The following was observed running javadoc on a sample API.

Notice files being generated twice (allclasses.html), seemingly similar files (all classes-index.html, all classes.html) and duplicate messages to the log ("Building index for all classes...")

Constructing Javadoc information...
Standard Doclet version 11-ea
Building tree for all the packages and classes...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/A.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/C.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/C.N.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/E.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/I.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/A.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/C.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/C.N.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/E.html...

Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/I.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/package-summary.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/p/package-tree.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/mA/module-summary.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/constant-values.html...
Building index for all the packages and classes...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/overview-tree.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/index-all.html...
Building index for all classes...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/allclasses-index.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/allpackages-index.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/deprecated-list.html...
Building index for all classes...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/allclasses.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/allclasses.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/index.html...
Generating build/test/apitest/APIReaderTest/testAPIReader/api/help-doc.html...