Use sensible AssertionError instead of ambiguous RuntimeException
Implement deprecated methods. Adds BUKKIT-5752
POM Changes

Basic changes to the build system which mark the artifact as Spigot, and the necessary code changes to ensure proper functionality. Also disables the auto updater provided by CraftBukkit as it is useless to us.
mc-dev imports

Imported files which are only modified by Spigot, not upstream. Files here should be completely unmodified aside from trivial changes such as adding throws statements to ensure proper compilation. You may need to add unrelated files in order to ensure a compilable result in the face of synthetic methods.
Skeleton API Implementations

This contains the basic, empty implementations for some Spigot-API extensions. They are included early in the patching progress so that compilation will still succeed midway despite the APIs only being provided by subsequent patches.
Obfuscation Helpers

Provides several friendly named methods which map to a obfuscated method. Obfuscated methods which are used frequently should be added to this file to ease with updates to new Minecraft versions.
Spigot Configuration

Provides the basic infrastructure to load and save the Spigot configuration file, spigot.yml
Better Chunk Tick Selection

An optimized chunk ticking algorithm which better selects chunks around players which are active on the server.
Crop Growth Rates

Allows configuring the growth rates of crops as a percentage of their normal growth rate.
More Efficient Chunk Save Queue

Optimizes the data structures behind the chunk save queue into ones more suitable for the type of data and access which they are used for.
Merge tweaks and configuration

This allows the merging of Experience orbs, as well as the configuration of the merge radius of items. Additionally it refactors the merge algorithm to be a better experience for players.
LongHash Tweaks

Tweaks the LongHash algorithm and provides a large array based map to look up values centered around the origin, ie the access normally seen on a Minecraft server.
Async Operation Catching

Catch and throw an exception when a potentially unsafe operation occurs on a thread other than the main server thread.
View Distance

This commit allows the user to select per world view distances, and view distances below 3. Be wary of the issues selecting a view distance of 1 or 2 may cause!
Spigot Timings

Overhauls the Timings System adding performance tracking all around the Minecraft Server
Fix Mob Spawning Relative to View Distance

Changes the mob spawning algorithm to properly account for view distance and the range around players.

Needs better documentation.
Handle Null Tile Entities
Entity Activation Range

This feature gives 3 new configurable ranges that if an entity of the matching type is outside of this radius of any player, will tick at 5% of its normal rate.

This will drastically cut down on tick timings for entities that are not in range of a user to actually be "used".
This change can have dramatic impact on gameplay if configured too low. Balance according to your servers desired gameplay.
Metrics
PlayerItemDamageEvent