Overwriting files not checked in version control

What version of Codex is running?

codex-cli 0.19.0

Which model were you using?

gpt-5

What platform is your computer?

Darwin 24.6.0 x86_64 i386

What steps can reproduce the bug?

I had previously written a custom Agents.MD, I forgot it was in .gitignore. When I ran the upgrade to codex 0.19 with Gpt5 it offered to /init I tought it's all under version control and try it and then maybe augment it with my old specific instructions but I just realized they were overwritten and not under version control. Hope this helps.

What is the expected behavior?

My file that I can't recover doesn't get overwritten.

What do you see instead?

old Agents.MD is gone.

Additional information

_No response_