I'm wondering if anyone has any special tools they use to specify a large site. Something that allows you to define page templates, transformations, page types, categories and relationships (just to name a few).
I've tried spreadsheets and databases and slickplan and airtable and a few other tools but none of them seem to really make it easy to take all of this information about the architecture of a large complex site out of my head.
I'm not sure I understand what exactly you're looking for... It sounds like you want to list all objects/features used in particular web site. If this is correct, starting from version 8, you can find this information under Sites -> select a site -> Assigned objects
This is for before the site is built.
I'm looking for suggested tools people use to architect the content on the site.
I am not sure if your concern is only content. If yes, did you take a look at Kentico Draft?
Kentico draft - https://kenticocloud.com/
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