Zhen - sorry to not make this clearer. I was working through the issue as I was writing this below.

The best thing would be to have the creating from template process modify on the fly the site type created via a template to whatever ur-type it is. So if a template with "affiliation" site type is picked, the resultant site should have a site type of "course".

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Thanks to https://sakaiproject.atlassian.net/browse/KNL-1016#icft=KNL-1016 one can now create many site types that resolve as "course" (that is - they are treated as a course). But the UI in many places is not checking the values set via https://sakaiproject.atlassian.net/browse/KNL-1016#icft=KNL-1016 and sakai.properties and instead is checking for the primitive "course"

When creating a site from a template with a site type that resolves as "isCourse" the resultant site is not treated as a course: it's title is editable, tools can be reordered (even when this is not allowed for courses), etc.

------------ ATTN ------------------
The simplest solution would be to modify on the fly the site type created via a template to the target site type. The type is defined through this config variable "<type>SiteTargetType":

For example:

courseSiteTargetType = course
projectSiteTargetType = project
...

If the <type>SiteSiteTargetType
-------------ATTN --------------------

At Michigan we are planing to use a collection of templates that have special site types (the site type is used to provide a categorized list of templates)

Course
Affiliation
Project
Specialized Courses
Specialized Projects

Of these the following (via sakai.properties) is considered a course:

courseSiteType.count=3
courseSiteType.1=course
courseSiteType.2=affiliation
courseSiteType.3=specialized_courses

-------------ATTN --------------------
So if a template with "affiliation" site type is picked, the resultant site should have a site type of "course" to keep things simple. Hah.
-------------ATTN --------------------

The other option is to nail down anywhere where the old way of checking for "isCourse" is still being used.

List of locales where this matters
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1. Site list (chef_site-list.vm) where it renders site type.
2. Site edit (chef_site-siteInfo-editInfo.vm), headers, site title editable, Appearance (Theme)
3. Tools edit (chef_site-newSiteFeatures.vm, as well as the other templates for tool groupings), header, tool selection?
4. Site info page (chef_site-siteInfo-list.vm), toolbar choices.

...or search the codebase!