I've a single C# file with a cspp extension.  In the config file, I've set:

EXTENSION_MAPPING      = cspp=CSharp
and
FILE_PATTERNS          = *.cs *.cspp

When I run Doxygen with these settings, it states:

"Adding custom extension mapping: .cspp will be treated as language csharp" 

However, the file is not fully processed.  It documents the first enum listed in the file, and then quits.  I see the exact same behavior when I exclude the EXTENSION_MAPPING line altogether.

However, if I change the file's extension to cs, everything is documented properly, and more information is reported to the command window.

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I have the exact same setup for a Java file with a jpp extension. In the config file, I've set:

EXTENSION_MAPPING      = jpp=Java
and
FILE_PATTERNS          = *.java *.jpp

However, in this case, everything works perfectly.