Have you tried to install each of the IDEs(Arduino, Eclipse and XDK) individually? You can also download the Flash Tool Lite separately and/or you can use the flashall script to flash the image.
You can find all the download links in here: IoT - Intel® Edison Board Download | Intel® Developer Zone
First, start with downloading the Flash Tool Lite (Manual - IoT - Flash Tool Lite User Manual | Intel® Developer Zone). For this you will need to also download the Release 2.1 Yocto* complete image
Available IDEs: IoT - IDEs | Intel® Developer Zone
Let us know if this works.