From Deepak Bhole dbhole at redhat.com,
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A javadoc user recently reported a bug for Fedora whereby they were
seeing .class files being compiled by the javadoc tool:
https://bugzilla.redhat.com/show_bug.cgi?id=719118

I have been able to successfully reproduce this locally as well.

 From what I can tell, the issue is that the scanner function searches
for .class files in addition to .java files:

http://hg.openjdk.java.net/jdk7/tl/langtools/file/a72412b148d7/src/share/classes/com/sun/tools/javadoc/JavadocTool.java

(line 270 and 276).

After changing 270 to scan for java files and removing class file kind from
276, I can no longer reproduce the issue as only .java files are
considered then.