Right now you can deploy a base line to see if system have all the require local apps. Would be nice if you allow the system to have remediation for the missing application, that is specify by the company. As of now the only thing you can have baseline auto fix is Registry value & Script (by running remediation script) & WQL Query. If it could auto and manually fix application that would be outstanding. I would allow it in these two ways, if the system detects it missing an app it auto deploys that package ID to itself (Check box when setting up configuration item). You could also make when you make a right click on a baseline deployment and click create collection, during that process you pick what configuration item you want to re-mediate (where the red arrow is). I think both ways would be very helpful to get an environment corrected.