KNOWN_ISSUES

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Mapping Files to Modules:

Because a single @module is supported for a set of files, the parser expects that all files in 
the input directory belong to the same module.  If multiple modules exist either in the source
directory or in any subdirectory, files may get mapped to modules incorrectly.

For example:

sourcedir/
    module1.js
    module2.js

sourcedir/
    module1/
        foo.js
    module2/
        bar.js

$ yuidoc.py sourcedir

The workaround is to use the second pattern and pass the source directory for each module to yuidoc

$ yuidoc.py module1 module2

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