I am working on my first major (several hundred pages) website design and development project. I want to create subdirectories for each of the website's categories, which in turn have their own subdirectories for easy user navigation.

Example: website.com/directory. I am aware that by placing an index.html file within each directory, the browser automatically detects and navigates to that page, but that seems like a messy solution (having multiple index.html files, albeit in distinct folders), and I cannot imagine everyone does that.

So my question is...how do you properly organize and use subdirectories?