CMake with Make

I have a Makefile project which the source code is on Windows, but a library I need is on WSL-Ubuntu.

For VS Code, I can download the source code into Ubuntu, and use the remote-SSH option to open the source code directly located on Ubuntu.

For CLion, as far as my search goes, all remote options requires the source code to be on the local machine, which is my Windows. What I have done is set up my toolchain, set up my CMake to use my Ubuntu toolchain, and set up my deployment -> mappings to the folder where I would have had the source code if it was on Ubuntu. However, in some of the code, it includes some headers that are in the Ubuntu library:

<llvm/IR/abc.h>

However, CLion warns me: "unable to find declaration to go to", there are also a lot of red code, and the folder is not deployed

I understand that I need CMake, so I created a CMake file, but CLion refuses to pick up the CMakeLists.txt file.

I did find a solution.

I deleted the .idea folder, and moved the Makefile elsewhere. When reopened, CLion prompted me to create a new CMakeList.txt, and after that, I moved back my Makefile, and everything worked smoothly.

Why is CLion not picking up the CMake that I manually created? Is there a setting that I need to change somewhere? Also, is there a way to force CLion to generate a CMake file for me, instead of having to delete .idea and the Makefile.