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The `.config` folder is a big headache when trying to be strategic about backups due to apps putting gigs of session data there.
"session data" is not "config", consarnit! An app's "config" shouldn't be gigs large. Grumble grumble, grouse grouse, and so on. :^)
The one that upsets me the most is the default directory for go modules `~/go`. This frustrates me so much. I refused to install any go apps or use it for development for years. I've unfortunately had to give in, and it can at least be overridden by setting `GOPATH`, but it is a terrible, terrible default.
In short, it scans all your programs and determines if you can configure it to respect the xdg standards. It doesn't work for everything, but most applications do seem to have such an option.
Pictures are better sorted with EXIF keywords. So, metadata stored in the picture itself, perhaps even in the MIME type. Thus, if a picture is family related, just tag it #family, or #personx and so on. This is why I store them in the same folder on a per-date basis. The rest is keywords edited with programs such as Adobe Bridge and so on.
As for document file name structure, text files and the like, I've used both `Date then Descrpition.txt` or `Keyword Title or Description and then Date.txt` with the date obviously being an ISO date such that `YYYY-MM-DD-hhmm` with `-hhmm` being optional, also for sorting reasons. Sometimes I like sorting on "topics" i.e. keywords or titles, but other times, such as in logs, I like the date first because it's more essential to know when you logged something, and not necessarily the topic.
You should think the date is superfluous since it's also stored in the system. However, my experience that when you move around a file, the date eventually changes, and certainly if you make a mistake along the way. Meanwhile a filename date doesn't change. Also it helps with list sorting where applicable.
My home directory is nearly empty, because all the files I work with are in OwnCloud (so the real question is: what is the directory structure in OwnCloud). Local Git repositories are on a completely separate partition.
Since KeepassXC now handles SSH keys, the keys from .ssh are now in the Keepass-file, which is on OwnCloud. That was a huge simplification, and now there is nothing in my home directory that I really care much about.