[support] Approaches to project documentation

[Hadubard]

Hi all,

I have to create a complete documentation of a rather huge Drupal based web project. My first idea has been to use the API module to use in-code comments to create an easy way to step through the code. I really like this in the drupal API documentation. But I also require a more general approach to fill the gaps between distinct parts in code in order to provide a general overview of how the pieces of the project are tight together, what assumptions and general ideas the project is based on, flow charts, etc ...
I thought about using the doxygen @ingroup tag for that too (to create topics pages if I understand correctly), but my client argued that the use of accompanying images (flow charts, database schemas, etc ...) would be too difficult to include using this approach.
What I really like about it is the possibility to have all the doc in our VCS.

I would be interested to hear about your approaches regarding this kind of project documentation.
If you have any interesting resources or websites covering this topic I would be glad for a hint too. My search didn't yield very specific approaches but rather a general "yes, document what you do". But I'm more interested in a more or less detailed real life approach:
- What software do you use?
- How do you create cross references between code doc and general doc?
- Where do you store the doc?
- ...

best regards to all