When an error or warning occurs in an overview file passed
in with the -overview option, they do not contain the
filename (or line number) of the overview file.
The same is probably true of package.html files.

This is important, because they can contain @see,
{@link} and other tags that generate warnings/errors.

You can reproduce this by putting a link in overview.html
to a non-existent class, such as:

   {@link com.package1.XXXXXXX}

Notice in the following messages how the source filename
appears in warnings for *.java files but not for the
very last message, which corresponds with the above error.

Generating html-jamie/deprecated-list.html...
/home/jamieh/stddoclettests/sample-src/com/package1/NewClass1.java:316:
warning - Tag @link: can't find publicMethod() in com.package1.NewClass1
/home/jamieh/stddoclettests/sample-src/com/package1/Class1.java:332:
warning - Tag @link: can't find publicMethod() in com.package1.Class1
Building index for all classes...
Generating html-jamie/allclasses-frame.html...
Generating html-jamie/allclasses-noframe.html...
Generating html-jamie/index.html...
Generating html-jamie/packages.html...
Generating html-jamie/overview-summary.html...
javadoc: warning - Tag @link: Class or Package not found:
com.package1.XXXXXXX

Please also check to see if a warning or error in a package.html
file has the same problem.