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Messed up file system

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If i go to the sd card or phone memory...the folders are so cluttered up. This has to be the most irritating part of android. No discipline whatsoever. Kind of ridiculous. Any application i install almost inevitably ends up creating a folder right at the root of the memory.

For example, In windows we have
1. Windows folder - system files.
2. Program files - installed programs.
3. %appdata% / %programdata% - application / user settings.

Is there some way i can organize my file system? Is it possible to force android to be more disciplined? Since i'm going down this road in a day or so, any custom ROM's?
 
For example, In windows we have
1. Windows folder - system files.
2. Program files - installed programs.
3. %appdata% / %programdata% - application / user settings.
These elements are not so different in most cases:

System apps live in the /system folder.
User installed apps live in /data/app
App data live in /data/data/%app%

However, that's all in the internal storage, and if you are not rooted you probably can't even see that. The point is that the root of the SD card (or the /sdcard partition, which is part of the internal storage and not actually an SD car) is not the root of the filesystem but the root of a general media storage area.

Where apps do store stuff in the sd card (either the real SD card or the "internal sd card") some apps let you select the location via the app's settings. If the app doesn't let you do that, if you move the data it may not know where to find them (though you can usually organise stuff like music or photos as you like as the apps that use them will search the whole card).

As an aside, I'm always annoyed by desktop OSes and apps which assume that I want to keep all my documents in an undifferentiated folder called "Documents" - I sort my files by their content, context or purpose as the most important classification, not which app produced them, so have to constantly overrule what to me is a stupid default behaviour ;)
 
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