Munki and Jamf run as root, so scripts they execute execute as root, not user.
One great way around this is to use Outset‘s login scripts (login-once, login-every), but sometimes you may have occasion to actually run a script immediately as the logged-in user.
Obviously, you’ll want to get the currently logged-in user into a variable you can use—several methods for that are described in How To: Get the currently logged in user, in a more Apple approved way—and you’ll want to watch out for the “logged in user” being _mbsetupuser, root, or just blank.
Then, you can use su to substitute a user identity:
/usr/bin/su -l "$loggedInUser" -c "commandyouwanttorunastheuser"
This is kind of a hack, so whether you’re using this as a postinstall_script in a Munki nopkg or a script that a Jamf policy is calling, you’ll definitely want to thoroughly test it to make sure it does what you want it to do