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Question about creating a junction before/during Windows installation

I'm exploring the possibility of installing Windows so that it thinks that the Users directory is on the C: drive when it's actually on another physical drive. I haven't been able to find anything online that answers the question, so I thought I'd try here (among other places).

I'm currently splitting work between my desktop and my laptop. Most of the work is synced using Dropbox and doesn't cause a problem, but I keep coming up with issues because the file paths are not consistent between the two systems.

The desktop has four drives: OS, data, games and storage. This is the setup I've been using for years. I used to duplicate it over to my old laptop using multiple partitions, each being a reasonable size of the single HDD. After a while I decided to change it to use small partitions that then held junctions back to the large partition so that I wasn't splitting the HDD's empty space across multiple partitions. This worked OK because all of the drive letters were consistent between the two machines.

I recently replaced the laptop with a Surface Pro. I didn't really have the time or inclination to faff around with partitioning again, so I just left it with the standard installation on a single C: partition. The first problem was that every time I duplicated my Opus config to the laptop, half of my buttons no longer pointed to the correct location. I was fixing these slowly as and when I became aware of them, plus using tricks like %USERPROFILE% and /hostpictures in file paths.

A second problem was that the path to my Dropbox folder was no longer the same. I fixed that by creating another junction C:\Dropbox on each PC and using that path for any software that was sensitive to paths. Since this seemed to work OK, I thought that the next time I rebuild my desktop, I could do something similar: for example, keep my storage drive as F: but only access the contents via a junction at C:\Storage. On the single-drive Surface, the data would actually be held in the C:\Storage folder and the paths would be consistent.

I've not rebuilt the desktop yet because I don't know how to handle the Users directory. I usually use an answer file when installing windows, redirecting Users to another drive: I still want Users to be on a different physical drive to the OS on the desktop, but in order to keep the paths consistent across the two computers, I want the OS to think that the folder is at C:\Users, not E:\Users. I don't know how to do this. I did think about prepping the system by formatting the drives before installing windows, then maybe using the Troubleshooting options in the Windows installation to access the command line in order to create a junction before starting the installation, but I figure that even if the installer doesn't insist on reformatting the drives itself, there's a good chance that something would spook it.

I was also wondering if it would be possible to install Windows as normal, without moving the Users folder, then boot from a USB, move the folder, create the link, and reboot into Windows. My suspicion is that it wouldn't be that easy.

So does anyone have a suggestion as to how this might be done, or if it's even possible, or if it's a really bad idea? Thanks in advance.

Can you explain in one sentence what you are aiming for? o)

I think here you can find some useful hints:

I thought the first sentence in my post did that. I want to do a clean installation of Windows with the Users folder on a different physical drive to the OS but with Windows accessing the folder using C:\Users instead of D:\Users.

Further information: I want to do it during installation rather than afterwards because it's generally a pain to move system folders after installation. I therefore ideally want a way to create a junction or mount a drive as a folder before the installation starts, without the installer undoing whatever it is I've done.

That seems similar to one of the things I was thinking of trying, namely booting from USB so that all the OS files are unlocked, then moving the folder and creating the link. I was hoping someone here might have tried something similar and knew if it was likely to work.