I'm using the command line. I have also updated to Eclipse Kepler. It seems to execute javadoc differently? I'm investigating. But try this:
read the javadoc manual. It's confusing and doesn't tell you what to do, but, here's an example that should get you going.
Create a file called "options"
Add to the file this:
-d target-bin
-stylesheetfile style.css
-use
-splitindex
-windowtitle 'My Project Name Class Specification'
-doctitle 'My Project Name Class Specification'
-header '<b>My Project Name</b><br><font size="-1">0.1.5-alpha</font>'
-bottom 'Copyright 2014 My Company or Myself. All rights reserved.'
-group "Group Of Packages" "com.mypackage.*"
-overview overview.html
-exclude 'android'
-subpackages 'com.mypackage:android'
-charset utf-8
-encoding UTF8
-quiet
-sourcepath ../myProject/src;..\..\..\android-sdks\sources\android-19
Then on the command line type:
javadoc @options
Now, in Kepler, the "Generate Javadoc" dialog box says "What is the javadoc command line"...I suspect I'll have to type something like this. But don't know.
Hopefully this quick example will give you a start on how to get it done for your purposes.
By the way, I created a generic Eclipse project called "javadoc" in my Workspace so I could manage the files.