java.lang.AssertionError
at com.sun.tools.javac.util.Assert.error(Assert.java:155)
at com.sun.tools.javac.util.Assert.checkNull(Assert.java:54)
at com.sun.tools.javac.code.Symtab.enterModule(Symtab.java:752)
at com.sun.tools.javac.comp.Modules.enterModule(Modules.java:241)
at com.sun.tools.javac.comp.Modules.enterModules(Modules.java:222)
at com.sun.tools.javac.comp.Modules.enter(Modules.java:191)
at com.sun.tools.javac.main.JavaCompiler.readSourceFile(JavaCompiler.java:838)
at com.sun.tools.javac.main.JavaCompiler.readSourceFile(JavaCompiler.java:800)
at com.sun.tools.javac.main.JavaCompiler.access$100(JavaCompiler.java:93)
at com.sun.tools.javac.main.JavaCompiler$1.complete(JavaCompiler.java:331)
at com.sun.tools.javac.code.ClassFinder.fillIn(ClassFinder.java:362)
at com.sun.tools.javac.code.ModuleFinder.findSingleModule(ModuleFinder.java:211)
at com.sun.tools.javac.comp.Modules.setCompilationUnitModules(Modules.java:330)
at com.sun.tools.javac.comp.Modules.enter(Modules.java:193)
at jdk.javadoc.internal.tool.JavadocTool.getEnvironment(JavadocTool.java:190)
at jdk.javadoc.internal.tool.Start.parseAndExecute(Start.java:400)
at jdk.javadoc.internal.tool.Start.begin(Start.java:274)
at jdk.javadoc.internal.tool.Start.begin(Start.java:220)
at jdk.javadoc.internal.tool.Main.execute(Main.java:70)
at jdk.javadoc.internal.tool.Main.main(Main.java:52)

This error was experienced with a bad merge and fixed by:
http://hg.openjdk.java.net/jigsaw/jake/rev/ee7c28c82b0d

To make it easy have attached a reproducer, modify the variables for your top-level repo and build directory.