Prevent prep and logs from being captured when collecting logs

Resolve awk warnings in collect-logs.sh

refs #4624
refs #4411

Change-Id: I2fdb385f12374864f572e3529c837cbaa51fdfb2
diff --git a/Vagrantfile b/Vagrantfile
index 56bb131..95c0ab1 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -11,6 +11,8 @@
 $setup_integ = <<SCRIPT
 cp -R /vagrant integration-tests
 cd integration-tests && ./install_apps.py install_all 2>&1 | tee install.log
+rm -rf prepare
+cd install_helpers/tools && make clean
 SCRIPT
 
 $setup_ssh = <<SCRIPT