..The new javadoc correctly does not allow non ".java" files as they were in old Javadoc. Any file with non ".java" extension is rejected. But the error message needs more clarity. Please find the command and the message attached below.
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blr-sunray:/home/vr128054/jdk-latest/jdk1.4.0/src/javax/swing 654 % java   -Dfile.encoding=EUC-JP   -Xbootclasspath/p:/home/vr128054/gj/gjclasses3   -classpath /home/vr128054/gj/gjclasses3   com.sun.tools.javadoc.Main JPanel.xxx
Loading source files for package JPanel.xxx...
javadoc: No source files for package JPanel/xxx 
1 error
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While it is perfectly valid to reject .xxx extension, by default, a "." shouldnt
be considered a package name delimiter. A filename level error message could be more informative.

N/A

On the contrary: the "." IS the package delimiter.  We only
make a special case of handling ".java" to treat it as a file name.

However, in a command such as
	javadoc a/b.c
where a/b.c could neither be a valid source file name nor a package name, we
should just say so.

 xxxxx@xxxxx  2001-04-11

I dont think this is a bug. 
Anything else but .java files should not be given to the 
javadoc command. I feel there are rare occasions where 
this might appropriate, but a foo.xjava file is not 
correctly treated by the compiler anyway.
This new "feature" now leads to errors if the last package 
in the tree is named java, like com.foo.bar.java
Now, javadoc looks for a file called com/foo/bar.java and 
fails.