Linux Directory Structure also known as FHS (Filesystem Hierarchy Standard) and 'RootFs' defines the main directories and their contents in Linux operating systems, including Puppy. In frugal installation it is held in a series of compressed files BaseSFS, Pup SaveFile and other SFSs.

/mnt
Any media or filesystem that is mounted will have a folder here including hard-drive partitions, cds, usbs and archive files such as SFSs. In frugal mode only files saved in this directory will be outside the PupSave file.

/usr/share/applications
Installed applications with a menu entry will have a link file here, see .desktop files.

/proc
Broadly speaking contains two main groups. Numerically named directories corresponding to the process ID (PID) of a process currently executing on the system. The second file non-numerically named directories and regular files describe some aspect of kernel operation.

Linux Foundation's FHS (2011)
FHS page - links for version 2.2 and 2.3 (2004)
FHS 2.2 page (2001)
FHS manual page
WikiPedia:Filesystem_Hierarchy_Standard
The Linux /proc Filesystem as a Programmers' Tool