After an investigation I found out that account which is used by IIS app pool must have windows user profile (files/folders). I believe that Microsoft.Xrm.Tooling is using user profile location and if you use service account that doesn’t have user profile it won’t work. Details on how to configure IIS app pool identities are here: http://www.iis.net/learn/manage/configuring-security/application-pool-identities
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