Full documentation for SonarQube has moved to a new location: http://docs.sonarqube.org/display/SONAR

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Only password-checking is done against PAM. Authorization (access control) is still fully managed in SonarQube. A SonarQube account must be created first for each new user wishing to use SonarQube. The System administrator should also During the first authentication trial, if the password is correct, the SonarQube database is automatically populated with the new user.  The System administrator should assign the user to the desired groups in order to grant him necessary rights. If one a password exists , the password in the SonarQube account SonarQube database, it will be ignored because the external system password will override it.