Interesting, do you keep a copy of the index document form of repos or is that done on the fly during indexing? Is your custom index format a binary format? I have no idea whether that's standard practice, or just a compressed text format is enough. I guess that non-binary formats would be enormous though, and given that an index is by definition relatively unique it probably wouldn't compress that well.
I do feel the development velocity thing. I've felt something similar on my smaller scale projects. Being able to fully re-index the corpus in less than a day definitely seems like it would provide a lot of opportunities to experiment and try stuff out without it being too costly.
Scale up in terms of what? Is the current system not indexing all of GitHub, or you mean you want to index on more things (E.g. commits, PRs, etc)?