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IdentityFiles can be passed to ssh via `-i`, not `-l`.
The next paragraph mentions the correct argument.

ref commit 52c8324fa2,
part of PR drduh/YubiKey-Guide#65
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Michael 2019-01-20 18:48:59 +00:00 committed by GitHub
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@ -1258,7 +1258,7 @@ ssh-rsa AAAAB4NzaC1yc2EAAAADAQABAAACAz[...]zreOKM+HwpkHzcy9DQcVG2Nw== cardno:000
## (Optional) Save public key for identity file configuration
By default, SSH attempts to use all the identities available via the agent. It's often a good idea to manage exactly which keys SSH will use to connect to a server, for example to separate different roles or [to avoid being fingerprinted by untrusted ssh servers](https://blog.filippo.io/ssh-whoami-filippo-io/). To do this you'll need to use the command line argument `-l [identity_file]` or the `IdentityFile` and `IdentitiesOnly` options in `.ssh/config`.
By default, SSH attempts to use all the identities available via the agent. It's often a good idea to manage exactly which keys SSH will use to connect to a server, for example to separate different roles or [to avoid being fingerprinted by untrusted ssh servers](https://blog.filippo.io/ssh-whoami-filippo-io/). To do this you'll need to use the command line argument `-i [identity_file]` or the `IdentityFile` and `IdentitiesOnly` options in `.ssh/config`.
The argument provided to `IdentityFile` is traditionally the path to the _private_ key file (for example `IdentityFile ~/.ssh/id_rsa`). For the YubiKey - indeed, in general for keys stored in an ssh agent - `IdentityFile` should point to the _public_ key file, `ssh` will select the appropriate private key from those available via the ssh agent. To prevent `ssh` from trying all keys in the agent use the `IdentitiesOnly yes` option along with one or more `-i` or `IdentityFile` options for the target host.