I'm using Windows x64 and I'm not able to make msysgit to work using pagent authentication.

Here are some details:

The problem is that:

 plink -v -a -ssh git@github.com git version
 FATAL ERROR: Network error: Connection timed out
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up vote 2 down vote accepted

As silly at it may seam the reason for this problem is that plink will use the default hostname/ip from the Default Settings and will ignore command line parameters.

The solution is to remove hostname/ip from Default settings.

Also if you fail to connect due to fingerprint you should first connect one time using putty in order to store the fingerprint, just run putty git@github.com.

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