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I've been using "PSAppDeployToolkit" in SCCM for a while now to manage conflicting processes. It would be great to have these additional features:
1). The dialog box that says the apps which need to be closed before installing, it would be great to allow other windows to go on top of it, until a set time before the deadline, to then make it always be on top.
2). When installing/upgrading an app, to have the ability to show a dialog box with custom text (see attached install.png)
#2 already exists, you are able to set custom text in the progress dialogs.
As for having the window move to the top after a certain amount of time - that's a good suggestion, however you can kind of do that already by configuring the prompt to not be topmost (-TopMost $false in v3, or -NotTopMost in v4) in combination with the -PersistPrompt switch (which will surface the prompt to the top at regular intervals defined in the config file).
+1