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As to file manager, yes, all of them (as far as I know) work on top of the shell. However, this doesn't mean that all of them hide the shell behind a menu-based interface (aka curses interface, like mc or ranger, which, if I correctly understood your question, is not what you want). CliFM, for example, works on top of the shell, true, but, being a Command Line Interface File Manager, it gives you a prompt by default (unlike other file managers) where you can run shell commands as usual (plus file-management specific commands built-in in CliFM itself).
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