I tried moving the WA includes into a /includes/ folder at the root and updated all import paths. this worked fine and I can maybe continue doing this where possible.
If I then try to amend the scripts (i.e change a forms design) things break a bit but I expected that.
I'm quite fussy about keeping a neat and tidy directory structure hence wanting everything in an includes folder!
Also, if presenting the site to other developers to work on it looks more professional.
I think being able to specify a directory for all WA extension includes would be a VERY useful feature (and not too difficult?). Any chance of this being considered for future releases?