I see your problem; somewhere recently he changed the Wizard to use an CB "Global Variable" instead of Linking file/folder solution; but, I did NOT do that change on Linux.
(But, I forgot if I tested the wizard on Linux or not after he asked.)
I will see what the Global Variable is supposed to be.
The base location of the Global Variable needed to be "/home/stahta01/devel/open_source_code/version_control/arduino_ide-git" for me.
( I just tested this location "/home/stahta01/devel/open_source_code/version_control/arduino_ide-git/build/linux/work" and it also worked for me.)
The results of the above list needs to contain at least the folders "hardware" and "libraries".
My folders below.
app arduino-core build examples_formatter.conf format.every.sketch.sh hardware libraries lib_sync license.txt README.md work
In doing my solution I had to edit an header search path in the Wizard created project
Sorry, about the confusion; I missed when he did the change to Global Variable under Linux.
To create a CB "Global Variable" use
Setting -> "Global Variables ..."
Click on "New" (By the current variable) enter "arduino" for the name of the variable.
I have attached an image of the window below.