Auto-indexing: directly support multi-root projects

[keynmol]

To reduce the number of jobs being scheduled, I propose we move multi-root support into the tool itself, peraps as a separate command that delegates to regular index

For example, in this repo: https://github.com/in28minutes/spring-boot-examples we are currently inferencing 1 indexer job per folder.

That's quite wasteful, not only because of CPU cycles, but also because of lack of persistent dependency cache.

Instead, we can add index-batch [options] root1 root2 root3 command which can index each root independently and possible in parallel, and then merge the resulting SCIP indexes.

Merging should be done in simplest way possible - basically concatenating lists of documents, assuming that subfolders are independent of each other. This can be lossy, but good enough.