Now for the question : is it possible to have the game ignore system files/directories ?
You can tell the game to ignore specific folders modifying the file named settings.ini located at C:\Users\<USERNAME>\AppData\Local\AdventurOS\settings.ini and adding a new parameter called banned and each entry separated with the | character. it will look something like this:
banned = "foldername|documents|pictures|"
The game will not create doors that go to directories with that name.
I mean, on C:/ there is a lot hidden system files and directories i can't access with the normal explorer, and i don't like not being able to "map ahead" what's in what room. So if there could be an option or something to disable the use of hidden system files in the future that would be great :).
There is no way of hiding the default systemwide hidden files for now, but is something that we will take a look on implementing in future updates.
Regarding the out of place mosnter, thanks for the report, the screenshot really helps! We will address this issue on the next content update