`wstool` has assumptions about workspaces (hence the name). It also requires one to operate on (or initialise one). From the usage doc string:
> wstool is a command to manipulate ROS workspaces. wstool replaces its predecessor rosws.
Successor to `wstool` is [vcstool](
https://github.com/dirk-thomas/vcstool), which completely decouples "downloading repositories" from workspace management. Part of the rationale would seem to be exactly the points you raise.
`vcstool` uses `.repos` files (to avoid the confusion with ROS) and only supports `.rosinstall` files for convenience / historical reasons.
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