[embedder] Fix crash when flutter/flutter is updated.

git pull/checkout by default will not update submodules so
third_party/dart-pkg/flutter is sticking at the old version
when you pull changes that update third_party/dart-pkg/flutter. This leads to third_party/dart-pkg/flutter using
a different version of flutter engine from our copy of
libengine_flutter.so.

The fix is to configure git to update submodules when pulling new
changes in this repo.

Also it seemed scripts/bootstrap_bazel.sh got broken at some point.
Switching to calling it directly instead of symlinking it which
fixes the issue (in addition to making it easier to debug).

Change-Id: I4e13e866d33cc8007bfec515387dd18e4dc4591b
diff --git a/scripts/bootstrap.sh b/scripts/bootstrap.sh
index df8cdd7..31f6091 100755
--- a/scripts/bootstrap.sh
+++ b/scripts/bootstrap.sh
@@ -26,8 +26,13 @@
 echo-info "Initializing submodules..."
 git -C $FUCHSIA_EMBEDDER_DIR submodule update --recursive --init
 
+echo-info "Configuring git to update submodules when pulling changes in this repo..."
+echo-info "(This is necessary to keep libflutter_engine.so and third_party/dart-pkg/flutter aligned"
+echo-info "to avoid crashes from Dart SDK incompatibilities)"
+git -C $FUCHSIA_EMBEDDER_DIR config submodule.recurse true
+
 echo-info "Bootstrapping Bazel..."
-$FUCHSIA_EMBEDDER_DIR/scripts/bootstrap_bazel.sh
+$FUCHSIA_EMBEDDER_DIR/third_party/sdk-integration/bazel_rules_fuchsia/scripts/bootstrap_bazel.sh
 $FUCHSIA_EMBEDDER_DIR/tools/bazel clean
 
 echo-info 'Building the embedder to fetch external dependencies (clang)...'
diff --git a/scripts/bootstrap_bazel.sh b/scripts/bootstrap_bazel.sh
deleted file mode 120000
index 925a6b1..0000000
--- a/scripts/bootstrap_bazel.sh
+++ /dev/null
@@ -1 +0,0 @@
-../third_party/sdk-integration/bazel_rules_fuchsia/bootstrap/bootstrap.sh
\ No newline at end of file