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I'd defintely go with an M.2 SSD, you can get 1tb for 50€ and 2tb for 100€ now and they're much faster, more reliable and take up way less space.

For ML/AI stuff, you might be just fine using an AMD GPU. AMD GPUs are a lot easier to use on Linux and are also a good bit cheaper. I use Fedora with an AMD GPU and I just installed the packages for OpenCL and HIP and now I can run LLMs on my PC using my GPU. I've also used Stable Diffusion with that GPU on Linux before. If there's something specific you want to do regarding that, I'd look up first if you need an Nvidia GPU for that but from my experience AMD GPUs work just fine.

I'd take a look at AMD CPUs again. Last time I checked they were even cheaper (including mobo price) than Intel even though they're also more efficient (faster and less power draw). Prices might have changed tho. You should probably use a Ryzen 5, a Ryzen 7 will only make sense if you use all cores because game performance is pretty much the same. A Ryzen 3 is more of a budget option tho, I wouldn't use that. If it's in your budget, you should also use the newest generation that uses the AM5 socket because you'll be able to upgrade your CPU without needing a new mobo. I think it also only supports DDR5 RAM, which is more expensive than DDR4. If you use a Ryzen generation that uses the AM4 socket, it's gonna be cheaper but if you want to upgrade you'll need a new mobo with AM5 and new DDR5 RAM in addition to the new CPU.

As for Linux distros, my recommendations are Linux Mint if you want something very easy, EndeavourOS if you want something Arch-based or Fedora if you want something that's not quite as easy as Mint but more up-to-date. I personally use Fedora but I used EndeavourOS before. I detailed why I switched to Fedora in a reply here somewhere.

A lot of great suggestions here already. But nobody is mentioning that if you really want to future-proof, you should go fully quantum.

The responsiveness between a hard drive and an SSD is night and day. NVMe is even faster but not noticeable unless you move a hell of a lot of data around. A motherboard having at least 1 M.2 NVMe slot is common, so installing the OS on it is an option. Hard drives have more storage per price, but unless space is significant factor I suggest using SSDs (also quieter than a spinning disk!). More info on storage formats in this video

Recent generations of motherboards use DDR5 RAM, which were very expensive on release. I think the price has come down but I am not up to date this generation. You may be able to save money making a DDR4 system but you'll be stuck on a less supported platform.

AMD had like ~10 years of bad/power hungry processors and Intel stagnated, re-releasing 4-core processors over and over. AMD made a big comeback with their Ryzen series becoming best bang for buck, then even over taking Intel. I think it's pretty even now.

If you don't intend to game or do certain compute workloads then you can avoid buying a GPU. Integrated CPUs have come quite far (still low end compared to a dedicated GPU). Crypto mining, Covid and now AI has made the GPUs market expensive and boring. Nvidia has more higher-end cards, mid range is way more expensive for both and low end sucks ass. On Linux AMD GPUs drivers come with the OS, but Nvidia you have to get their proprietary drivers (Linux gaming has come a long way).

I went through the same process myself a couple years ago, first PC build in a while. The biggest shock for me was finding out hard drives (SSD, HHD, etc) were outdated: its all about NVMe cards which look like a stick of RAM and plug directly on the motherboard.