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I have an ssh config file with something like this that I am not understanding.

Host my_alias
    HostName me@myserver.com
    HostName %h
    ProxyCommand ssh -W %h:%p me2.myserver.com

I thought %h stood for Hostname. What is the meaning of HostName %h?

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You would typically use Hostname %h like

Host my-*
    Hostname %h.site.dom

which would expand any host starting with my- (e.g. my-test) to the FQDN (e.g. my-test.site.dom)

Hostname %h on it's own won't do anything.

As you also define HostName me@myserver.com first (and ssh_config says "For each parameter, the first obtained value will be used.") the entry will be ignored.

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