Your zipped up application files
During deployment:
/tmp/deployment/application folder
Once running:
/var/app/current
This is for boith worker and web server environments. A good way to prove it is to use this php in a page:
die("All done, path to api: " . getcwd(). ", PHP executible path: " . PHP_BINDIR);
Logs
/var/log/
Feel free to comment if you can add help to this page or point out issues and solutions you have found. I do not provide support on this site, if you need help with a problem head over to stack overflow.