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Based on various tests with InspectIT and documentation the best instrumentation point for Apache Tomcat , or other products that use the Coyote Connector , was determined:

Its the function org.apache.coyote.http11.Http11Processor.prepareRequest() which is responsible to convert a received request to such a format, that it can be further processed by Tomcat's internal engine.

You need only to instrument this function so, that the following the header is access accessed and removed at the end of the method:

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The headers are stored in the variable "headers". Its class provides the functions to access and remove:

            headers.getValue("InspectITID"); // To access the ID
            headers.removeHeader("InspectITID"); // To remove the header
        }