How can I close windows when quitting an application - but leave desktop windows open?

In Mavericks...
Is there any way to close the windows of application (when quitting - ie System Preferences => General) BUT not have this affect the finder application.
I want the windows I have opened in the finder to remain opened, but everything else to close upon quitting

Well, for some time now (since I upgraded to Mavericks) my startup goes on and on.
It will, on occasion, finish correctly and I can go on with my work, but usually, it hangs.
I can restart the finder 2 or 3 times and get it to finish loading.
If I go into System Preferences => General => and turn “Close windows when quitting an application” on, then restart, the finder usually starts up faster and does not hang
Obviously, there is some operation that is running in the background that is trying to restore itself to some unknown state that is holding up the finder application.
I have uninstalled and turned off all sort of applications that run in the background, but have not yet been able to locate the culprit.
So, I’d like to be able to have “Close windows when quitting an application” on because everything else on the machine can revert to a clean start-up state -- but I want the windows I leave opened in the finder to remain opened and where I put them.

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