In our instance the reason this an issue is that we call the ls.exe utility
from PHP web code and have found that Windows XP is creating system hidden
files in some of our subdirectories (usually the XP auto-created thumbnail
databases). We have also found other ls.exe implementations that do
properly ignore hidden files. The MKS Toolkit for instance does properly
ignore these file types.
It just seems odd that ls.exe shows files that would not be listed with
standard command line "dir".
I agree that the proper way to implement this in cygwin would be to hide
system hidden files by default and have a switch to allow ls.exe to show
these files if requested (like "ls --show-hidden-files" and "ls
--show-system-files").