I use a homogenized file structure across all of my devices and use symbolic links or scripts to move files that the operating system or programs want in specific places. This allows me to always find files quickly without relying on a search tool. This also makes it very easy to backup and restore all of my data. Images of pre-configured systems automatically begin syncing with the main server when they are re-installed from a backup. The master version of this structure is stored on the server and are synced to the devices they are needed on with syncthing or rsync depending on system. This entire common folder is backed up by having a full copy saved to a hard drive once per week, with this drive being rotated and stored off-site. The entire file system is also mirrored to a second server capable of supporting the same syncing in case the first server goes offline.

The backup folder contains several folders for backups.

Dot files are organized into folders based on the system they are applicable to.

The download folder has two sub-folders. One folder serves as the download location for the server. The second is a download folder that is synced across all devices so that something downloaded on my phone is also available on my laptop and all other devices.

The git folder is the root for all projects. Every project I do, whether code or not, is revisioned with git. Even this wiki is stored as a folder in the git directory. The git folder is subdivided into folders by organization similar to how this wiki is divided.

Each of the literature sub-folders are Calibre libraries.