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Run apt update and see if it works. Meaning to look what sources it connects to, if it doesn't fail.
If this fails, then ofc you have to create the file with the Trixie sources. There has to be a dummy file somewhere for you to copy.
I don't really understand your post, you claim to have updated, but it's a new usb install?
Not sure if this answers your question, on my fresh install of Debian 13 it seems to default to using
/etc/apt/sources.list
For example, I had to go in there to enable non-free and it worked fine.
There is a newer/recommended format of sources files ending in .sources in the same folder. The newer format is supported as of Debian 13 but for whatever reason Debian 13 doesn't actually default to installing the newer version on fresh installs. I'm a bit confused by that but Debian's own docs do discuss it.
https://wiki.debian.org/SourcesList
On my fresh install the /etc/apt/sources.list.d still exists, it looks like other software still create their own sources .list files in there when adding their own repos. Debian 13 itself does not seem to generate any files there.
Debian 13 itself does not seem to generate any files there
I noticed that too.
I did it manually, deleted the old list file, it works fine.
You will need some sort of source if you ever want to update. Trixie has support for the new format. see: https://ostechnix.com/migrate-to-deb822-format-debian-13-trixie/
You don’t need a /etc/apt/sources.list anymore, but you need something in /etc/apt/sources.list.d/ as per the above.
This helped
sudo apt modernize-sources
I wish I'd known this was a thing before I spent 15 minutes searching the manpages and manually upgrading my sources...
Here is the section of the release notes that deals with the source list.
Also see this man page for further details and examples.