com.sun.source.util.JavacTask has a method for getting the abstract syntax trees:

    public abstract Iterable<? extends CompilationUnitTree> parse()
        throws IOException;

Also, there is a method for analyzing which may cause source files to be loaded
from source path:

    public abstract void analyze() throws IOException;

Perhaps the method should be modified to return all the trees (including those
loaded from source path):

    public abstract Iterable<? extends CompilationUnitTree> analyze()
        throws IOException;

If a client of the API tries to collect dependency information, the code could
follow this template:

task.parse();
for (CompilationUnitTree unit : task.analyze()) {
    // collect dependency information (using com.sun.source.util.TreeScanner)
}
task.generate();