Empty analysis of projects after upgrade to sonarqube 4.0

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After sonar upgrade from 3.5.1 to sonarqube 4.0, all the Soanr projects analysis become blank.

I am unable to create the sonar-project.properties file on the project root folder, so instead I created linux soft-link to the source code and located it on the project.properties file directory.

This configuration worked perfectly before the upgrade, but now, on the analysis log I get WARN messages such bellow to all of the source files:

20:58:13.290 WARN  - File '/asthome/ast/ccast/mb_ccast/bb/ccrm9Client/v79_9/com/astro/crm/cim/desktop/XNoLinkedWebAccount.java' is not in basedir '/asthome/ast/ccast/sonar/sonar/crm'

I am using sonar-runner 2.3.
Can you please help me to solve this issue?

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