General

Can run classes and code to build be hosted in separate projects ?

Of course yes. If you prefer that your Jerkar run code lies in a distinct project, create a Jerkar project in a sibling folder and mention where is located the project to build.

...
@Override
protected void setup() {  // project to build lies in a sibling folder. 
      Path projectPath = this.baseDir().resolve("../myProject");   
      project().setSourceLayout(JkProjectSourceLayout.ofMavenStyle().withBaseDir(projectPath));
      ...

My run class does not compile so I can't invoke any Jerkar method as 'help' or 'scaffold#run'. What can I do ?

You can specify a built-in run class to run. This way, compilation won't occur. For example jerkar -RunClass=JkRun help or jerkar -RC=JkRun scaffold#run java#".

Compilation

How can I choose the JDK used to compile ?

Jerkar uses the JDK it is running on to compile production or test code. If code must be build on a another JDK version, you can specify JDK path for different version. Just mention it as option, for example in your [JERKAR HOME]/options.properties file.

jdk.6=/software/jdk6
jdk.7=/software/jdk7
jdk.9=/software/jdk9
...

This way, if one of your project source code is declared to be in a specific Java version, the relevant JDK version will be used automatically to compile it.

How can I use Eclipse compiler in Jerkar ?

Jerkar can use any JSR199 Java compiler to compile your Java code. Just set the compiler instance you need as :

import org.eclipse.jdt.internal.compiler.tool.EclipseCompiler;

@JkImport("org.eclipse.jdt.core.compiler:ecj:4.6.1")
public class Build extends JkRun {
    ...
    maker().setCompiler(JkJavaCompiler.of(new EclipseCompiler()));
    ...
}