Fix order of redirection in compile.sh

This avoid having garbage warning when compiling Java code because
we use the internal API of Javac.
Also add a run_silent around the protobuf compilation.

Fixes #239

--
MOS_MIGRATED_REVID=95707763
diff --git a/scripts/bootstrap/buildenv.sh b/scripts/bootstrap/buildenv.sh
index 20192ed..2a64d8c 100755
--- a/scripts/bootstrap/buildenv.sh
+++ b/scripts/bootstrap/buildenv.sh
@@ -45,7 +45,7 @@
 
 function run_silent() {
   echo "${@}" >${errfile}
-  "${@}" 2>&1 >>${errfile}
+  "${@}" >>${errfile} 2>&1
   rm ${errfile}
 }
 
diff --git a/scripts/bootstrap/compile.sh b/scripts/bootstrap/compile.sh
index 826dd20..6f663b6 100755
--- a/scripts/bootstrap/compile.sh
+++ b/scripts/bootstrap/compile.sh
@@ -252,7 +252,7 @@
 if [ -z "${BAZEL_SKIP_JAVA_COMPILATION}" ]; then
   log "Compiling Java stubs for protocol buffers..."
   for f in $PROTO_FILES ; do
-    "${PROTOC}" -Isrc/main/protobuf/ --java_out=${OUTPUT_DIR}/src "$f"
+    run_silent "${PROTOC}" -Isrc/main/protobuf/ --java_out=${OUTPUT_DIR}/src "$f"
   done
 
   java_compilation "Bazel Java" "$DIRS" "$LIBRARY_JARS" "${OUTPUT_DIR}"