Dealing with Folders

I've been trying to figure out a way to deal with user created folders. 
Its very common for users in my organization to work with a set of databases in IDEA and then create a folder to organize them within the current directory. They will create a folder and then move the databases over. The problem though is many of the scripts that I have been written can not find those databases moved into those folders. The scripts will pull all the databases in the current directory unless they are within a folder. 
Is there anyway to have it look into those folders and give the user the option to select those?