They pretty much are.
All your files should be in the applications folder. But there may be
a few exception most you don't have to worry about.  At least I
haven't worried in the last 2 years or more. :D
When you create an application with the internal system you get all
the files as scaffolding for your application, but you don't have to
use it. I for one have my own scaffolding app that I use.

On Sep 27, 7:51 pm, apple <simo...@gmail.com> wrote:
> I sometimes have to remind myself which files in an application are
> "my files" versus "web2py files". In particular this becomes an issue
> with upgrades. It is not clear when the web2py files in applications
> have been updated.
>
> For example the latest release has made changes to files and added
> files to static/js and static/css. As a result if you add new features
> such as smartgrid, it will not worked as expected without updating
> these files.
>
> Wouldn't it be better to set up the directories so that all of the "my
> files" are in one directory and the "web2py files" in another?

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