Indexing with remote server build (Yocto, C++, SDK, Docker)

I have some specific problem. In general I work with environment where many projects are using the same, or mostly the same sources. Deployment images are build using Yocto project. For ease of work we are using SDKs generated for certain recipes. Unfortunately I need to have at least two (or even more) SDKs active.

CLion must be started in environment while Yocto SDK is loaded to properly use it. It it impossible to start multiple standalone instances (I haven't tried brute force method with copying CLion binaries - I'm even not sure if license will work that way) and each instance "popped out" of original one inherits environment.

My solution was to deploy those SDKs in Docker containers with SSH login enabled. I was successful and such SDKs can be used by CLion as remote toolchains.

Problem is that those SDKs contains not only libraries themselves but also lists of includes (all, C++ standard as well as product specific). Once project is configured all those references are lost, indexing does not work and sources are "full red" what makes managing such big project, well maybe not impossible, but really hard.

Is there any solution to this problem? I'm I missing something?

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