Sonar properties files

You have to specify the projectBaseDir if the module name doesn't match you module directory.

Since both your module are located in ".", you can simply add the following to your sonar-project properties:

module1.sonar.projectBaseDir=.
module2.sonar.projectBaseDir=.

Sonar will handle your modules as components of the project:

EDIT

If both of your modules are located in the same source directory, define the same source folder for both and exclude the unwanted packages with sonar.exclusions:

module1.sonar.sources=src/main/java
module1.sonar.exclusions=app2code/**/*

module2.sonar.sources=src/main/java
module2.sonar.exclusions=app1code/**/*

More details about file exclusion