I'm still not understanding why you need version control for a lookup file and .index file. So, my answer might not be proper to your question.
If your app requires to keep track of all changes users updated lookup csv files, you need your own way to do it. Current Splunk does not have such feature.
Splunk automatically create index files (tsidx files) when csv file is large. tsidx file will improve search performance. If a lookup is updated, Splunk needs to create a new tsidx files. Splunk will not keep those tsidx files. tsidx files. They are binary files. So, when you say version control, I assume you keep all of them because diff would be really difficult. So, size of the app will eventually become very large depending on how much version records will be kept.
What is purpose of version control? Do you have a real use cases and examples? Do you need to revert back to different versions? Do you need something to check diff or merge lookup files by your own app's feature, not Splunk feature?
Because I do not understand your use case for requiring "version control" of lookup files, I believe my answer is not proper.
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