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All paths are from the install directory where the jtinstall script was directed to place the installation, which is saved as the $WTHOME environment variable in the setup file. 

pi/bin is the directory where most system administrative tasks are performed. The file in that directory called "setup" contains system environment variable value that should be in the install users environment whenever performing operations with the CLI such as backupdb and restoredb. CLI operation must only be performed under the user id that installs Journyx. You can source the setup file in the install user's ~/.profile or ~/.bashrc or equivalent, or simply source the file prior to performing any system maintenance as the installing user. 

cd <install directory>/pi/bin

. ./setup

that's a dot, then a space then dot slash setup. Or alternatively,

source <install directory>/pi/bin/setup

Usually it's easier to add the sourcing of the setup file (the above command) to a shell profile file such as ~/.bashrc so you don't have to remember to do it every time you log into this account. you should do this under the Linux account where you installed Journyx. On windows everything is keyed off the %WTHOME% environment variable instead. 

cgi, timesheet, and wtlib under $WTHOME/pi/pylib are the directories where the application logic Python modules reside.In the event that a patch is require for a Journyx software problem, the likely resolution will involve replacing a module in one of these directories. Do not attempt to manipulate any files in these directories without the direction of Journyx Support.Normally all patches are provide with an installer script which copies the files to the right directories.

SavedReportFiles and jtfs, special directories used to save user information in previous release are no longer used as of Version 8.9 see the notes on the restoredb command below for more information.