Hi, Nicholas.
I recommend using the Integration Server’s built-in package management to promote packages between environments. The convenience of a single ZIP file and webMethods ability to extract and activate code from the ZIP makes this simple.
There are some folks who have developed fairly sophisticated Flow to manage migration procedures and to meet the requirements set by system administrators.
Regarding configuration files, you should be able to find more information in these conversations:
#webMethods#webMethods-General#webMethods-Upgrade#Integration-Server-and-ESB