[MCHECKSTYLE-299] build type check goal ignored source options when using phases "test site"

**[Johannes Wienke](https://issues.apache.org/jira/secure/ViewProfile.jspa?name=languitar)** opened **[MCHECKSTYLE-299](https://issues.apache.org/jira/browse/MCHECKSTYLE-299?redirect=false)** and commented

I have a project where we enforce a zero-warnings policy. For this purpose we have included a call to `checkstyle:check` in the build phase using the following configuration:

```xml

org.apache.maven.plugins
maven-checkstyle-plugin
2.15

${project.basedir}/codecheck/checkstyle.xml
config_loc=${project.basedir}/codecheck
true
true
warning
true
${project.basedir}/src



checkstyle-validate
validate

check

```

Additionally, checkstyle is set up as a reporting goal in the reporting section:

```xml

org.apache.maven.plugins
maven-checkstyle-plugin
2.15

${project.basedir}/codecheck/checkstyle.xml
config_loc=${project.basedir}/codecheck
true
${project.basedir}/src

```

The project contains multiple source trees and some contain generated code. Therefore it is necessary to restrict checkstyle to only one of these trees where the manually maintained code lives. Otherwise, the build would fail due to warnings being detected in generated code.

This shown configuration works well when calling maven all of the following ways:

```
mvn compile
mvn test
mvn site
mvn test site
```

However, when changing the deprecated `sourceDirectory` elements to the list syntax with `sourceDirectories`, the last call `mvn test site` starts to fail and ignores the specified source directories. All previous other calls still work as expected.

When looking at the effective configuration using `mvn -X` I could see, that in the last call version with "test site", the `sourceDirectories` list of the check goal is again the complete list of source trees instead of the specified one.

Since we are also using some plugins to include the generated code etc., a reference to the complete POM might be helpful for debugging:
https://code.cor-lab.org/projects/rsb/repository/rsb-java/revisions/master/entry/pom.xml

---

**Affects:** 2.15

Reproduce the configuration with Maven using the commands listed, especially `mvn test site`, and inspect the effective configuration with `mvn -X`. Compare the `sourceDirectories` handling in the check goal against the deprecated `sourceDirectory` behavior; done means `mvn test site` checks only the configured source trees rather than all source trees.

Written by the indexing model from the issue text.