diff --git a/libexec/pyenv b/libexec/pyenv
index a1266c1f..fbdd880c 100755
--- a/libexec/pyenv
+++ b/libexec/pyenv
@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 set -e
-unset CDPATH
 
 if [ "$1" = "--debug" ]; then
   export PYENV_DEBUG=1
@@ -22,7 +21,8 @@ abort() {
 
 if enable -f "${BASH_SOURCE%/*}"/../libexec/pyenv-realpath.dylib realpath 2>/dev/null; then
   abs_dirname() {
-    local path="$(realpath "$1")"
+    local path
+    path="$(realpath "$1")"
     echo "${path%/*}"
   }
 else
@@ -69,6 +69,11 @@ if [ -z "${PYENV_DIR}" ]; then
     export PYENV_DIR
     unset PYENV_FILE_ARG
   fi
+else
+  [[ $PYENV_DIR == /* ]] || PYENV_DIR="$PWD/$PYENV_DIR"
+  cd "$PYENV_DIR" 2>/dev/null || abort "cannot change working directory to \`$PYENV_DIR'"
+  PYENV_DIR="$PWD"
+  cd "$OLDPWD"
 fi
 
 if [ -z "${PYENV_DIR}" ]; then
@@ -121,7 +126,13 @@ case "$command" in
   ;;
 * )
   command_path="$(command -v "pyenv-$command" || true)"
-  [ -n "$command_path" ] || abort "no such command \`$command'"
+  if [ -z "$command_path" ]; then
+    if [ "$command" == "shell" ]; then
+      abort "shell integration not enabled. Run \`pyenv init' for instructions."
+    else
+      abort "no such command \`$command'"
+    fi
+  fi
 
   shift 1
   if [ "$1" = --help ]; then
diff --git a/libexec/pyenv-commands b/libexec/pyenv-commands
index 547fd265..283ce44b 100755
--- a/libexec/pyenv-commands
+++ b/libexec/pyenv-commands
@@ -28,15 +28,15 @@ shopt -s nullglob
     for command in "${path}/pyenv-"*; do
       command="${command##*pyenv-}"
       if [ -n "$sh" ]; then
-        if [ ${command:0:3} = "sh-" ]; then
-          echo ${command##sh-}
+        if [ "${command:0:3}" = "sh-" ]; then
+          echo "${command##sh-}"
         fi
       elif [ -n "$nosh" ]; then
-        if [ ${command:0:3} != "sh-" ]; then
-          echo ${command##sh-}
+        if [ "${command:0:3}" != "sh-" ]; then
+          echo "${command##sh-}"
         fi
       else
-        echo ${command##sh-}
+        echo "${command##sh-}"
       fi
     done
   done
diff --git a/libexec/pyenv-help b/libexec/pyenv-help
index a63bd7d6..8270993e 100755
--- a/libexec/pyenv-help
+++ b/libexec/pyenv-help
@@ -42,6 +42,7 @@ extract_initial_comment_block() {
 }
 
 collect_documentation() {
+  # shellcheck disable=SC2016
   $(type -p gawk awk | head -1) '
     /^Summary:/ {
       summary = substr($0, 10)
@@ -86,7 +87,8 @@ collect_documentation() {
 }
 
 documentation_for() {
-  local filename="$(command_path "$1")"
+  local filename
+  filename="$(command_path "$1")"
   if [ -n "$filename" ]; then
     extract_initial_comment_block < "$filename" | collect_documentation
   fi
@@ -114,7 +116,7 @@ print_help() {
   eval "$(documentation_for "$command")"
   [ -n "$help" ] || help="$summary"
 
-  if [ -n "$usage" -o -n "$summary" ]; then
+  if [ -n "$usage" ] || [ -n "$summary" ]; then
     if [ -n "$usage" ]; then
       echo "$usage"
     else
diff --git a/libexec/pyenv-init b/libexec/pyenv-init
index df196295..659d1f4c 100755
--- a/libexec/pyenv-init
+++ b/libexec/pyenv-init
@@ -138,7 +138,7 @@ esac
 if [ "$shell" != "fish" ]; then
 IFS="|"
 cat <<EOS
-  command="\$1"
+  command="\${1:-}"
   if [ "\$#" -gt 0 ]; then
     shift
   fi
diff --git a/libexec/pyenv-rehash b/libexec/pyenv-rehash
index 47c64c7c..0c822e51 100755
--- a/libexec/pyenv-rehash
+++ b/libexec/pyenv-rehash
@@ -16,7 +16,7 @@ mkdir -p "$SHIM_PATH"
 # to stderr and exit with a non-zero status.
 set -o noclobber
 { echo > "$PROTOTYPE_SHIM_PATH"
-} 2>/dev/null ||
+} 2>| /dev/null ||
 { if [ -w "$SHIM_PATH" ]; then
     echo "pyenv: cannot rehash: $PROTOTYPE_SHIM_PATH exists"
   else
@@ -83,7 +83,7 @@ remove_outdated_shims() {
 list_executable_names() {
   local version file
   pyenv-versions --bare --skip-aliases | \
-  while read version; do
+  while read -r version; do
     for file in "${PYENV_ROOT}/versions/${version}/bin/"*; do
       echo "${file##*/}"
     done
@@ -136,6 +136,7 @@ shopt -s nullglob
 # executables.
 create_prototype_shim
 remove_outdated_shims
+# shellcheck disable=SC2046
 make_shims $(list_executable_names | sort -u)
 
 
diff --git a/libexec/pyenv-root b/libexec/pyenv-root
index 6669caa2..b4a135f3 100755
--- a/libexec/pyenv-root
+++ b/libexec/pyenv-root
@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 # Summary: Display the root directory where versions and shims are kept
-echo $PYENV_ROOT
+echo "$PYENV_ROOT"
diff --git a/libexec/pyenv-whence b/libexec/pyenv-whence
index d551e567..fddcf112 100755
--- a/libexec/pyenv-whence
+++ b/libexec/pyenv-whence
@@ -20,7 +20,7 @@ fi
 
 whence() {
   local command="$1"
-  pyenv-versions --bare | while read version; do
+  pyenv-versions --bare | while read -r version; do
     path="$(pyenv-prefix "$version")/bin/${command}"
     if [ -x "$path" ]; then
       [ "$print_paths" ] && echo "$path" || echo "$version"
diff --git a/src/configure b/src/configure
index 10d0ff57..54b33798 100755
--- a/src/configure
+++ b/src/configure
@@ -34,16 +34,16 @@ esac
 eval "$("$src_dir"/shobj-conf -C "$CC" -o "$host_os")"
 
 sed "
-  s,@CC@,${CC},
-  s,@CFLAGS@,${CFLAGS},
-  s,@LOCAL_CFLAGS@,${LOCAL_CFLAGS},
-  s,@DEFS@,${DEFS},
-  s,@LOCAL_DEFS@,${LOCAL_DEFS},
-  s,@SHOBJ_CC@,${SHOBJ_CC},
-  s,@SHOBJ_CFLAGS@,${SHOBJ_CFLAGS},
-  s,@SHOBJ_LD@,${SHOBJ_LD},
-  s,@SHOBJ_LDFLAGS@,${SHOBJ_LDFLAGS//,/\\,},
-  s,@SHOBJ_XLDFLAGS@,${SHOBJ_XLDFLAGS//,/\\,},
-  s,@SHOBJ_LIBS@,${SHOBJ_LIBS},
-  s,@SHOBJ_STATUS@,${SHOBJ_STATUS},
+  s#@CC@#${CC}#
+  s#@CFLAGS@#${CFLAGS}#
+  s#@LOCAL_CFLAGS@#${LOCAL_CFLAGS}#
+  s#@DEFS@#${DEFS}#
+  s#@LOCAL_DEFS@#${LOCAL_DEFS}#
+  s#@SHOBJ_CC@#${SHOBJ_CC}#
+  s#@SHOBJ_CFLAGS@#${SHOBJ_CFLAGS}#
+  s#@SHOBJ_LD@#${SHOBJ_LD}#
+  s#@SHOBJ_LDFLAGS@#${SHOBJ_LDFLAGS}#
+  s#@SHOBJ_XLDFLAGS@#${SHOBJ_XLDFLAGS}#
+  s#@SHOBJ_LIBS@#${SHOBJ_LIBS}#
+  s#@SHOBJ_STATUS@#${SHOBJ_STATUS}#
 " "$src_dir"/Makefile.in > "$src_dir"/Makefile
diff --git a/test/shell.bats b/test/shell.bats
index 82383aad..0871065c 100644
--- a/test/shell.bats
+++ b/test/shell.bats
@@ -2,6 +2,17 @@
 
 load test_helper
 
+@test "shell integration disabled" {
+  run pyenv shell
+  assert_failure "pyenv: shell integration not enabled. Run \`pyenv init' for instructions."
+}
+
+@test "shell integration enabled" {
+  eval "$(pyenv init -)"
+  run pyenv shell
+  assert_success "pyenv: no shell-specific version configured"
+}
+
 @test "no shell version" {
   mkdir -p "${PYENV_TEST_DIR}/myproject"
   cd "${PYENV_TEST_DIR}/myproject"
diff --git a/test/version-file.bats b/test/version-file.bats
index 84ceba5d..c46fb389 100644
--- a/test/version-file.bats
+++ b/test/version-file.bats
@@ -9,7 +9,7 @@ setup() {
 
 create_file() {
   mkdir -p "$(dirname "$1")"
-  touch "$1"
+  echo "system" > "$1"
 }
 
 @test "detects global 'version' file" {
diff --git a/test/version-origin.bats b/test/version-origin.bats
index be6d6f93..cd7ec563 100644
--- a/test/version-origin.bats
+++ b/test/version-origin.bats
@@ -26,7 +26,7 @@ setup() {
 }
 
 @test "detects local file" {
-  touch .python-version
+  echo "system" > .python-version
   run pyenv-version-origin
   assert_success "${PWD}/.python-version"
 }
diff --git a/test/which.bats b/test/which.bats
index 5dd10164..5145cdb4 100644
--- a/test/which.bats
+++ b/test/which.bats
@@ -60,12 +60,11 @@ create_executable() {
 }
 
 @test "doesn't include current directory in PATH search" {
-  export PATH="$(path_without "kill-all-humans")"
   mkdir -p "$PYENV_TEST_DIR"
   cd "$PYENV_TEST_DIR"
   touch kill-all-humans
   chmod +x kill-all-humans
-  PYENV_VERSION=system run pyenv-which kill-all-humans
+  PATH="$(path_without "kill-all-humans")" PYENV_VERSION=system run pyenv-which kill-all-humans
   assert_failure "pyenv: kill-all-humans: command not found"
 }
 
@@ -91,9 +90,8 @@ OUT
 }
 
 @test "no executable found for system version" {
-  export PATH="$(path_without "py.test")"
-  PYENV_VERSION=system run pyenv-which py.test
-  assert_failure "pyenv: py.test: command not found"
+  PATH="$(path_without "rake")" PYENV_VERSION=system run pyenv-which rake
+  assert_failure "pyenv: rake: command not found"
 }
 
 @test "executable found in other versions" {