get CLion compilation database project to automatically choose which files to index?

I work with a very large bazel project and was excited to learn about compilation database support as I would like a more stable alternative to the intellij bazel plugin (which seems to get out of sync with new releases of CLion).

I spent some time adapting this tool:

https://github.com/grailbio/bazel-compilation-database

to allow me to specify a subset of build targets and it works. However, when I load a project from the resulting compilation database, CLion begins to index everything, despite the fact that the compilation database only concerns a subset of the targets within the project.

I think it'd make sense to only index the files that are referenced in the targets in the compilation database; otherwise I need to hand exclude / include the directories of interest.

Might this be possible? Are there any suggestions for how I might automate the process of building a CLion project that only indexes a subset of files in conjunction with the compilation database?