Falling back to patching base and 3-way merge...
CONFLICT (modify/delete): src/main/java/net/minecraft/server/MinecraftServer.java deleted in HEAD and modified in Obfuscation Helpers. Version Obfuscation Helpers of src/main/java/net/minecraft/server/MinecraftServer.java left in tree.
Patch failed at 0004 Obfuscation Helpers
The copy of the patch that failed is found in: .git/rebase-apply/patch
When you have resolved this problem, run "git am --continue".
If you prefer to skip this patch, run "git am --skip" instead.
To restore the original branch and stop patching, run "git am --abort".
  Something did not apply cleanly to Spigot-Server.
  Please review above details and finish the apply then
  save the changes with rebuildPatches.sh
Error compiling Spigot. Please check the wiki for FAQs.
If this does not resolve your issue then please pastebin the entire BuildTools.log.txt file when seeking support.
java.lang.RuntimeException: Error running command, return status !=0: [sh, applyPatches.sh]
        at org.spigotmc.builder.Builder.runProcess0(Builder.java:637)
        at org.spigotmc.builder.Builder.runProcess(Builder.java:595)
        at org.spigotmc.builder.Builder.main(Builder.java:476)
        at org.spigotmc.builder.Bootstrap.main(Bootstrap.java:23)