What do I need to install on my machine so that I can run Powershell scripts against our Office365 SharePoint farm? I want to be able to spider for our Sites and then the folder tree in each.

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You need windows Powershell & .net Framework & Office 365 Sign-in Assistant.

Install and Configure the Office 365 PowerShell Cmdlets

Also check this anwser: http://community.office365.com/en-us/f/148/t/21214.aspx

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