The solution is pretty straight forward as the question stated the flow.
Cloud --> RPi --> Arduino.
Step 1
Upload the sketch in the Cloud Instance (ftp or http)
Step 2
In the windows IoT Core, wget the sketch file and Install Arduino IDE
wget http://cloud-server/sketches/program1.ino
sudo apt-get update
sudo apt-get install arduino
Step 3
Reboot the RPi
sudo reboot
Step 4
When the RPi rebooted,
open the Arduino IDE and select the port to upload the sketch
/dev/tty/USB0
If the Step 2 wont go successful then try to install windows gnu tool chain
http://gnutoolchains.com/raspberry/
to compile and install piduino as follows
mkdir hardware/RaspberryPi
cd hardware/RaspberryPi
git clone https://github.com/me-no-dev/RasPiArduino piduino