MacOS – How to close all windows of Mac OS X Finder

At the risk of stating an idea too obvious to merit an answer, I will point out that ever since OS X 10.9 Mavericks, tags are perhaps the most obvious way to take "several related files in different folders" and "combine them in the same view" as stated in the original question.

In the Finder, select any item and then use the Tags... menu item (to which you can assign a keyboard shortcut in the Keyboard system preferences pane), or the Edit Tags button in the toolbar of any Finder window, to assign a tag to that item. You can then click on the name of that tag in the recent tags list (in the sidebar of any Finder window) to see a list of all files tagged with that tag. Or you can search for that tag and save the search as a smart folder. You can tag any items that appear in Spotlight search results, including email, contacts, reminders, etc. For more information about working with tags, see my answer to this question about tags best practices.

If you hold down option while resizing the window and then close it, the next time you open it from the dock it will open at the new default size.

You will need to do this with the other ways of opening the finder window, such as clicking the HD icon on the desktop of after closing a window going to file -> new finder window.

Once these have all been done you will not have to do it again.