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I tried updating PuTTY, but it didn't quite have the desired effect.
I had PuTTY 0.71 installed, and 0,73 is the repository version.
Here's the output from the Command:

System looks to be online, executing command.

App Manager Running Agent Update Checks for [PuTTY release 0.71 (64-bit)].....
Chocolatey v0.10.15
Upgrading the following packages:
putty
By upgrading you accept licenses for the packages.
putty v0.73 is the latest version available based on your source(s).

Progress: Downloading putty 0.73... 10%
Progress: Downloading putty 0.73... 33%
Progress: Downloading putty 0.73... 55%
Progress: Downloading putty 0.73... 77%
Progress: Downloading putty 0.73... 99%
Progress: Downloading putty 0.73... 100%

putty v0.73 (forced) [Approved]
putty package files upgrade completed. Performing other installation steps.
The upgrade of putty was successful.
Software install location not explicitly set, could be in package or
default install location if installer.

Chocolatey upgraded 1/1 packages.
See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).


And now I do see PuTTY 0.73 in C:\ProgramData\chocolatey\lib\putty.portable\tools
But that didn't replace the installed PuTTY 0.71 version. It just added these files, but they don't run by default or from command line. So when I load up PuTTY, it's still the old 0.71 version.
How do we get it to actually upgrade an app rather than installing a portable version?

I'm assuming Habitat is supposed to pass the software install location for the 0.71 version?

You must select the correct "package" from the Chocolatey repos.

The one you chosen is a portable version of the program, try finding the "full installed putty" version of the package and then update the search with the new install title.

This will the cause putty to be physically installed on agent and seen in the installed Applications and Softwares of the Windows OS which is then inventoried by Automate and as such updates our "installed" version with in the plugin.

We get our version data of software installed directly from Automate then we use Chocolatey to query what they have on repos for your package title. If versions differ older to newer we call on Chocolatey to install new version. We then force a software inventory on agent and our data should then update to show newer versions.

But this only works if your installing full repo packages and not specialty packages.

Here are the 3 putty repo packages available, try one of the other 2 packages.

Reading the fine print, I found this on the main putty package:
This meta package depends on putty.portable rather then putty.install for historical reasons. Since this may violate expectation of certain users, consider installing the latter directly.
So I'll try putty.install instead.