I am organizing PHP Project files in following way. I don’t know this is standard or not. But it makes my life easier. If anyone knows any standard for organizing PHP files please share with us.
/webroot
/image (all images)
/dev (scripts and images under development – this is a mess)
/doc (document and pdf files that is uploaded or my work description)
/etc (configuration, i.e. database un&pw, etc – restricted perms)
/home (this is where most of the website lives)
/inc (included files)
/func (included functions)
/class (included class)
index.php
I organized the project I am working on like a *nix file system. /etc for config, /usr for core files /usr/lib for common stuff thats kinda generic to the project. /usr/classes for classes and so on. /var for logs. /srv contains images, js, css and anything else that is server directly. I manage the path in such a way that everything could actually be outside the web root except for the srv folder and index.php.