diff --git a/.gitignore b/.gitignore
index 658890931..143c73b2a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,7 +22,16 @@ build/
 bin/
 dist/
 manifest.mf
-work/
+
+work/1.*
+work/BuildData
+work/Bukkit
+work/CraftBukkit
+work/Paperclip
+work/Spigot
+work/Spigot-Server
+work/Spigot-API
+work/*.jar
 
 # Mac filesystem dust
 .DS_Store/
@@ -37,15 +46,11 @@ work/
 *~
 
 # other stuff
-Spigot-API
-Spigot-Server
+
 Paper-Server
 Paper-API
 PaperSpigot-Server
 PaperSpigot-API
-Bukkit
-CraftBukkit
-Paperclip
 Paperclip.jar
 paperclip.jar
 paperclip-*.jar
diff --git a/.gitmodules b/.gitmodules
index f8d5e238f..758536e06 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,15 +1,15 @@
-[submodule "Bukkit"]
-	path = Bukkit
+[submodule "work/Bukkit"]
+	path = work/Bukkit
 	url = https://hub.spigotmc.org/stash/scm/spigot/bukkit.git
-[submodule "CraftBukkit"]
-	path = CraftBukkit
+[submodule "work/CraftBukkit"]
+	path = work/CraftBukkit
 	url = https://hub.spigotmc.org/stash/scm/spigot/craftbukkit.git
-[submodule "BuildData"]
-	path = BuildData
+[submodule "work/BuildData"]
+	path = work/BuildData
 	url = https://hub.spigotmc.org/stash/scm/spigot/builddata.git
-[submodule "Paperclip"]
-	path = Paperclip
-	url = https://github.com/PaperMC/Paperclip.git
-[submodule "Spigot"]
-	path = Spigot
+[submodule "work/Spigot"]
+	path = work/Spigot
 	url = https://hub.spigotmc.org/stash/scm/spigot/spigot.git
+[submodule "work/Paperclip"]
+	path = work/Paperclip
+	url = https://github.com/PaperMC/Paperclip.git
diff --git a/Paperclip b/Paperclip
deleted file mode 160000
index 6bff72410..000000000
--- a/Paperclip
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 6bff72410effad0b2b0b0d8471a477f42bd484ff
diff --git a/build.sh b/build.sh
deleted file mode 100755
index 00eb9131e..000000000
--- a/build.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-(git submodule update --init && ./remap.sh && ./decompile.sh && ./init.sh && ./applyPatches.sh) || (
-	echo "Failed to build Paper"
-	exit 1
-) || exit 1
-if [ "$1" == "--jar" ]; then
-	(mvn clean install && ./paperclip.sh) || exit 1
-fi
diff --git a/init.sh b/init.sh
deleted file mode 100755
index 95dc3b37c..000000000
--- a/init.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-PS1="$"
-basedir=`pwd`
-workdir="$basedir/work"
-minecraftversion=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-decompiledir="$workdir/$minecraftversion"
-nms="$decompiledir/net/minecraft/server"
-cb=src/main/java/net/minecraft/server
-
-paperjar="Paper-Server/target/paper-${minecraftversion}.jar"
-vanillajar="work/${minecraftversion}/${minecraftversion}.jar"
-
-echo -e "mcver=${minecraftversion}\npaperjar=../${paperjar}\nvanillajar=../${vanillajar}\n" > paperclip.properties
-
-patch=$(which patch 2>/dev/null)
-if [ "x$patch" == "x" ]; then
-    patch=$basedir/hctap.exe
-fi
-
-echo "Applying CraftBukkit patches to NMS..."
-cd "$basedir/CraftBukkit"
-git checkout -B patched HEAD >/dev/null 2>&1
-rm -rf $cb
-mkdir -p $cb
-for file in $(ls nms-patches)
-do
-    patchFile="nms-patches/$file"
-    file="$(echo $file | cut -d. -f1).java"
-
-    echo "Patching $file < $patchFile"
-    sed -i 's/\r//' "$nms/$file" > /dev/null
-
-    cp "$nms/$file" "$cb/$file"
-    "$patch" -s -d src/main/java/ "net/minecraft/server/$file" < "$patchFile"
-done
-
-git add src >/dev/null 2>&1 || exit 1
-git commit -m "CraftBukkit $ $(date)" >/dev/null 2>&1 || exit 1
-git checkout -f HEAD^ >/dev/null 2>&1 || exit 1
diff --git a/paper b/paper
new file mode 100755
index 000000000..340acf43d
--- /dev/null
+++ b/paper
@@ -0,0 +1,146 @@
+#!/usr/bin/env bash
+
+# get base dir regardless of execution location
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ "$SOURCE" != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+SOURCE=$([[ "$SOURCE" = /* ]] && echo "$SOURCE" || echo "$PWD/${SOURCE#./}")
+basedir=$(dirname "$SOURCE")
+
+paperstash() {
+    STASHED=$(git stash)
+}
+
+paperunstash() {
+    if [[ "$STASHED" != "No local changes to save" ]] ; then
+        git stash pop
+    fi
+}
+
+case "$1" in
+    "rbp" | "rebuild")
+    (
+        set -e
+        cd "$basedir"
+        scripts/rebuildPatches.sh "$basedir"
+    )
+    ;;
+    "p" | "patch")
+    (
+        set -e
+        cd "$basedir"
+        scripts/build.sh "$basedir"
+    )
+    ;;
+    "j" | "jar")
+    (
+        set -e
+        cd "$basedir"
+        scripts/build.sh "$basedir" "--jar"
+    )
+    ;;
+    "make")
+    (
+        if [[ "$2" = "bacon" ]] ; then
+            set -e
+            cd "$basedir"
+            scripts/build.sh "$basedir" "--jar"
+        fi
+    )
+    ;;
+    "r" | "root")
+        cd "$basedir"
+    ;;
+    "a" | "api")
+        cd "$basedir/Paper-API"
+    ;;
+    "s" | "server")
+        cd "$basedir"
+    ;;
+    "e" | "edit")
+        case "$2" in
+            "s" | "server")
+            export LAST_EDIT="$basedir/Paper-Server"
+            cd "$basedir/Paper-Server"
+            (
+                set -e
+
+                paperstash
+                git rebase -i upstream/upstream
+                paperunstash
+            )
+            ;;
+            "a" | "api")
+            export LAST_EDIT="$basedir/Paper-API"
+            cd "$basedir/Paper-API"
+            (
+                set -e
+
+                paperstash
+                git rebase -i upstream/upstream
+                paperunstash
+            )
+            ;;
+            "c" | "continue")
+            cd "$LAST_EDIT"
+            unset LAST_EDIT
+            (
+                set -e
+
+                git add .
+                git commit --amend
+                git rebase --continue
+
+                cd "$basedir"
+                scripts/rebuildPatches.sh "$basedir"
+            )
+            ;;
+            *)
+                echo "You must edit either the api or server."
+            ;;
+        esac
+    ;;
+    "setup")
+        if [[ -f ~/.bashrc ]] ; then
+            NAME="paper"
+            if [[ ! -z "${2+x}" ]] ; then
+                NAME="$2"
+            fi
+            (grep "alias $NAME=" ~/.bashrc > /dev/null) && (sed -i "s|alias $NAME=.*|alias $NAME='. $SOURCE'|g" ~/.bashrc) || (echo "alias $NAME='. $SOURCE'" >> ~/.bashrc)
+            alias "$NAME=. $SOURCE"
+            echo "You can now just type '$NAME' at any time to access the paper tool."
+        fi
+    ;;
+    *)
+        echo "PaperMC build tool command. This provides a variety of commands to build and manage the PaperMC build"
+        echo "environment. For all of the functionality of this command to be available, you must first run the"
+        echo "'setup' command. View below for details. For essential building and patching, you do not need to do the setup."
+        echo ""
+        echo " Normal commands:"
+        echo "  * rbp, rebuild | Rebuild patches, can be called from anywhere."
+        echo "  * p, patch     | Apply all patches to the project without building it. Can be run from anywhere."
+        echo "  * j, jar       | Apply all patches and build the project, paperclip.jar will be output. Can be run from anywhere."
+        echo ""
+        echo " These commands require the setup command before use:"
+        echo "  * r, root      | Change directory to the root of the project."
+        echo "  * a. api       | Move to the Paper-API directory."
+        echo "  * s, server    | Move to the Paper-Server directory."
+        echo "  * e, edit      | Use to edit a specific patch, give it the argument \"server\" or \"api\""
+        echo "                 | respectively to edit the correct project. Use the argument \"continue\" after"
+        echo "                 | the changes have been made to finish and rebuild patches. Can be called from anywhere."
+        echo ""
+        echo "  * setup        | Add an alias to .bashrc to allow full functionality of this script. Run as:"
+        echo "                 |     . ./paper setup"
+        echo "                 | After you run this command you'll be able to just run 'paper' from anywhere."
+        echo "                 | The default name for the resulting alias is 'paper', you can give an argument to override"
+        echo "                 | this default, such as:"
+        echo "                 |     . ./paper setup example"
+        echo "                 | Which will allow you to run 'example' instead."
+    ;;
+esac
+
+unset -f paperstash
+unset -f paperunstash
diff --git a/paperclip.sh b/paperclip.sh
deleted file mode 100755
index fe255bfa9..000000000
--- a/paperclip.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env bash
-basedir=`pwd`
-workdir=$basedir/work
-mcver=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-
-cd ./Paperclip
-mvn clean package
-cd ..
-cp ./Paperclip/target/paperclip-${mcver}.jar ./paperclip.jar
-
-echo ""
-echo ""
-echo ""
-echo "Build success!"
-echo "Copied final jar to $(pwd)/paperclip.jar"
diff --git a/applyPatches.sh b/scripts/applyPatches.sh
similarity index 76%
rename from applyPatches.sh
rename to scripts/applyPatches.sh
index 62b82e5b2..d4ab2fbef 100755
--- a/applyPatches.sh
+++ b/scripts/applyPatches.sh
@@ -1,12 +1,15 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
-basedir=`pwd`
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
 echo "Rebuilding Forked projects.... "
 
 function applyPatch {
     what=$1
-    what_name=$(basename $what)
+    what_name=$(basename "$what")
     target=$2
     branch=$3
 
@@ -21,7 +24,7 @@ function applyPatch {
     cd "$basedir/$target"
     echo "Resetting $target to $what_name..."
     git remote rm upstream > /dev/null 2>&1
-    git remote add upstream $basedir/$what >/dev/null 2>&1
+    git remote add upstream "$basedir/$what" >/dev/null 2>&1
     git checkout master 2>/dev/null || git checkout -b master
     git fetch upstream >/dev/null 2>&1
     git reset --hard upstream/upstream
@@ -39,8 +42,8 @@ function applyPatch {
 }
 
 # Move into spigot dir
-pushd Spigot
-basedir=$basedir/Spigot
+cd "$workdir/Spigot"
+basedir=$(pwd)
 # Apply Spigot
 (
 	applyPatch ../Bukkit Spigot-API HEAD &&
@@ -50,19 +53,20 @@ basedir=$basedir/Spigot
 	exit 1
 ) || exit 1
 # Move out of Spigot
-popd
-basedir=$(dirname "$basedir")
+basedir="$1"
+cd "$basedir"
 
 echo "Importing MC Dev"
 
-./importmcdev.sh
+./scripts/importmcdev.sh "$basedir"
 
 # Apply paper
+cd "$basedir"
 (
-	applyPatch Spigot/Spigot-API Paper-API HEAD &&
-	applyPatch Spigot/Spigot-Server Paper-Server HEAD
+	applyPatch "work/Spigot/Spigot-API" Paper-API HEAD &&
+	applyPatch "work/Spigot/Spigot-Server" Paper-Server HEAD
 ) || (
 	echo "Failed to apply Paper Patches"
 	exit 1
 ) || exit 1
-
+)
diff --git a/scripts/build.sh b/scripts/build.sh
new file mode 100755
index 000000000..0d0827982
--- /dev/null
+++ b/scripts/build.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+(
+set -e
+basedir="$(cd "$1" && pwd -P)"
+
+(git submodule update --init && ./scripts/remap.sh "$basedir" && ./scripts/decompile.sh "$basedir" && ./scripts/init.sh "$basedir" && ./scripts/applyPatches.sh "$basedir") || (
+	echo "Failed to build Paper"
+	exit 1
+) || exit 1
+if [ "$2" == "--jar" ]; then
+	mvn clean install && ./scripts/paperclip.sh "$basedir"
+fi
+)
diff --git a/decompile.sh b/scripts/decompile.sh
similarity index 58%
rename from decompile.sh
rename to scripts/decompile.sh
index 81947e1c7..e56736beb 100755
--- a/decompile.sh
+++ b/scripts/decompile.sh
@@ -1,11 +1,13 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
-basedir=`pwd`
-workdir=$basedir/work
-minecraftversion=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-decompiledir=$workdir/$minecraftversion
-classdir=$decompiledir/classes
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
+minecraftversion=$(cat "$workdir/BuildData/info.json"  | grep minecraftVersion | cut -d '"' -f 4)
+decompiledir="$workdir/$minecraftversion"
+classdir="$decompiledir/classes"
 
 echo "Extracting NMS classes..."
 if [ ! -d "$classdir" ]; then
@@ -22,9 +24,10 @@ fi
 echo "Decompiling classes..."
 if [ ! -d "$decompiledir/net/minecraft/server" ]; then
     cd "$basedir"
-    java -jar BuildData/bin/fernflower.jar -dgs=1 -hdc=0 -asc=1 -udv=0 "$classdir" "$decompiledir"
+    java -jar "$workdir/BuildData/bin/fernflower.jar" -dgs=1 -hdc=0 -asc=1 -udv=0 "$classdir" "$decompiledir"
     if [ "$?" != "0" ]; then
         echo "Failed to decompile classes."
         exit 1
     fi
 fi
+)
diff --git a/importmcdev.sh b/scripts/importmcdev.sh
similarity index 73%
rename from importmcdev.sh
rename to scripts/importmcdev.sh
index 9900c11dc..398e9a740 100755
--- a/importmcdev.sh
+++ b/scripts/importmcdev.sh
@@ -1,19 +1,21 @@
 #!/usr/bin/env bash
 
+(
+set -e
 nms="net/minecraft/server"
 export MODLOG=""
 PS1="$"
-basedir=`pwd`
+basedir="$(cd "$1" && pwd -P)"
 
-workdir=$basedir/work
-minecraftversion=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-decompiledir=$workdir/$minecraftversion
+workdir="$basedir/work"
+minecraftversion=$(cat "$workdir/BuildData/info.json"  | grep minecraftVersion | cut -d '"' -f 4)
+decompiledir="$workdir/$minecraftversion"
 
 export importedmcdev=""
 function import {
 	export importedmcdev="$importedmcdev $1"
 	file="${1}.java"
-	target="$basedir/Spigot/Spigot-Server/src/main/java/$nms/$file"
+	target="$workdir/Spigot/Spigot-Server/src/main/java/$nms/$file"
 	base="$decompiledir/$nms/$file"
 
 	if [[ ! -f "$target" ]]; then
@@ -24,7 +26,7 @@ function import {
 }
 
 (
-	cd Spigot/Spigot-Server/
+	cd "$workdir/Spigot/Spigot-Server/"
 	lastlog=$(git log -1 --oneline)
 	if [[ "$lastlog" = *"mc-dev Imports"* ]]; then
 		git reset --hard HEAD^
@@ -59,8 +61,7 @@ import PathfinderGoalFloat
 import PersistentVillage
 import TileEntityEnderChest
 
-(
-	cd Spigot/Spigot-Server/
-	git add src -A
-	echo -e "mc-dev Imports\n\n$MODLOG" | git commit src -F -
+cd "$workdir/Spigot/Spigot-Server/"
+git add src -A
+echo -e "mc-dev Imports\n\n$MODLOG" | git commit src -F -
 )
diff --git a/scripts/init.sh b/scripts/init.sh
new file mode 100755
index 000000000..51110efb7
--- /dev/null
+++ b/scripts/init.sh
@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+
+(
+set -e
+PS1="$"
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
+minecraftversion=$(cat "$workdir/BuildData/info.json"  | grep minecraftVersion | cut -d '"' -f 4)
+decompiledir="$workdir/$minecraftversion"
+nms="$decompiledir/net/minecraft/server"
+cb="src/main/java/net/minecraft/server"
+
+patch=$(which patch 2>/dev/null)
+if [ "x$patch" == "x" ]; then
+    patch="$basedir/hctap.exe"
+fi
+
+echo "Applying CraftBukkit patches to NMS..."
+cd "$workdir/CraftBukkit"
+git checkout -B patched HEAD >/dev/null 2>&1
+rm -rf "$cb"
+mkdir -p "$cb"
+for file in $(ls nms-patches)
+do
+    patchFile="nms-patches/$file"
+    file="$(echo "$file" | cut -d. -f1).java"
+
+    echo "Patching $file < $patchFile"
+    set +e
+    sed -i 's/\r//' "$nms/$file" > /dev/null
+    set -e
+
+    cp "$nms/$file" "$cb/$file"
+    "$patch" -s -d src/main/java/ "net/minecraft/server/$file" < "$patchFile"
+done
+
+git add src >/dev/null 2>&1
+git commit -m "CraftBukkit $ $(date)" >/dev/null 2>&1
+git checkout -f HEAD^ >/dev/null 2>&1
+)
diff --git a/makemcdevsrc.sh b/scripts/makemcdevsrc.sh
similarity index 50%
rename from makemcdevsrc.sh
rename to scripts/makemcdevsrc.sh
index 375127b05..a83515abe 100755
--- a/makemcdevsrc.sh
+++ b/scripts/makemcdevsrc.sh
@@ -1,14 +1,16 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
 
-workdir=work
-minecraftversion=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-decompiledir=$workdir/$minecraftversion
-nms=$decompiledir/net/minecraft/server
-cb=src/main/java/net/minecraft/server
-papernms=Paper-Server/src/main/java/net/minecraft/server
-mcdevsrc=${decompiledir}/src/net/minecraft/server
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
+minecraftversion=$(cat "$basedir/BuildData/info.json"  | grep minecraftVersion | cut -d '"' -f 4)
+decompiledir="$workdir/$minecraftversion"
+nms="$decompiledir/net/minecraft/server"
+papernms="Paper-Server/src/main/java/net/minecraft/server"
+mcdevsrc="${decompiledir}/src/net/minecraft/server"
 rm -rf "${mcdevsrc}"
 mkdir -p "${mcdevsrc}"
 cp ${nms}/*.java "${mcdevsrc}/"
@@ -23,3 +25,4 @@ do
     fi
 done
 echo "Built $decompiledir/src to be included in your project for src access";
+)
diff --git a/scripts/paperclip.sh b/scripts/paperclip.sh
new file mode 100755
index 000000000..071fe06cc
--- /dev/null
+++ b/scripts/paperclip.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+(
+set -e
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
+mcver=$(cat "$workdir/BuildData/info.json" | grep minecraftVersion | cut -d '"' -f 4)
+paperjar="../../Paper-Server/target/paper-$mcver.jar"
+vanillajar="../$mcver/$mcver.jar"
+
+(
+    cd "$workdir/Paperclip"
+    mvn clean package "-Dmcver=$mcver" "-Dpaperjar=$paperjar" "-Dvanillajar=$vanillajar"
+)
+cp "$workdir/Paperclip/target/paperclip-${mcver}.jar" "$basedir/paperclip.jar"
+
+echo ""
+echo ""
+echo ""
+echo "Build success!"
+echo "Copied final jar to $(cd "$basedir" && pwd -P)/paperclip.jar"
+)
diff --git a/rebuildPatches.sh b/scripts/rebuildPatches.sh
similarity index 62%
rename from rebuildPatches.sh
rename to scripts/rebuildPatches.sh
index 003269f6a..0bc21a87a 100755
--- a/rebuildPatches.sh
+++ b/scripts/rebuildPatches.sh
@@ -1,7 +1,10 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
-basedir=`pwd`
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
 echo "Rebuilding patch files from current fork state..."
 git config core.safecrlf false
 
@@ -9,24 +12,26 @@ function cleanupPatches {
     cd "$1"
     for patch in *.patch; do
         echo "$patch"
-        gitver=$(tail -n 2 $patch | grep -ve "^$" | tail -n 1)
-        diffs=$(git diff --staged $patch | grep -E "^(\+|\-)" | grep -Ev "(From [a-z0-9]{32,}|\-\-\- a|\+\+\+ b|.index)")
+        gitver=$(tail -n 2 "$patch" | grep -ve "^$" | tail -n 1)
+        diffs=$(git diff --staged "$patch" | grep -E "^(\+|\-)" | grep -Ev "(From [a-z0-9]{32,}|\-\-\- a|\+\+\+ b|.index)")
 
         testver=$(echo "$diffs" | tail -n 2 | grep -ve "^$" | tail -n 1 | grep "$gitver")
         if [ "x$testver" != "x" ]; then
+            set +e
             diffs=$(echo "$diffs" | sed 'N;$!P;$!D;$d')
+            set -e
         fi
 
         if [ "x$diffs" == "x" ] ; then
-            git reset HEAD $patch >/dev/null
-            git checkout -- $patch >/dev/null
+            git reset HEAD "$patch" >/dev/null
+            git checkout -- "$patch" >/dev/null
         fi
     done
 }
 
 function savePatches {
     what=$1
-    what_name=$(basename $what)
+    what_name=$(basename "$what")
     target=$2
     echo "Formatting patches for $what..."
 
@@ -42,5 +47,6 @@ function savePatches {
     echo "  Patches saved for $what to $what_name-Patches/"
 }
 
-savePatches Spigot/Spigot-API Paper-API
-savePatches Spigot/Spigot-Server Paper-Server
+savePatches "$workdir/Spigot/Spigot-API" "Paper-API"
+savePatches "$workdir/Spigot/Spigot-Server" "Paper-Server"
+)
diff --git a/remap.sh b/scripts/remap.sh
similarity index 53%
rename from remap.sh
rename to scripts/remap.sh
index 3bd79f3ba..5bccafb0c 100755
--- a/remap.sh
+++ b/scripts/remap.sh
@@ -1,15 +1,17 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
-basedir=`pwd`
-workdir=$basedir/work
-minecraftversion=$(cat BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
-minecrafthash=$(cat BuildData/info.json | grep minecraftHash | cut -d '"' -f 4)
-accesstransforms=BuildData/mappings/$(cat BuildData/info.json | grep accessTransforms | cut -d '"' -f 4)
-classmappings=BuildData/mappings/$(cat BuildData/info.json | grep classMappings | cut -d '"' -f 4)
-membermappings=BuildData/mappings/$(cat BuildData/info.json | grep memberMappings | cut -d '"' -f 4)
-packagemappings=BuildData/mappings/$(cat BuildData/info.json | grep packageMappings | cut -d '"' -f 4)
-jarpath=$workdir/$minecraftversion/$minecraftversion
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
+minecraftversion=$(cat ${workdir}/BuildData/info.json | grep minecraftVersion | cut -d '"' -f 4)
+minecrafthash=$(cat ${workdir}/BuildData/info.json | grep minecraftHash | cut -d '"' -f 4)
+accesstransforms="$workdir/BuildData/mappings/"$(cat ${workdir}/BuildData/info.json | grep accessTransforms | cut -d '"' -f 4)
+classmappings="$workdir/BuildData/mappings/"$(cat ${workdir}/BuildData/info.json | grep classMappings | cut -d '"' -f 4)
+membermappings="$workdir/BuildData/mappings/"$(cat ${workdir}/BuildData/info.json | grep memberMappings | cut -d '"' -f 4)
+packagemappings="$workdir/BuildData/mappings/"$(cat ${workdir}/BuildData/info.json | grep packageMappings | cut -d '"' -f 4)
+jarpath="$workdir/$minecraftversion/$minecraftversion"
 
 echo "Downloading unmapped vanilla jar..."
 if [ ! -f  "$jarpath.jar" ]; then
@@ -36,7 +38,7 @@ fi
 
 echo "Applying class mappings..."
 if [ ! -f "$jarpath-cl.jar" ]; then
-    java -jar BuildData/bin/SpecialSource-2.jar map -i "$jarpath.jar" -m "$classmappings" -o "$jarpath-cl.jar" 1>/dev/null
+    java -jar "$workdir/BuildData/bin/SpecialSource-2.jar" map -i "$jarpath.jar" -m "$classmappings" -o "$jarpath-cl.jar" 1>/dev/null
     if [ "$?" != "0" ]; then
         echo "Failed to apply class mappings."
         exit 1
@@ -45,7 +47,7 @@ fi
 
 echo "Applying member mappings..."
 if [ ! -f "$jarpath-m.jar" ]; then
-    java -jar BuildData/bin/SpecialSource-2.jar map -i "$jarpath-cl.jar" -m "$membermappings" -o "$jarpath-m.jar" 1>/dev/null
+    java -jar "$workdir/BuildData/bin/SpecialSource-2.jar" map -i "$jarpath-cl.jar" -m "$membermappings" -o "$jarpath-m.jar" 1>/dev/null
     if [ "$?" != "0" ]; then
         echo "Failed to apply member mappings."
         exit 1
@@ -54,7 +56,7 @@ fi
 
 echo "Creating remapped jar..."
 if [ ! -f "$jarpath-mapped.jar" ]; then
-    java -jar BuildData/bin/SpecialSource.jar --kill-lvt -i "$jarpath-m.jar" --access-transformer "$accesstransforms" -m "$packagemappings" -o "$jarpath-mapped.jar" 1>/dev/null
+    java -jar "$workdir/BuildData/bin/SpecialSource.jar" --kill-lvt -i "$jarpath-m.jar" --access-transformer "$accesstransforms" -m "$packagemappings" -o "$jarpath-mapped.jar" 1>/dev/null
     if [ "$?" != "0" ]; then
         echo "Failed to create remapped jar."
         exit 1
@@ -62,9 +64,10 @@ if [ ! -f "$jarpath-mapped.jar" ]; then
 fi
 
 echo "Installing remapped jar..."
-cd CraftBukkit # Need to be in a directory with a valid POM at the time of install.
+cd "$workdir/CraftBukkit" # Need to be in a directory with a valid POM at the time of install.
 mvn install:install-file -q -Dfile="$jarpath-mapped.jar" -Dpackaging=jar -DgroupId=org.spigotmc -DartifactId=minecraft-server -Dversion="$minecraftversion-SNAPSHOT"
 if [ "$?" != "0" ]; then
     echo "Failed to install remapped jar."
     exit 1
 fi
+)
diff --git a/upstreamMerge.sh b/scripts/upstreamMerge.sh
similarity index 58%
rename from upstreamMerge.sh
rename to scripts/upstreamMerge.sh
index c3d5db20a..9b05f170e 100755
--- a/upstreamMerge.sh
+++ b/scripts/upstreamMerge.sh
@@ -1,10 +1,13 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
+(
+set -e
 PS1="$"
-basedir=`pwd`
+basedir="$(cd "$1" && pwd -P)"
+workdir="$basedir/work"
 
 function update {
-    cd "$basedir/$1"
+    cd "$workdir/$1"
     git fetch && git reset --hard origin/master
     cd ../
     git add $1
@@ -13,3 +16,4 @@ function update {
 update Bukkit
 update CraftBukkit
 update Spigot
+)
diff --git a/BuildData b/work/BuildData
similarity index 100%
rename from BuildData
rename to work/BuildData
diff --git a/Bukkit b/work/Bukkit
similarity index 100%
rename from Bukkit
rename to work/Bukkit
diff --git a/CraftBukkit b/work/CraftBukkit
similarity index 100%
rename from CraftBukkit
rename to work/CraftBukkit
diff --git a/work/Paperclip b/work/Paperclip
new file mode 160000
index 000000000..90e566f21
--- /dev/null
+++ b/work/Paperclip
@@ -0,0 +1 @@
+Subproject commit 90e566f21456fb83ba33a8910ee99c2e426c6de7
diff --git a/Spigot b/work/Spigot
similarity index 100%
rename from Spigot
rename to work/Spigot