Source Control
We have 20 or 30 projects being built into 4 or 5 discrete solutions. We are using Subversion for SCM.
1) We have one tree in SVN containing all the projects organised logically by namespace and project name. There is a .sln at the root that will build them all, but that is not a requirement.
2) For each actual solution we have a new trunks folder in SVN with SVN:External references to all the required projects so that they get updated from their locations under the main tree.
3) In each solution is the .sln file plus a few other required files, plus any code that is unique to that solution and not shared across solutions.
Having many smaller projects is a bit of a pain at times (for example the TortoiseSVN update messages get messy with all those external links) but does have the huge advantage that dependancies are not allowed to be circular, so our UI projects depend on the BO projects but the BO projects cannot reference the UI (and nor should they!).
Architecture
We have completely switched over to using MS SCSF and CAB enterprise pattern to manage the way our various projects combine and interact in a Win Forms interface. I am unsure if you have the same problems (multiple modules need to share space in a common forms environment) but if you do then this may well bring some sanity and convention to how you architect and assemble your solutions.
I mention that because SCSF tends to merge BO and UI type functions into the same module, whereas previously we maintained a strict 3 level policy:
FW - Framework code. Code whose function relates to software concerns.
BO - Business Objects. Code whose function relates to problem domain concerns.
UI - Code which relates to the UI.
In that scenario dependancies are strictly UI -> BO -> FW
We have found that we can maintain that structure even while using SCSF generated modules so all is good in the world :-)
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