diff --git a/README.md b/README.md
index d7ad02c2..9d2dbc99 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 ### Setup
 
 ```
-./bootstrap.sh
+./scripts/bootstrap.sh
 ```
 
 ### Example
diff --git a/bootstrap.sh b/bootstrap.sh
deleted file mode 100755
index d8059df5..00000000
--- a/bootstrap.sh
+++ /dev/null
@@ -1,129 +0,0 @@
-#!/usr/bin/env bash
-# Copyright 2015 Peter Goodman (peter@trailofbits.com), all rights reserved.
-
-
-# Fetch all dependencies.
-echo "${GREEN}Updating aptitude.${RESET}"
-sudo apt-get update
-
-echo "${GREEN}Downloading dependencies.${RESET}"
-sudo apt-get install -y binutils-dev build-essential
-sudo apt-get install -y cmake
-sudo apt-get install -y libgflags-dev libgflags2
-sudo apt-get install -y libgoogle-glog-dev libgoogle-glog0
-sudo apt-get install -y protobuf-compiler libprotobuf-dev libprotobuf8 python-protobuf
-
-RED=`tput setaf 1`
-GREEN=`tput setaf 2`
-YELLOW=`tput setaf 3`
-RESET=`tput sgr0`
-
-# Directory in which this script resides (i.e. McSema root dir).
-DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-
-# Versions of things.
-LLVM_VERSION=3.7.0
-PIN_VERSION=2.14-71313-gcc.4.4.7-linux
-
-
-echo "${GREEN}Downloading third-party code.${RESET}"
-mkdir -p $DIR/third_party
-
-# Download LLVM.
-echo "${YELLOW}Downloading LLVM ${LLVM_VERSION}.${RESET}"
-wget http://llvm.org/releases/3.7.0/llvm-${LLVM_VERSION}.src.tar.xz
-tar xf llvm-$LLVM_VERSION.src.tar.xz
-rm llvm-$LLVM_VERSION.src.tar.xz
-
-
-# Download Clang.
-echo "${YELLOW}Downloading Clang ${LLVM_VERSION}.${RESET}"
-wget http://llvm.org/releases/3.7.0/cfe-${LLVM_VERSION}.src.tar.xz
-tar xf cfe-${LLVM_VERSION}.src.tar.xz
-rm cfe-${LLVM_VERSION}.src.tar.xz
-
-
-# Download PIN.
-echo "${YELLOW}Downloading PIN ${PIN_VERSION}.${RESET}"
-wget http://software.intel.com/sites/landingpage/pintool/downloads/pin-2.14-71313-gcc.4.4.7-linux.tar.gz
-tar xf pin-${PIN_VERSION}.tar.gz
-rm pin-${PIN_VERSION}.tar.gz
-
-
-# Move things around.
-mv llvm-$LLVM_VERSION.src $DIR/third_party/llvm
-mv cfe-${LLVM_VERSION}.src $DIR/third_party/llvm/tools/clang
-mv pin-${PIN_VERSION} $DIR/third_party/pin
-
-
-# Compile LLVM & Clang.
-echo "${GREEN}Compiling LLVM and Clang.${RESET}"
-mkdir $DIR/third_party/llvm/build
-cd $DIR/third_party/llvm/build
-
-CFLAGS="-g3" CXXFLAGS="-g3" LDFLAGS="-g" \
-cmake ../ \
-    -DCMAKE_BUILD_TYPE:STRING=Debug \
-    -DLLVM_ENABLE_RTTI:BOOL=ON \
-    -DLLVM_TARGETS_TO_BUILD:STRING="X86;ARM;AArch64" \
-    -DLLVM_ENABLE_ASSERTIONS:BOOL=ON \
-    -DLLVM_ENABLE_THREADS:BOOL=ON
-make
-
-# Create the generated files directories.
-echo "${GREEN}Creating aut-generated files.${RESET}"
-cd $DIR
-mkdir -p $DIR/generated
-mkdir -p $DIR/generated/Arch
-mkdir -p $DIR/generated/Arch/X86
-mkdir -p $DIR/generated/CFG
-
-
-# Generate 32- and 64-bit x86 machine state modules for importing by
-# `cfg_to_bc`.
-echo "${YELLOW}Generating architecture-specific state files.${RESET}"
-cd $DIR
-$DIR/third_party/llvm/build/bin/clang++ -x c++ -std=gnu++11 -I$DIR -DMCSEMA_STATE_REG=Reg32 -E - \
-    < $DIR/mcsema/Arch/X86/State.inc \
-    > $DIR/generated/Arch/X86/State32.cpp
-    
-$DIR/third_party/llvm/build/bin/clang++ -x c++ -std=gnu++11 -I$DIR -DMCSEMA_STATE_REG=Reg64 -E - \
-    < $DIR/mcsema/Arch/X86/State.inc \
-    > $DIR/generated/Arch/X86/State64.cpp
-
-$DIR/third_party/llvm/build/bin/clang++ -std=gnu++11 -g3 -m32 -emit-llvm \
-    -c $DIR/generated/Arch/X86/State32.cpp \
-    -o $DIR/generated/Arch/X86/State32.bc
-
-$DIR/third_party/llvm/build/bin/clang++ -std=gnu++11 -g3 -m64 -emit-llvm \
-    -c $DIR/generated/Arch/X86/State64.cpp \
-    -o $DIR/generated/Arch/X86/State64.bc
-
-
-# Generate the protocol buffer file for the CFG definition. The lifter will
-# read in CFG protobuf files and output LLVM bitcode files.
-echo "${YELLOW}Generating protocol buffers.${RESET}"
-cd $DIR/generated/CFG
-cp $DIR/mcsema/CFG/CFG.proto $DIR/generated/CFG
-protoc --cpp_out=. CFG.proto
-protoc --python_out=. CFG.proto
-
-
-# Build McSema. McSema will be built with the above version of Clang.
-echo "${GREEN}Compiling McSema.${RESET}"
-cd $DIR
-mkdir $DIR/build
-cd $DIR/build
-cmake -G "Unix Makefiles" -DMCSEMA_DIR=$DIR ..
-make all
-
-
-# Find IDA.
-
-#echo "${GREEN}Finding IDA.${RESET}"
-#IDA=`locate idal64 | head -n 1`
-#if [ ! -e $IDA ] ; then
-#    echo "${RED}Error: Could not find IDA."
-#fi
-
-