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My threshold of pain seems to be about 1500 files per directory. You can have as many as you want, just seems to be too slow after that point.
How do you divide them up? Some people dived them by project, some by product line, some by customer, some by part number and others by vendor. It really depends on the type of business you are in.
I personally like to keep the drawings with their parts/assemblies when I can.
If you have good searches designed, the directory's structure's value is diminished.
Personally, I would worry to much about structure since PDM manages the files in a different way on the back-end. The results are only database results and so the more the longer it takes.
You might consider not really living in the Explorer view too much and really use the searching ability. In the SW scenerio any assembly or drawing can give you a complete list of references by version, configuration,etc... on bom or contains tab...
We work on very large designs so my current project involves close to 15K unique files at the top level assembly. We do break our folder structure down into a few different departments but there's just a lot of data to manage - which is kind of where Workgroup lost it's abilities - a check in/out would involved about a half hour or more for a simple change.
I really don't use the Explorer view that much, but I want to replace a part in an assembly it always seems to be in the giant project folder and I have to wait for the browser, or when I want to save a new component there I am, in that giant project folder again.
It seems to me that it's just something we'll need to get used to in the future!