diff --git a/scripts/bootstrap/bootstrap.sh b/scripts/bootstrap/bootstrap.sh
index 3832692..c50afc2 100755
--- a/scripts/bootstrap/bootstrap.sh
+++ b/scripts/bootstrap/bootstrap.sh
@@ -62,7 +62,8 @@
         --javacopt="-g -source ${JAVA_VERSION} -target ${JAVA_VERSION}" "${@}"
   }
 else
-  function _run_bootstrapping_bazel() { local command=$1
+  function _run_bootstrapping_bazel() {
+    local command=$1
     shift
     ${BAZEL} --bazelrc=${BAZELRC} ${BAZEL_DIR_STARTUP_OPTIONS} $command \
         ${_BAZEL_ARGS} --verbose_failures \
diff --git a/scripts/bootstrap/buildenv.sh b/scripts/bootstrap/buildenv.sh
index 39a15c4..197eef9 100755
--- a/scripts/bootstrap/buildenv.sh
+++ b/scripts/bootstrap/buildenv.sh
@@ -77,22 +77,22 @@
   fi
   ;;
 
-msys*|mingw*)
+msys*|mingw*|cygwin*)
   # Use a simplified platform string.
-  PLATFORM="mingw"
+  PLATFORM="windows"
   PATHSEP=";"
   # Find the latest available version of the SDK.
-  JAVA_HOME="${JAVA_HOME:-$(ls -d /c/Program\ Files/Java/jdk* | sort | tail -n 1)}"
+  JAVA_HOME="${JAVA_HOME:-$(ls -d C:/Program\ Files/Java/jdk* | sort | tail -n 1)}"
   # Replace backslashes with forward slashes.
   JAVA_HOME="${JAVA_HOME//\\//}"
 esac
 
 EXE_EXT=""
-if [ "${PLATFORM}" == "mingw" ]; then
+if [ "${PLATFORM}" == "windows" ]; then
   # Extension for executables.
   EXE_EXT=".exe"
 
-  # Fix TMPDIR on msys
+  # Fix TMPDIR on windows
   default_tmp=${TMP:-$(cygpath -mO)/Temp}
   TMPDIR=$(cygpath -ml "${TMPDIR:-$default_tmp}")
 fi
@@ -235,13 +235,13 @@
 }
 
 function git_sha1() {
-  if [ -x "$(which git || true)" ] && [ -d .git ]; then
+  if [ -x "$(which git 2>/dev/null)" ] && [ -d .git ]; then
     git rev-parse --short HEAD 2>/dev/null || true
   fi
 }
 
 function git_date() {
-  if [ -x "$(which git || true)" ] && [ -d .git ]; then
+  if [ -x "$(which git 2>/dev/null)" ] && [ -d .git ]; then
     git log -1 --pretty=%ai | cut -d " " -f 1 || true
   fi
 }
diff --git a/scripts/bootstrap/compile.sh b/scripts/bootstrap/compile.sh
index 08687ac..eec6123 100755
--- a/scripts/bootstrap/compile.sh
+++ b/scripts/bootstrap/compile.sh
@@ -272,8 +272,7 @@
 function build_jni() {
   local -r output_dir=$1
 
-  case "${PLATFORM}" in
-  msys*|mingw*)
+  if [ "${PLATFORM}" = "windows" ]; then
     # We need JNI on Windows because some filesystem operations are not (and
     # cannot be) implemented in native Java.
     log "Building Windows JNI library..."
@@ -297,13 +296,10 @@
     chmod 0555 "$output"
 
     JNI_FLAGS="-Dio.bazel.EnableJni=1 -Djava.library.path=${output_dir}"
-    ;;
-
-  *)
+  else
     # We don't need JNI on other platforms.
     JNI_FLAGS="-Dio.bazel.EnableJni=0"
-    ;;
-  esac
+  fi
 }
 
 build_jni "${ARCHIVE_DIR}/_embedded_binaries"
@@ -319,6 +315,12 @@
   cp tools/osx/xcode_locator_stub.sh ${ARCHIVE_DIR}/_embedded_binaries/xcode-locator
 fi
 
+function get_cwd() {
+  local result=${PWD}
+  [ "$PLATFORM" = "windows" ] && result="$(cygpath -m "$result")"
+  echo "$result"
+}
+
 function run_bazel_jar() {
   local command=$1
   shift
@@ -369,7 +371,7 @@
       --install_base=${ARCHIVE_DIR} \
       --output_base=${OUTPUT_DIR}/out \
       --install_md5= \
-      --workspace_directory=${PWD} \
+      --workspace_directory="$(get_cwd)" \
       --nofatal_event_bus_exceptions \
       ${BAZEL_DIR_STARTUP_OPTIONS} \
       ${BAZEL_BOOTSTRAP_STARTUP_OPTIONS:-} \
@@ -378,6 +380,6 @@
       --startup_time=329 --extract_data_time=523 \
       --rc_source=/dev/null --isatty=1 \
       "${client_env[@]}" \
-      --client_cwd=${PWD} \
+      --client_cwd="$(get_cwd)" \
       "${@}"
 }