Re: create a blank .flag file when a file is picked up.

Then you will need to write a pipeline component.  There is a simple example of a pipeline component in the BizTalk Install directory at SDK\Samples\Pipelines\CustomComponent.  

Also, here is a pretty good online tutorial..

http://blogs.msdn.com/brajens/archive/2006/11/25/how-to-develop-biztalk-custom-pipeline-components-part1.aspx

http://blogs.msdn.com/brajens/archive/2006/11/25/how-to-develop-biztalk-custom-pipeline-components-part2.aspx

http://blogs.msdn.com/brajens/archive/2006/11/25/how-to-develop-biztalk-custom-pipeline-components-part3.aspx

Your code to write out this .flag file is going to most likely end up in the Execute method of your pipeline component. 

-Ben