The filesystems are organized in a hierarchy starting at the root directory (which has the path '/'). Unlike on typical UNIX systems, the root filsystem is not a mass storage filesystem that the OS was booted from. Instead, it is a virtual filesystem that can only contain directories, symbolic links, and mountpoints.
All the other filesystems are mounted as subdirectories of the root filesystem or further down in the file hierarchy.
The booted filesystem (what would be the rootfs in a typical UNIX) is mounted in '/boot'. For convenience, several links are created in the rootfs to well-known directories ('/bin', '/var', etc). These point into the corresponding directories in /boot/system, which are managed by packagefs.
The packagefs is a read-only union filesystem that makes available the content of various software packages (installed as .hpkg files) to constitute the entire /boot/system directory. The files can be accessed either as a complete filesystem hierarchy directly in /boot/system, or by referencing specific packages exposed in /boot/system/package-links (each directory is a view of the packagefs, containing only the files for a given package and all its dependencies). In theory, this allows packages to be exposed in the package-links directory even while they are not actually "activated" in the main system hierarchy. It also allows to access a version of a file provided by a specific package, in the case that two packages provide identically named files.
While packagefs is mostly read-only, some directories (called "shine-through") are actually exposing the content of the underlying filesystem. This includes for example the "config" directory (for configuration files) and the "non-packaged" directory, where a mirror of the standard filesystem hierarchy is available for non packaged software. This can be used to install software locally that is not available yet in HPKG form (for example, as a destination for "make install").
For a complete list of directories and how to access them in a way that is safe to future filesystem reorganizations, see find_path, and BPathFinder.