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We have Citrix XenApp 4.0/4.5/5.0 farms with hundreds of published applications which we will need to edit, preferably through a scriptable command-line tool. I've searched the Citrix Administrator's Guides and their troubleshooting tool list, but I'm returning empty-handed.

Can someone recommend any tools that can view and edit Citrix published app permissions, besides the normal GUI?

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This would have been great. I never stumbled upon a really useful tool which could do that. Thomas Koetzing has a almost complete Resource Kit which contains many tools any (citrix) admin may find helpful.

But I always ended up scripting using the Citrix SDK

A really good guide covering the Citrix SDK

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I'm checking out the SDKs now... The abandoned PowerShell Commands CTP looks like it would be great; but the MFCOM will probably work for all versions we have. Thanks, Tom! –  ewall Jan 19 '12 at 14:34
    
For Xenapp 6 and 6.5 the official Citrix-Powershell-Snapin is great. Don't know if there is a snapin for 5. For 4.5 or lower there is no official snapin available. You're welcome –  Tom Jan 19 '12 at 14:58

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