What are some replacements to the features Keybase offers?
*proper e2e, not in the lame way Zoom described its interpretation of e2e...
Association of keys with identity -> https://keys.pub/
Git -> Github via git-remote-gcrypt
IM -> Telegram. Not a proper replacement, but works for most of my contacts. Something really secret can be shared via GPG. I guess for your small business a self-hosted Mattermost instance will fit.
Files and directories sharing -> syncthing. I use it mostly between my devices.
Technically the cryptographic links can still be verified even if Keybase doesn't exist anymore, but they did provide a user-friendly interface to set them up, etc.
Both of the above alternatives are end to end encrypted (E2EE)
As for the social keys aspect of Keybase, hope that Keybase open sources their solution.
As it is, I'm probably going to add a well-known to my personal website with my keys.
On your own server, you can host your own git repos, your own IRC server, and your own file storage.