In com.blamejared.compat.thaumcraft.handlers.handlers.Crucible
on line 90
You should check whether output is null before checking whether it is empty.

Here is the relevant piece from my log:

[AVAILABLE][CLIENT][INFO] Altering Crucible Recipe(s) for Unknown item
[AVAILABLE][CLIENT][ERROR] Error while applying actions
java.lang.NullPointerException
at com.blamejared.compat.thaumcraft.handlers.handlers.Crucible$Remove.apply(Crucible.java:90)
at crafttweaker.runtime.CrTTweaker.apply(CrTTweaker.java:57)
at crafttweaker.CraftTweakerAPI.apply(CraftTweakerAPI.java:146)
at java.lang.Iterable.forEach(Unknown Source)
at com.blamejared.ModTweaker.loadComplete(ModTweaker.java:41)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at net.minecraftforge.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:624)
at sun.reflect.GeneratedMethodAccessor10.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:91)
at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:150)
at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:76)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:71)
at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:116)
at com.google.common.eventbus.EventBus.post(EventBus.java:217)
at net.minecraftforge.fml.common.LoadController.sendEventToModContainer(LoadController.java:219)
at net.minecraftforge.fml.common.LoadController.propogateStateMessage(LoadController.java:197)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:91)
at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:150)
at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:76)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:71)
at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:116)
at com.google.common.eventbus.EventBus.post(EventBus.java:217)
at net.minecraftforge.fml.common.LoadController.distributeStateMessage(LoadController.java:136)
at net.minecraftforge.fml.common.Loader.initializeMods(Loader.java:752)
at net.minecraftforge.fml.client.FMLClientHandler.finishMinecraftLoading(FMLClientHandler.java:336)
at net.minecraft.client.Minecraft.func_71384_a(Minecraft.java:535)
at net.minecraft.client.Minecraft.func_99999_d(Minecraft.java:3931)
at net.minecraft.client.main.Main.main(SourceFile:123)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at net.minecraft.launchwrapper.Launch.launch(Launch.java:135)
at net.minecraft.launchwrapper.Launch.main(Launch.java:28)

Or you could follow our template and make all of our lives easier. If you don't do anything stupid, the output shouldn't be null.

Sorry about not using the template. I would have done that if I was merely reporting the bug.

Instead, I decided to look at the code and debug it myself, so I was just telling you about the fix that I came up with.

A different way to fix it would be to change that "if" to an "else if".