Build Documentation Choose Version
Retrieve a list of available git tags.
Use git checkout to select the preferred version (or git branch) to build.
git checkout 126.96.36.199.4-stable
Replace 188.8.131.52.4 with the actual version chosen for the build: the stable, testers-only or developers version. Common sense is required when choosing the right version number. For example, the latest available version number is not necessarily the most stable or suitable. To learn more about current Whonix versions, follow the Whonix News Blog.
Clean Up and Sanitize
This step is also important for security.
Retrieve the list of extraneous files and folders. 
git clean -ndff
See if the output looks sane; it generally should, unless Whonix source code is modified by advanced users (who understand git better anyhow). If the output looks like the following, everything is fine.
Would remove packages/apparmor-profile-gwenview/ Would remove packages/kde-privacy/
Remove these folders.
git clean -dff
The output should show.
Removing packages/apparmor-profile-gwenview/ Removing packages/kde-privacy/
Be sure to check out the right commit for each git submodule.
git submodule update --init --recursive
Check there are no extraneous files. This is important for security.
The output should show the following:
nothing to commit (working directory clean)
If the directory is not clean, the extra files should be removed first.