Can you use CloudWatch Agent on Windows to create a measure which is the number of files in a directory

You can publish a custom metric to CloudWatch in the form of a script output doing a simple file count in your windows directory.

Have a small script running via task scheduler that checks the number of files in the directly and makes a put-metric-data call to CloudWatch and publishes the file count.

See here for how to publish a custom metric: http://docs.aws.amazon.com/AmazonCloudWatch/latest/DeveloperGuide/publishingMetrics.html