Newest version has better support literally for any generated Makefiles, through the compiledb
Three steps:
install compiledb
pip install compiledb
run a dry make
compiledb -n make
(do the autogen, configure if needed)
there will be a compile_commands.json file generated open the project and you will see CLion will load info from the json file. If you your CLion still try to find CMakeLists.txt and cannot read compile_commands.json, try to remove the entire folder, re-download the source files, and redo step 1,2,3
Orignal post: Working with Makefiles in CLion using Compilation DB