We start the sonar from msbuild and pass (among other things) the command line argument: -D sonar.sources = "../../Source/"
C: \ Projects \ MyProject \ build \ Tools \ SonarRunner.2.3 \ Bin ..
SonarQube Runner 2.3
Java 1.7.0_51 Oracle Corporation (64-bit)
Windows 8 6.2 amd64
INFO: Runner configuration file: C: \ Projects \ Project \ assembly \ Tools \ SonarRunner.2.3 \ Bin .. \ conf \ sonar-runner.properties
INFO: project configuration file: NONE
INFO: default locale: "en_GB", source encoding: "UTF-8"
INFO: Working Directory: C: \ projects \ project \ Build \ Scripts.sonar
INFO: SonarQube 4.3 Server
13: 13: 43.706 INFO - Download batch parameters
13: 13: 43.924 INFO - User cache: C: \ Users \ username.sonar \ cache
13: 15: 16.155 INFO - quality setting is not performed.
13: 15: 16.356 INFO - Base directory: C: \ projects \ project \ Build \ Scripts
13: 15: 16.356 INFO - Working directory: C: \ projects \ project \ Build \ Scripts.sonar
13: 15: 16.356 INFO - Source dirs: C: \ projects \ project \ Source
13: 15: 16.356 INFO - Source encoding: UTF-8, default language: en_GB
13: 15: 16.356 INFO - Index files
13: 15: 16.358 INFO - Excluded tests:
13: 15: 16.358 INFO - /. Integration Tests / /.*
13: 15: 16.358 INFO - /. UnitTests / /.*
13: 15: 17.287 WARN - The file '% s' is ignored. It is not in module r '% s'.