The tools get their configuration from /Library/Preferences/ManagedInstalls.plist
If the file is missing munki uses these defaults:

prefs['ManagedInstallDir'] = "/Library/Managed Installs"
prefs['ManifestURL'] = "http:/munki/repo/manifests/"
prefs['SoftwareRepoURL'] = "http:/munki/repo"
prefs['LoggingLevel'] = 1
prefs['ClientIdentifier'] = (fully-qualified hostname)
prefs['InstallAppleSoftwareUpdates'] = False
prefs['SoftwareUpdateServerURL'] = None
prefs['UseClientCertificate'] = False
