$atuin doctor provides some useful info.
On my systems (Linux Mint Cinnamon (mine), Fedora and Ubuntu (work)) the config files are spread all over the place(s). My memory resembles Swiss cheese, so remembering their locations is a challenge.
if doctor also provided the location of the configs and the files it likes to modify to make it work, it may remove some load off the forums(?) by people like me 
e.g. the AI when queried, dumped the following on this particular system (my dev box, one of … uummm, four!)
Here’s the full picture of Atuin on your system:
Binary
- /home/atomicrobot/.atuin/bin/atuin — installed via cargo-dist (v18.18.1)
Config files
- /home/atomicrobot/.config/atuin/config.toml — main config
- /home/atomicrobot/.config/atuin/permissions.ai.toml — AI permission grants
- /home/atomicrobot/.config/atuin/atuin-receipt.json — install receipt (metadata)
Data files
/home/atomicrobot/.local/share/atuin/ — all databases live here:
history.db — your command history
ai_sessions.db — AI session continuity
records.db, meta.db, kv.db, scripts.db — sync & internal state
key — encryption key
dotfiles/ — synced shell aliases
Logs
/home/atomicrobot/.atuin/logs/ — with the config we just added:
ai.log.YYYY-MM-DD — AI requests/responses (debug level)
daemon.log.YYYY-MM-DD — daemon logs
search.log.YYYY-MM-DD — search logs
Shell init (atuin lives in three shells)
- fish: ~/.config/fish/config.fish — atuin init fish | source
- bash: ~/.bashrc — sources env + atuin init bash
- zsh: ~/.zshrc — sources env + atuin init zsh
Env script
- /home/atomicrobot/.atuin/bin/env — shared env setup sourced by bash/zsh