diff --git a/scripts/decompile.sh b/scripts/decompile.sh
index a1b06a1f1d..d90a6de9da 100755
--- a/scripts/decompile.sh
+++ b/scripts/decompile.sh
@@ -73,7 +73,7 @@ if [ ! -d "$classdir" ]; then
     mkdir -p "$classdir"
     cd "$classdir"
     set +e
-    jar xf "$decompiledir/$minecraftversion-mapped.jar" net/minecraft/server
+    jar xf "$decompiledir/$minecraftversion-mapped.jar" net/minecraft
     if [ "$?" != "0" ]; then
         cd "$basedir"
         echo "Failed to extract NMS classes."
diff --git a/scripts/importmcdev.sh b/scripts/importmcdev.sh
index 0051a75308..597f797c1f 100755
--- a/scripts/importmcdev.sh
+++ b/scripts/importmcdev.sh
@@ -2,7 +2,7 @@
 
 (
 set -e
-nms="net/minecraft/server"
+nms="net/minecraft"
 export MODLOG=""
 PS1="$"
 basedir="$(cd "$1" && pwd -P)"
@@ -24,6 +24,7 @@ function import {
     if [[ ! -f "$target" ]]; then
         export MODLOG="$MODLOG  Imported $file from mc-dev\n";
         #echo "Copying $base to $target"
+        mkdir -p "$(dirname "$target")"
         cp "$base" "$target" || exit 1
     else
         echo "UN-NEEDED IMPORT: $file"
@@ -59,10 +60,9 @@ function importLibrary {
 )
 
 
+files=$(cat "$basedir/Spigot-Server-Patches/"* | grep "+++ b/src/main/java/net/minecraft/" | sort | uniq | sed 's/\+\+\+ b\/src\/main\/java\/net\/minecraft\///g')
 
-files=$(cat "$basedir/Spigot-Server-Patches/"* | grep "+++ b/src/main/java/net/minecraft/server/" | sort | uniq | sed 's/\+\+\+ b\/src\/main\/java\/net\/minecraft\/server\///g' | sed 's/.java//g')
-
-nonnms=$(grep -R "new file mode" -B 1 "$basedir/Spigot-Server-Patches/" | grep -v "new file mode" | grep -oE "net\/minecraft\/server\/.*.java" | grep -oE "[A-Za-z]+?.java$" --color=none | sed 's/.java//g')
+nonnms=$(grep -R "new file mode" -B 1 "$basedir/Spigot-Server-Patches/" | grep -v "new file mode" | grep -oE "net\/minecraft\/**\/.*.java" | grep -oE "[A-Za-z]+?.java$" --color=none | sed 's/.java//g')
 function containsElement {
 	local e
 	for e in "${@:2}"; do
@@ -74,7 +74,8 @@ set +e
 for f in $files; do
 	containsElement "$f" ${nonnms[@]}
 	if [ "$?" == "1" ]; then
-		if [ ! -f "$workdir/Spigot/Spigot-Server/src/main/java/net/minecraft/server/$f.java" ]; then
+		if [ ! -f "$workdir/Spigot/Spigot-Server/src/main/java/net/minecraft/$f" ]; then
+      f="$(echo "$f" | sed 's/.java//g')"
 			if [ ! -f "$decompiledir/$nms/$f.java" ]; then
 				echo "$(color 1 31) ERROR!!! Missing NMS$(color 1 34) $f $(colorend)";
 			else
diff --git a/scripts/init.sh b/scripts/init.sh
index 3b85343d6c..9c51762ae6 100755
--- a/scripts/init.sh
+++ b/scripts/init.sh
@@ -7,8 +7,8 @@ basedir="$(cd "$1" && pwd -P)"
 workdir="$basedir/work"
 minecraftversion=$(cat "$workdir/BuildData/info.json"  | grep minecraftVersion | cut -d '"' -f 4)
 spigotdecompiledir="$workdir/Minecraft/$minecraftversion/spigot"
-nms="$spigotdecompiledir/net/minecraft/server"
-cb="src/main/java/net/minecraft/server"
+nms="$spigotdecompiledir"
+cb="src/main/java"
 gitcmd="git -c commit.gpgsign=false"
 
 # https://stackoverflow.com/a/38595160
@@ -45,31 +45,31 @@ done
 echo "Applying CraftBukkit patches to NMS..."
 cd "$workdir/CraftBukkit"
 $gitcmd checkout -B patched HEAD >/dev/null 2>&1
-rm -rf "$cb"
-mkdir -p "$cb"
+rm -rf "$cb/net"
 # create baseline NMS import so we can see diff of what CB changed
-for file in $(ls nms-patches)
+while IFS= read -r -d '' file
 do
-    patchFile="nms-patches/$file"
-    file="$(echo "$file" | cut -d. -f1).java"
+    patchFile="$file"
+    file="$(echo "$file" | cut -d "/" -f2- | cut -d. -f1).java"
+    mkdir -p "$(dirname $cb/"$file")"
     cp "$nms/$file" "$cb/$file"
-done
+done <   <(find nms-patches -type f -print0)
 $gitcmd add src
 $gitcmd commit -m "Minecraft $ $(date)" --author="Vanilla <auto@mated.null>"
 
 # apply patches
-for file in $(ls nms-patches)
+while IFS= read -r -d '' file
 do
-    patchFile="nms-patches/$file"
-    file="$(echo "$file" | cut -d. -f1).java"
+    patchFile="$file"
+    file="$(echo "$file" | cut -d "/" -f2- | cut -d. -f1).java"
 
     echo "Patching $file < $patchFile"
     set +e
     strip_cr "$nms/$file" > /dev/null
     set -e
 
-    "$patch" -s -d src/main/java/ "net/minecraft/server/$file" < "$patchFile"
-done
+    "$patch" -d src/main/java -p 1 < "$patchFile"
+done <   <(find nms-patches -type f -print0)
 
 $gitcmd add src
 $gitcmd commit -m "CraftBukkit $ $(date)" --author="CraftBukkit <auto@mated.null>"