Toolchain feature "Enviroment file" does not work in 2025.3, works in 2025.2
Hi, I use Clion toolchains feature “Add environment from file” for loading Intel OneAPI paths into environment. This has always worked with all earlier Clion editions. But in 2025.3 the environment paths from the OneApi “setvars.sh” is not loaded, meaning my include paths for same project working in 2025.2 is not finding what it needs when loaded using 2025.3
I do use Cmake preset file with the vendor option to load specific tool chain (with a environment file). I have only tested with Intel OneApi setvars.sh
How to reproduce, setup Clion 2025.2 with a toolchain that uses OneApi setvars.sh file and load/create a project using Cmake presets file with Clion vendor specific toolchain option, notice see Header search paths for OneApi included.
Do the same in 2025.3 and notice OneApi header search paths missing.

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In my honest opinion, the usage of the toolchain files and the handling of environment variables that in theory should persist into the CMake configuration, is very poorly documented and does not work most of the time.
I find the usage of this file to be vague, some sources claim it should be setup as file containing only KEY=VALUE type of environment configurations, while others claim it can be run as a shell script.
Ok thx for your input, strange because this has always worked with all earlier Clion editions, never been a issue until 2025.3
I dont see how Cmake configuration should be a issue. Vendor options in Cmake preset files i have used a long time for both Microsoft vendor options and Jetbrains Clion options and always worked.
For now its fixed same way as i load enviroment for desktop starting VScode and Neovim, just a custom desktop file to execute a sh file that sources the OneApi setvars.sh and then runs the executable. I guess it aint stupid if it works…
create a startclion.sh file:
Change clion.desktop to:
Hi Irrada12!
You might be facing CPP-47813. We hope to include the fix in CLion 2025.3.1, which is expected to be released this week.
Feel free to comment or upvote CPP-47813 to get updates. See https://intellij-support.jetbrains.com/hc/en-us/articles/207241135-How-to-follow-YouTrack-issues-and-receive-notifications if you are not familiar with YouTrack.