Is it bad practice to have a dot file and an adjacent identically named file without dot?
Background: We already create a $HOME/.ourapp directory where we store various configuration files, log files, etc. but we are debating where to put files that the user would add, create, and modify, either from outside the app or from within it, using various tools. It would seem most natural have these in $HOME/ourapp but that might be bad practice or confusing.
Is it bad practice to have a dot file and an adjacent identically named file without dot?
No. The "semantics" of dotfiles are (and this is very conventional and not very consistent) that they store user configuration, so they'd go along fine with "user-visible" non-dot-directories.
We already create a $HOME/.ourapp directory where we store various configuration files, log files, etc
I'd recommend against that – that's not good practice, which would be having a folder $XDG_CONFIG_HOME/ourapp (typically or if unset, $XDG_CONFIG_HOME is $HOME/.config) for configuration, $XDG_RUNTIME_DIR/ourapp for temporary files, $XDG_STATE_HOME/ourapp/logs (if unset, $XDG_STATE_HOMEis $HOME/.local/state) for state that should persist reboots, but isn't essential, like logs.
See https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html#variables
That way, you
but we are debating where to put files that the user would add, create, and modify, either from outside the app or from within it, using various tools.
Important discussion!
I'd recommend asking the executable xdg-user-dir DOCUMENTS (or VIDEOS, or one of the other choices documented in man xdg-user-dir), and use e.g. $(xdg-user-dir DOCUMENTS)/ourapp for user-modified data: That would make sure the files are put where the user intuitively looks for them.
It would seem logical to an English speaker to put all such file simply into $HOME/Documents, but on non-English user accounts, these directories are typically called differently ($HOME/Dokumente on German gnome, for example); judging by the non-ASCII character in your name, I'd guess you're just like me all too aware of how annoying not being able to localize software is.
$HOME/.ourapp since 2012, and secondly, we want to be consistent across OSs, even non-free ones, us supporting both AIX and macOS. Using $HOME/.local/share/ourapp doesn't seem very user friendly. $HOME with %appdata for config files and use the Windows API to find Document folders! Regarding 12 years of legacy: I know that feeling, but really, you can write a few lines of code that first look in the "new" XDG directory, then in the "old" ~/.ourapp. If you know users never downgrade, you can also auto-migrate old to new location. .ourapp for things the user shouldn't fiddle with, and now need a location for things the user should fiddle with. I don't understand XDG's opinion that user-fiddlable things go to $HOME/.local/share/ourapp since that's also inside a dot directory.