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Since the dawn of graphical user interfaces, there has been almost no change in now we manage and organize files and folders. The file managers of today are fundamentally identical to the file managers 20 years ago. All of the file namagers of today - in any operating system, including mobile - have severe limitations. Two of those limitations are mention below. A concept for a new, radically different file manager, free of those limitations is then presented.

1) Suppose you have some personal file or a file from work that you want to save to your computer. However, you can't quite decide in which of your folders to put the file. Perhaps you have three directories in which that file would belong equally well. You have a couple of options. A) you make a choice and put the file in one of those three folders, or B) you really want that file to be in those other two folders as well, so you place shortcuts in those other two folders. Suppose you choose B). After a year you go back to that file. You find the folder that contains the actual copy but you want to know in which other folder you put a shortcut to that file. In some file managers and operating systems you can do that (although it will take time), in others you cannot.

2) For many of us, one of the most annoying tasks is file management. Many of us have external backup drives where at least a couple of times annually we simply dump everthing important from our computers. Pehaps we just put everthing in a single folder or two, or do some minimal organization, and put it in the backup drive. We always think that once we find some free time we will organize those files, but we never find that time. As a result, after a couple of years our backup drives begin to resemble the contents of a garbage truck in terms of how messy everything is. After a certain point, we might even begin feeling that organizing the contents in the backup drive is simply a hopeless task that would take weeks to accomplish.
Why is that? What makes file management such a difficult and time consuming task? The answer I have come to is the following. The file managers of the present force us to make one choice when there might be several equally valid choice. Here is what I mean. Suppose you have a thousand files - of various kinds - that you want to organize. There is probably tens of ways of organizing those files. Let's give more specific examples. Suppose you are doing academic research and those 1000 files are all related to your research - shortcuts of websites, research papers, your papers, videos, pictures, algorithms, code, etc. One way of organizing them is by type - you have a folder for each file type. Another way is to separate the files by subtopic. Or maybe you want to organize them by source - perhaps you want to put the research papers and programs from different universities in different folders. Let's suppose you overcome this challenge and decide to organize the files by topic - a folder for each topic. Then you come to a second problem. Some files - say some research papers - belong to two or more topics (folders). The task of organizing the files becomes very difficult, therefore. There are many equally valid ways of organizing those 1000 files but the file managers force one to make a single choice. What if we did not have this limitation. What if we were able to make all of those choices simultaneously.

The aforementioned are two of many limitations that the file managers of the present have. I came up with a concept of a file manager that is free from the those and other limitation. A file manager that does not force the user to make a single choice when organizing files but allows the user to make all the possible choices. A file manager which would transform the task of organizing our backup drives from being a dreadful and impossible task to becoming a task that is enjoyable and quick.

The concept I am proposing is best explained with pictures but I will try my best to explain it in words while relying on the reader's imagination.
I am proposing a file manager which displays files in two different ways "Galactic View" and "Singular View". These are virtual views - I will explain what I mean later.

Galactic View -
imagine a galaxy where each star is a file (this can be either 3D or 2D). You have the ability to zoom in and out. The distance between two files represents how closely related those files are according to the judgement of the user. Suppose you have 1000 files that are unorganized. The picture you should be having in your mind is that of the Andromeda Galaxy but with only 1000 stars or files. The first step toward organizing those files would be to start moving them around. Think of it as moving stars in a galaxy, or maybe creating multiple galaxies from those stars. Say you make 5 galaxies from your files. You can zoom in and out so you can see any number of files or groups depending how far you zoomed. But suppose you have about a dozen files that you think should belong to more than one group. No problem. This is a virtual representation of the files. What you are seeing in this Galactic view is simply 'shadows' of the files. Therefore, in this galactic view you can have as many 'shadows' of a file as you want. Hence for your problem where you want to put those files in more than one group, you can just make more shadows of those files and put them into as many groups as you wich. OK, now that you have 5 galaxies, you go to the next step, You can start organizing each one of them further. If you think that a file is closely related to another file, you put those two files close to one another. If a third file is slightly less related to those two, you put that file a little bit farther away but still slose to them - think about it as moving stars in a galaxy. Suppose now you want to isolate some files. Then you can simply put them inside a bubble and name the bubble - a bubble would be the analogy of a folder - but think of that bubble as being 50% transparent so you can see the files inside the bubble and some of those outside it. Depending on your zoom level, you can be either inside or outside the bubble. Imagine now you are seeing the bubble from outside - and you can see the three files that you have in the bubble. But at the same time, you are seeing some of the files that are close to the bubble. The distances between the files still represent how closely related they are according to your judgement. If you think that a file is closely related to the files in the bubble but should not be in the bubble, you simply place that file close to the bubble. You can also have bubbles inside other bubbles - analogous to folders within folders.
You may also have lines that connect two files - think of those as lines between stars in a galaxy. Maybe those lines would also represent relationships between files. This would be just an additional way of expressing how related certain files are. It would be to the user to decide whether to connect certain files by lines and what purpose to ascribe to those lines.

Singular View -
Think in terms of the Galactic View still. Suppose you are looking at a certain file. But as we said in the previous paragraph, you may have that file (or to be more precise the 'shadow' of that file) in several different bubbles (folders) simultaneously. Once you single-click on a file the following will happen. Before clicking the file, you were seeing it as a star in a galaxy (Galactic View). After single-clicking the file the view changes to "Singular View" where the file you clicked is displayed at the center of the screen, and to it are attached the bubbles (folders) in which it appears. Say for instance your file is named "a" and it belongs to the bubbles (folders) "F1", "F2", and "F3". And say Folder "F2" is insider a bigger folder named "BF1". What you would see in the "Singular VIew" for file "a" is the following:
"a" would be at the center of the screen and three branches would be attached to it - one branch leading to "F1", another one to "F2", and another to "F3". But since "F2" is inside "BF1" then a branch will be attached to "F2" that leads to "BF1". If you have trouble imagining what I just described, then do an online image seach for "network digram" or "idea digram", and you will seee immediately what I mean.

The aforementiond "Galactic View" and "Singular View" refer to how files are displayed to the user. These views would only be showing vitrual copies of the files - shadows of the files. Where the files are actually located - in which directory - that is a different story. We might have a third view "Directory Tree View". This would show where the files physically sit - and it might or might not be related to how the files are displayed in the "Galactic View". Organization of the ACTUAL files may be as simple as having one folder for each file type. And maybe inside those file-type folders there is a folder for each letter of the alphabet. Or the files may be organized the same way as they are organized in the Galactic View.

A name for such a file manager could be "Galactic File Manager".

Prior to posting the this idea, I spent some time searching whether something like this already exists. I could not find anything even close to what I have described. But if anyone knows of a file browser that already has the aforementioned features, please share it. Please share your comments.

Thank you for reading. It probably took you a while to read this, but to make you fell better, imagine how long it took me to write it .

There is another solution to this problem that has already been implemented: tags. You put the files wherever and use KDE's tagging system to tag the files. The file manager has ways of displaying the tags that are associated with a given file (Information Panel or Tags column), the tags that have been used for different files (tags:// kio) and the files that are associated with a given tag (tags://given_tag).

This idea might work well for some people who have a high aptitude for spatial cognition (this may not be the right term - the ability to organize and keep track of things using 2D or 3D spatial mapping), but I think that there are very few people who would be benefited by such a representation. I also see working with files in this manner as being a lot more cumbersome than even hierarchical folder based organization.

While it might make for pretty galaxy pictures, I don't think it would be easy or user friendly.

Having to manually drag and drop stuff around to show their relationship would be a lot more busywork then current filesystems. People barely bother with dragging and dropping everything into a folder called Backup, or mass-labeling half of them red, I think dragging relationships would be tedius for a lot of people.

Distance as the only measure of relationship doesn't really help if you don't remember the context in which that relationship was described.
(Did I place catpicture_1.jpg close to unknownpicture_2.jpg because they're both about cats? Or because they're both about silly things?) The bubbles do fix that to an extent, but bubbles are essentially the same as folders, so I don't see much added benefit.

Powerful searching and automatically generated tags are a much more descriptive and powerful way to look for files then positional display IMO.

Now perhaps a galaxy-view for searches, where the bubbles are automatically defined by the Tags associated with files? That might be interesting, at least visually.

This sounds very similar to this: http://youtu.be/M0ODskdEPnQ?t=17s
It is a virtual desktop with 3d books/files in a physics sandbox that can be stacked and manipulated.