If you use a tool like Process Monitor, you can see that when a directory is opened, explorer.exe performs a DirectoryQuery. I don't know if DirectoryQuery is specific to procmon, but I'm trying to see if I can capture those calls within C#. Or determine if there are any Win32 APIs I can PInvoke to get this info.

There are other tools like Clover that also do this. The functionality I'm trying to replicate is basically the same as Clover. Where I would redirect new directories to my application instead of Explorer.
If anyone can point me in the right direction, I would greatly appreciate it.
If you want to write your own File Explorer application then you can use the IExplorerBrowser object to do 90% of the work for you. Register a new default verb for the Directory and Folder ProgIds.
If you want to hook into Explorers File Explorer windows then you must implement a browser helper object (C# if you must) and tweak it so it only loads in Explorer.
DWebBrowserEvents2 will tell you about navigation events.
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