In C:\Windows\Temp there are many APT# folders; each having a different number after them, such as APT0, APT1, etc. These folders all appear to have the same file in them, which could be an installation of a specific Agent, such as Application Metering, Software Delivery Solution, etc.
Every time an Agent installation or upgrade task is executed, it creates an APT# folder with the MSI file in it. When the install task's policy is set to run multiple times on a schedule (every day, every hour, etc) and the collection always applies to every computer, it continually creates new folders.
In general, the practice for dealing with sub-agent installation or upgrades is to push it out to Run Once, and it is generally best to keep it like this, cloning the task if needed for future updates.
Note: In case that you have multiple machines that have a large amount of APT folders and you want to clean out your Temp directory in an automatic way rather than going to each single machine and delete them manually, you can create a Task Server Task or a DS job that runs the following VBscript on a regular basis (in most cases running this task once should be enough):
--VBScript to remove APT files from c:\Windows\Temp. Script is below:
Set oFSO = CreateObject("Scripting.FileSystemObject")
Set OFWindows = oFSO.GetFolder("c:\windows\temp")
Set OWinFolders = OFWindows.SubFolders
For Each OWinFolder in OWinFolders
if Ucase(left(OWinFolder.name , 3)) = "APT" then OWinFolder.delete force
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