Hi @ice3man543,
if you're worried that individual source files will be too large as single documents I think it is safe to say that you'll be fine. There is some discussion around the topic of max document size Maximum document size (albeit pretty old, but the general concepts around Lucene still apply).
Since you're searching on these files anyway, you'll have to index them in full I would assume (if you want to offer full text search on the source) so there is neither a need nor a point in storing them redundantly in another database IMO .