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How to create a simple File structure for a large project?

Update:10-11Source: network consolidation
Hi to all,
I've own and operated my own website design/development (a 1 woman office, plus many sub-contractors) over the period of 8 years. I started hand-coding HTML sites in 1997, before the creation DW (though I think the first ver was for Mac in '97). Over the recent years I've udated my skills to include CSS and enough Java/PHP to customize and/or troubleshoot current projects (learn as I go).
The majority of my clients have been other 1-10 person entrepreneur companies. I've recently won a bid to redesign a government site which consist of 30 departments, including their main site.
The purpose of this thread is to get some ideas on creating a file management/structure. Creating file management setup for smaller companies was a piece of cake, using a simple file mgmt structure within DW. Their current file structure is all over the place. I've read about a very good, simple file struture in a DW CS4 manual and wanted to get feedback on different methods that have worked, and have not worked, or your client:
Here's my thinking:
1. within the root dir place home.htm and perhaps a few .htm related only to home
    2. create the following folders off the root, "docs, imgs/global, CSS, FLA, Departments"
            - sub folders within docs for each dept
            - site wide css's placed into CSS
            - site wide FLAs into the FLA
            - sub-folders created within 'imgs' for each dept, including a 'global folder' for sitewide images and menu imgs (if needed)
- OR -
1. create same file structure for each dept folder, such as 'imgs/CSS/FLA/Docs'
Open for suggestions....

The Best Answer

It is a problem I have thought over at length and still feel what I use could be better. You are doing it the right way around researching before you start, as moving files once things are underway can course real problems. One issue is the use of similar assets across site(s), and version control if you have multiple versions of the same asset.
Can not say I have built a site(s) of that size but would recommend putting together a flow chart to help visualise the structure and find out better ways organising (works for me). Good luck, post back with your solution.