in reply to Directory independent processing
and make these programs aware of their immediate surrounding structures regardless of where in the directory tree the folder 'project' is placed ?.
"regardless" is a rather strong word; if your scripts should really find their project directory on their own, without any helping assumptions or config files, they'd have to recursively search all directories -- in general that's a very bad idea.
I know several approaches that some programs out there in the wild take (and often they take several of those in combination), listed in no particular order:
In the end, it all depends on what you want, and on the usualy work flow. Maybe you like some of the options I've listed.