboard-teams: false
velocity-support:
enabled: false
online-mode: false
secret: ''
watchdog:
early-warning-every: 5000
early-warning-delay: 10000
spam-limiter:
tab-spam-increment: 1
tab-spam-limit: 500
book-size:
page-max: 2560
total-multiplier: 0.98
async-chunks:
enable: true
threads: -1
messages:
no-permission: '&cI''m sorry, but you do not have permission to perform this command.
Please contact the server administrators if you believe that this is in error.'
kick:
authentication-servers-down: ''
connection-throttle: Connection throttled! Please wait before reconnecting.
flying-player: Flying is not enabled on this server
flying-vehicle: Flying is not enabled on this server
timings:
enabled: true
verbose: true
server-name-privacy: false
hidden-config-entries:
- database
- settings.bungeecord-addresses
history-interval: 300
history-length: 3600
server-name: Unknown Server
[/CODE]

Paper documentation

[CODE lang="yaml" title="server.properties"]#Minecraft server properties
#Sun May 17 07:15:31 CEST 2020
spawn-protection=16
max-tick-time=60000
query.port=25565
generator-settings=
force-gamemode=false
allow-nether=true
enforce-whitelist=false
gamemode=survival
broadcast-console-to-ops=true
enable-query=false
player-idle-timeout=0
difficulty=easy
spawn-monsters=true
broadcast-rcon-to-ops=true
op-permission-level=4
pvp=true
snooper-enabled=true
level-type=default
hardcore=false
enable-command-block=false
max-players=20
network-compression-threshold=256
resource-pack-sha1=
max-world-size=29999984
function-permission-level=2
rcon.port=25575
server-port=25565
debug=false
server-ip=
spawn-npcs=true
allow-flight=false
level-name=world
view-distance=10
resource-pack=
spawn-animals=true
white-list=false
rcon.password=
generate-structures=true
max-build-height=256
online-mode=true
level-seed=
use-native-transport=true
prevent-proxy-connections=false
enable-rcon=false
motd=A Minecraft Server
[/CODE]

Description at Minecraft gamepedia