I can't speak for everyone, but I tend to separate things like images, javascript, CSS, etc in to different folders.  Then make some sort of "include" folder.  The crux of this "include" folder are 2 files, normally called commonFunctions and databaseFunctions.  As you can imagine, anything that involves a transaction with the database goes in the databaseFunctions file and anything else (such as email processing and such) goes in the commonFunctions file.  If I have to build an admin panel with it as well, I put everything it needs in a separate directory so it is completely independent of any other files.

Perhaps the most important methodology I use though, is a white board.  Not just 1 white board, lots of them.  Every application I write is documented fully on white boards.  File layout, function layout, how the application flows, future thinking ideas, even some base pseudo-code is written on these white boards.  Once the website moves out of "construction" phase and is live, everything on the white boards gets photographed (I use a Nikon D5000 but you can use whatever you have to take high resolution pics) and digitized for future reference.  That way, anyone on the team can reference them at any time.  When an application comes up for a rewrite, everything that was written on the white boards either gets rewritten back on them, or are printed on poster printers and taped to the walls above the white board.

I totally agree with the whiteboard, my new office has a wall that is just a whiteboard.. By far the most useful wall ever built

Why take a picture of it (if you do it like rvtraveller)? That seems like a lot of disk space.

Quote from: Brad on January 29, 2012, 07:12:41 PM

I totally agree with the whiteboard, my new office has a wall that is just a whiteboard.. By far the most useful wall ever built

Why take a picture of it (if you do it like rvtraveller)? That seems like a lot of disk space.

Disk space is cheaper than wall space.

I really meant why not type them or something?

I take pictures, because it easily captures exactly what was laid out.  Sure, typing them is an option.  However, often times my whiteboards contain not only text but also flow diagrams and rough design sketches of how pages are to be laid out.  Sure, those details could also be replicated digitally.  In the end, it all comes down to what is the most efficient use of time and resources.  I could put all the details on the computer to begin with using something like OneNote to handle both text and drawing, but then that limits it to just me being able to view those notes.  But RVTraveller, why can't you use a projector and put them up on a big screen for all to see?  Answer:  I can't draw on presentation screens.

Remember, we aren't just talking about 1 person referencing notes like you might be for your personal website.  These notes might be viewed by 50+ people over the course of a project and this has been the most feasible way I have found to do this.  This same technique is used by companies around the world (such as Cisco, Treyarch Studios, Disney, and hundreds of other technical companies).

I will say, I have contemplated getting white boards that hook up to the computer and capture what you write as you write it, but I just haven't been convinced that this is the best route to go (not to mention, expensive).