How to resolve: files which are visible in Terminal, but invisible in the Finder?
Be sure you aren't looking in the root library, but your user library. Skype in Application Support and com.skype.plist are not invisible by default. Try changing the ~/Library/Application Support with /Users/&lt;username&gt;/Library/ Application Support, with  being your Username without the &lt;>. 

I find it easy to "Go to" with Shift+Command+G while there is Finder selected, and in the path type /Users/&lt;username&gt;/Library/Application Support/ and click Go. Then look for Skype. To find the plist, do the same, but with Preferences.

Also note that in terminal, the path to Application support would have a backslash (/Application\ Support), instead of only a Space