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cindex doesn't have any flags to exclude a folder from being indexed from a path like ST can exclude directories from a project path. But, it should be doable to expand the one path in ST to the directories and paths that ST has in the project.
Take the following directory structure
project/
|- dir-a/
| |- foo/
| |- bar/
| `- file.txt
|- dir-b/
| `- bar/
|- foo/
| `- bar/
`- file.txt
If I wanted to index project, yet exclude foo, I could transform this into the following paths for cindex to search:
project/dir-a/bar/
project/dir-a/file.txt
project/dir-b/
project/file.txt
This does add a lot of expansion, and I don't think cindex should have any issues with this, but it's worth keeping an eye out for.