FULL PRODUCT VERSION :
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 10.0.14393]

A DESCRIPTION OF THE PROBLEM :
javadoc throws NullPointerException when processing libraries that make use of class shadowing.

As mentioned at https://issues.apache.org/jira/browse/MJAVADOC-478 this issue is also reproducible under JDK9.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run attached testcase

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Following class shadowing rules, the first class in the classpath should shadow any classes that follow with the same name. As such:

one/com/MyClass should show up in the Javadoc output.
two/com/MyClass should be omitted from the Javadoc output.
ACTUAL -
javadoc: error - java.lang.NullPointerException

ERROR MESSAGES/STACK TRACES THAT OCCUR :
When running under jdk9:

Standard Doclet version 9-ea
Building tree for all the packages and classes...
javadoc: error - An internal exception has occurred.
        (java.lang.NullPointerException)
Please file a bug against the javadoc tool via the Java bug reporting page
(http://bugreport.java.com) after checking the Bug Database (http://bugs.java.com)
for duplicates. Include error messages and the following diagnostic in your report. Thank you.
java.lang.NullPointerException
        at jdk.compiler/com.sun.tools.javac.comp.Enter.getClassEnv(Enter.java:159)
        at jdk.compiler/com.sun.tools.javac.api.JavacTrees.getAttrContext(JavacTrees.java:885)
        at jdk.compiler/com.sun.tools.javac.api.JavacTrees.attributeDocReference(JavacTrees.java:422)
        at jdk.compiler/com.sun.tools.javac.api.JavacTrees.getElement(JavacTrees.java:407)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitReference(Checker.java:849)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitReference(Checker.java:102)
        at jdk.compiler/com.sun.tools.javac.tree.DCTree$DCReference.accept(DCTree.java:631)
        at jdk.compiler/com.sun.source.util.DocTreePathScanner.scan(DocTreePathScanner.java:71)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.visitLink(DocTreeScanner.java:296)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitLink(Checker.java:763)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitLink(Checker.java:102)
        at jdk.compiler/com.sun.tools.javac.tree.DCTree$DCLink.accept(DCTree.java:500)
        at jdk.compiler/com.sun.source.util.DocTreePathScanner.scan(DocTreePathScanner.java:71)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scanAndReduce(DocTreeScanner.java:83)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scan(DocTreeScanner.java:98)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scanAndReduce(DocTreeScanner.java:106)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.visitDocComment(DocTreeScanner.java:184)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitDocComment(Checker.java:231)
        at jdk.compiler/com.sun.tools.doclint.Checker.visitDocComment(Checker.java:102)
        at jdk.compiler/com.sun.tools.javac.tree.DCTree$DCDocComment.accept(DCTree.java:132)
        at jdk.compiler/com.sun.source.util.DocTreePathScanner.scan(DocTreePathScanner.java:50)
        at jdk.compiler/com.sun.tools.doclint.Checker.scan(Checker.java:193)
        at jdk.compiler/com.sun.tools.doclint.DocLint.scan(DocLint.java:348)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.WorkArounds.runDocLint(WorkArounds.java:108)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.getDocCommentTree0(Utils.java:3028)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.getDocCommentTree(Utils.java:3056)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils$WeakSoftHashMap.computeIfAbsent(Utils.java:3238)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.getCommentHelper(Utils.java:2871)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.hasBlockTag(Utils.java:2953)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.hasBlockTag(Utils.java:2949)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.Utils.isHidden(Utils.java:1553)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.ClassTree.buildTree(ClassTree.java:177)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.util.ClassTree.<init>(ClassTree.java:120)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.AbstractDoclet.startGeneration(AbstractDoclet.java:200)
        at jdk.javadoc/jdk.javadoc.internal.doclets.toolkit.AbstractDoclet.run(AbstractDoclet.java:115)
        at jdk.javadoc/jdk.javadoc.doclets.StandardDoclet.run(StandardDoclet.java:71)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.parseAndExecute(Start.java:604)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.begin(Start.java:424)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.begin(Start.java:341)
        at jdk.javadoc/jdk.javadoc.internal.tool.Main.execute(Main.java:63)
        at jdk.javadoc/jdk.javadoc.internal.tool.Main.main(Main.java:52)

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
one/com/MyClass.java:
------------------------------------------
package com;

/**
 * This class *should* show up in the Javadoc.
 */
public interface MyClass {
}
------------------------------------------

two/com/MyClass.java:
------------------------------------------
package com;

/**
 * This class should *not* show up in the Javadoc.
 *
 * The following link tag causes a NullPointerException: {@link Requirements}.
 */
public interface MyClass {
}
------------------------------------------

argfile:
------------------------------------------
'one/com/MyClass.java'
'two/com/MyClass.java'
------------------------------------------

options:
------------------------------------------
-d
'apidocs'
------------------------------------------

javadoc.bat:
------------------------------------------
javadoc.exe @options @argfile
------------------------------------------
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Remove either file from the argfile (prevent class shadowing from occurring).