diff --git a/.gitmodules b/.gitmodules
index 111c39c..ffb9af9 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "lib/pyyaml"]
 	path = lib/pyyaml
-	url = https://github.com/anishathalye/pyyaml
+	url = https://github.com/yaml/pyyaml
 	ignore = dirty
diff --git a/dotbot/cli.py b/dotbot/cli.py
index d77ab42..8febb26 100644
--- a/dotbot/cli.py
+++ b/dotbot/cli.py
@@ -14,10 +14,10 @@ def add_options(parser):
         help='suppress most output')
     parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',
         help='enable verbose output')
-    parser.add_argument('-d', '--base-directory', nargs=1,
+    parser.add_argument('-d', '--base-directory',
         dest='base_directory', help='execute commands from within BASEDIR',
         metavar='BASEDIR', required=True)
-    parser.add_argument('-c', '--config-file', nargs=1, dest='config_file',
+    parser.add_argument('-c', '--config-file', dest='config_file',
         help='run commands given in CONFIGFILE', metavar='CONFIGFILE',
         required=True)
     parser.add_argument('-p', '--plugin', action='append', dest='plugins', default=[],
@@ -55,10 +55,11 @@ def main():
         for plugin_path in plugin_paths:
             abspath = os.path.abspath(plugin_path)
             module.load(abspath)
-        tasks = read_config(options.config_file[0])
+        tasks = read_config(options.config_file)
         if not isinstance(tasks, list):
             raise ReadingError('Configuration file must be a list of tasks')
-        dispatcher = Dispatcher(options.base_directory[0])
+        os.chdir(options.base_directory)
+        dispatcher = Dispatcher(options.base_directory)
         success = dispatcher.dispatch(tasks)
         if success:
             log.info('\n==> All tasks executed successfully')
diff --git a/lib/pyyaml b/lib/pyyaml
index f30c956..7e026bf 160000
--- a/lib/pyyaml
+++ b/lib/pyyaml
@@ -1 +1 @@
-Subproject commit f30c956c11aa6b5e7827fe5840cc9ed40b938d17
+Subproject commit 7e026bfee9cc0bddeb1bbca0c4a0bcd826c2bfdf
diff --git a/test/Vagrantfile b/test/Vagrantfile
index 8ce1739..05d6747 100644
--- a/test/Vagrantfile
+++ b/test/Vagrantfile
@@ -2,8 +2,7 @@ Vagrant.configure(2) do |config|
   config.vm.box = 'debian/stretch64'
 
   # sync by copying for isolation
-  config.vm.synced_folder "..", "/dotbot", type: "rsync",
-    rsync__exclude: ".git/"
+  config.vm.synced_folder "..", "/dotbot", type: "rsync"
 
   # disable default synced folder
   config.vm.synced_folder ".", "/vagrant", disabled: true
diff --git a/test/test-lib.bash b/test/test-lib.bash
index 008c2f8..7b5e9ca 100644
--- a/test/test-lib.bash
+++ b/test/test-lib.bash
@@ -1,10 +1,6 @@
 DEBUG=${DEBUG:-false}
 USE_VAGRANT=${USE_VAGRANT:-true}
-if ${USE_VAGRANT}; then
-    DOTBOT_EXEC=${DOTBOT_EXEC:-"python /dotbot/bin/dotbot"}
-else
-    DOTBOT_EXEC=${DOTBOT_EXEC:-"/dotbot/bin/dotbot"}
-fi
+DOTBOT_EXEC=${DOTBOT_EXEC:-"python /dotbot/bin/dotbot"}
 DOTFILES="/home/$(whoami)/dotfiles"
 INSTALL_CONF='install.conf.yaml'
 INSTALL_CONF_JSON='install.conf.json'
@@ -51,17 +47,15 @@ initialize() {
 
 run_dotbot() {
     (
-        cd "${DOTFILES}"
-        cat > "${INSTALL_CONF}"
-        ${DOTBOT_EXEC} -d . -c "${INSTALL_CONF}" "${@}"
+        cat > "${DOTFILES}/${INSTALL_CONF}"
+        ${DOTBOT_EXEC} -d "${DOTFILES}" -c "${DOTFILES}/${INSTALL_CONF}" "${@}"
     )
 }
 
 run_dotbot_json() {
     (
-        cd "${DOTFILES}"
-        cat > "${INSTALL_CONF_JSON}"
-        ${DOTBOT_EXEC} -d . -c "${INSTALL_CONF_JSON}" "${@}"
+        cat > "${DOTFILES}/${INSTALL_CONF_JSON}"
+        ${DOTBOT_EXEC} -d "${DOTFILES}" -c "${DOTFILES}/${INSTALL_CONF_JSON}" "${@}"
     )
 }
 
diff --git a/test/test_travis b/test/test_travis
index 20ec1ae..79439e1 100755
--- a/test/test_travis
+++ b/test/test_travis
@@ -6,7 +6,7 @@ set -e
 # set -x
 # set -v
 
-BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+export BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 
 # Prevent execution outside of Travis CI builds
 if [[ "${TRAVIS}" != true || "${CI}" != true ]]; then
diff --git a/test/tests/plugin-dir.bash b/test/tests/plugin-dir.bash
index 299f144..f3a5e94 100644
--- a/test/tests/plugin-dir.bash
+++ b/test/tests/plugin-dir.bash
@@ -19,7 +19,7 @@ EOF
 '
 
 test_expect_success 'run' '
-run_dotbot --plugin-dir plugins <<EOF
+run_dotbot --plugin-dir ${DOTFILES}/plugins <<EOF
 - test: ~
 EOF
 '
diff --git a/test/tests/plugin.bash b/test/tests/plugin.bash
index 960e9ce..bdf0c7f 100644
--- a/test/tests/plugin.bash
+++ b/test/tests/plugin.bash
@@ -18,7 +18,7 @@ EOF
 '
 
 test_expect_success 'run' '
-run_dotbot --plugin test.py <<EOF
+run_dotbot --plugin ${DOTFILES}/test.py <<EOF
 - test: ~
 EOF
 '
diff --git a/test/tests/shim.bash b/test/tests/shim.bash
new file mode 100644
index 0000000..2ed7d54
--- /dev/null
+++ b/test/tests/shim.bash
@@ -0,0 +1,29 @@
+test_description='install shim works'
+. '../test-lib.bash'
+
+test_expect_success 'setup' '
+cd ${DOTFILES}
+git init
+if ${USE_VAGRANT}; then
+    git submodule add /dotbot dotbot
+else
+    git submodule add ${BASEDIR} dotbot
+fi
+cp ./dotbot/tools/git-submodule/install .
+echo "pear" > ${DOTFILES}/foo
+'
+
+test_expect_success 'run' '
+cat > ${DOTFILES}/install.conf.yaml <<EOF
+- link:
+    ~/.foo: foo
+EOF
+if ! ${USE_VAGRANT}; then
+    sed -i "" "1 s/sh$/python/" ${DOTFILES}/dotbot/bin/dotbot
+fi
+${DOTFILES}/install
+'
+
+test_expect_success 'test' '
+grep "pear" ~/.foo
+'
diff --git a/tools/git-submodule/install b/tools/git-submodule/install
index b1baa33..f11b48b 100755
--- a/tools/git-submodule/install
+++ b/tools/git-submodule/install
@@ -9,6 +9,7 @@ DOTBOT_BIN="bin/dotbot"
 BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 cd "${BASEDIR}"
+git -C "${DOTBOT_DIR}" submodule sync --recursive
 git submodule update --init --recursive "${DOTBOT_DIR}"
 
 "${BASEDIR}/${DOTBOT_DIR}/${DOTBOT_BIN}" -d "${BASEDIR}" -c "${CONFIG}" "${@}"