MS Visual Studio has Solution Explorer where I can see all project files, I can also create filters which are like folders for files to keep them in groups. The problem is - I w
If you click 'show all files' you switch solution explorer from showing a virtual filter of files to a physical filter of files.
No - SE and the Filing System hold independent copies of the structure/hierachy information.
I usually disable the filters and put files where I want them, so that the two structures remain in sync by default (indeed, any other way seems like madness if you want to have any kind of organisation of source code - I always group files for components inot separate folders).
Then (with filters disabled)...
If you create the folders in Solution Explorer, and use the context menu from that folder to "Add new item..." or "Add existing item" then the disk structure will reflect the solution explorer (existing items are copied rather than referenced from where they currently reside to ensure this, which can result in old copies of files being left around your project if you add to the wrong SE folder). Otherwise it is usually only if you "add as link" that VS will put an item in a different folder in the SE than it appears on disk.
To tidy things up, the easiest approaches are (after making a backup copy just in case):
Once they're in sync, only use the SE to manage the files, and be careful to add items using the context menu from the correct folder. If you move things about on disk, you'll break the links.
By filters I think you are referring to Solution Folders. Those are virtual folders that have no bearing on the file system. A trick I did is make a throw away project. Items added to project folders maintain their relationships. It is a hack, but it works. If someone knows a less hacky way to do it, I'd love to know, too.