Getting Pageant to save keys files?

Pageant cannot save the encryption keys for the key files. That would defeat the entire purpose of encrypting the keys in the first place...

However, if you edit the keys with PuTTYgen, you can store the keys unecrypted. Just leave the password field blank.

As mentioned already, you can add the key locations as command-line arguments to pageant. If you are running pageant from the Windows Start-Up folder, simply pass the key locations in as command-line arguments in the shortcut. For example:

"c:\program files\putty\pageant.exe" "c:\mykey.ppk"

For a comprehensive guide to setting this up, see the this page.

The simplest way to do this in Windows is to create a specially crafted shortcut inside the Startup folder (Start -> Programs -> Startup):

Note: This only works if you did not set a password on your key

1. go to Start menu, then "Programs", right click on the Startup folder and choose "Open"
2. right-click inside the folder and select "New", then "Shortcut"
3. browse to your PuTTY installation, for example "C:\Program Files (x86)\Atlassian\SourceTree\tools\putty" and select "pageant.exe"
4. name the shortcut whatever you want
5. right-click the newly created shortcut and select "Properties" You should see something like this:

Append its full path to your "Target" field like so: Target: "C:\Program Files (x86)\Atlassian\SourceTree\tools\putty\pageant.exe" C:\Git\Key.ppk

You should now see:

This particular set up is for GitFlow and Jira.