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I have recently build a new system with a 256GB SSD and a 3TB HDD. I want to save all my files on my HDD while my programs and Ubuntu 14.04 should run on my SSD to boost the performance. I might also be installing a Windows version later, but I am not so sure about that...

How can I do that? Is it possible to do that without reinstalling Ubuntu?

edit:

When I installed Ubuntu 14.04 64-bit on my system I chose Ubuntu to get installed on my SSD with the auto-partitioner. I have not yet copied my data from my ext. hard drive to my internal storage, as I want it to go to the HDD, while all my installs should go to my SSD. Later I might want another SSD-partition for Windows (if I install it) to use as my oprating system for gaming.

MalteK
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If you have already installed Ubuntu on SSD then after Windows installation you will need to run Boot Repair. The steps you take are described here:

How to install the Boot-Repair tool in an Ubuntu live disc?

If you already have Ubuntu on HDD, so I would recommend just to remorarily save your /home folder to another partition, then manage your partitions (maybe you want to delete the previous one which contained Ubuntu) with Gparted, which is included in Ubuntu and Live CD. The thread below has explanations how to manage partitions with Gparted.

How to resize partitions?

During the installation you could create or choose a partition for your /home folder, so you could place home on HDD having the / on SSD.

If you have already installed Ubuntu and want to move your home partition from SSD to HDD rather than reinstall Ubuntiu, then have a look at this thread:

How can I move my /home directory to another partition if it's already part of the / partition?