Hmm, at this stage having gone moreso public compared to this being an entirely internal project---I would say now is a good time to greatly back away from purely numerical versioning towards a mix of numerical and thematic with the latter being the overall leaning.
"V0.anything" will get just so much attention from an implied sense of "ready for fun", "v0.0.anything" stands to get at least an order of magnitude less to no tangible benefits. The project here is at the Beta level, ramping up as it does, so meeting and ideally exceeding public player expectations is the next good bit ahead.
Taking a page from ToME 4 itself, or Desktop Dungeons, and going with a Beta 4 "Sorcery Unleashed"....or some other indicative adjective as to the content is almost certainly a good way to go---you should be able to transition the ModDb page as you please in terms of filenames and whanot going forward given you are writing and submitting your own updates---and people will be far less inclined to look into earlier releases going forward versus the latest and greatest. This would also have the side benefit of helping to crystallize the "Title Goal(s)" to shoot for breaking each release up into, as opposed to just numerical decimal values increasing into the bleak horizon.
For those that somehow want to, a catch-all archive in chronological order with the old naming scheme should suffice just fine.
For Git I got nothing though.