This is useful info. Basically, your server or version of PHP is running a long outdated version of the libssh2 code.
One of the things WordPress 4.1 has that 4.0.1 did not is an improved language selector.
Specifically, whereas WordPress 4.0 would show you a list of the languages you already had installed, WordPress 4.1 will, if you have a writable filesystem, get the list of available languages from our API here, and allow you to choose, and then auto-install them for you. This makes it much easier to switch languages and the like.
So, when it's doing the filesystem work to try to use the SSH code, you're getting warnings and such because it's using an outdated version of libssh. You didn't get this in 4.0.1 because it didn't do any of that same filesystem code in the general settings screen.
Updating your server is the only real long-term solution here. Old versions of libraries like this can introduce security issues. Additionally, you may want to update your version of PHP as well. I'd say to use 5.4 or 5.5 at minimum.
Ultimately, no plugin is going to fix this for you. Not really. A plugin might be able to replace the parts that aren't working with other code, but a server problem is a server problem and needs to be fixed there. If the code is that old, it might have security ramifications to not update it as well.
Update PHP, update your SSH libraries, just do a general update of everything, really.
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