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I've been asked to create some custom themes for an on premise SharePoint 2013 environment, however I only have access to SharePoint 2013 online version, ie mydomain.sharepoint.com

Are there any major limitations or differences between the two versions from a development perspective?

  • do your question ficused only on custom themes? – Sascha May 10 '14 at 10:01
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The 2 platforms are considerably different in the way to approach them.

SharePoint Online (Office365):

  • It lives on the cloud
  • You don't have access to any physical assets/files
  • You can only work with files living in the database (i.e. libraries) or that are hosted in the cloud as well

SharePoint On Premises:

  • Lives on a physical server
  • You can host physical files on the Layouts folder (JS, CSS, Images, Application Pages, etc.)
  • Master Pages and Page Layouts can be Ghosted (this means they'll be read from the physical file while not-customized from the Web UI or SharePoint Designer)

My recommendation would be to do the work with an on-premises installation that matches the client's environment as close as possible, to avoid deployment conflicts after the theme is done.

In-depth (and first hand from Microsoft) information about the different versions of SharePoint: http://technet.microsoft.com/en-us/library/jj819267.aspx

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