Opt / Private Folder visible on HD?

Question

for some reason my /opt /private folders are not hidden anymore while the rest of my finder's hidden files are. What would cause these to be visible again, and how do I change them back? I know it has something to do with permissions, or fixing it might involve using "chflags"command.

update: so I fixed it after some searching around by using chflags

sudo chflags hidden /opt /private

though Im still curious what caused these files to change. Do you think it would have anything to do with developer tools or SDKs? I recently installed a bunch for mobile testing/development