fix regression from fcd39b851e52baf8f14dcc40a8e55058755a61b2 on not optimizing files when -c provided without an -o
Merge pull request #2804 from hamishwillee/incoming

Fixes to debugging, optimization, developers guide.
text update
improve FAQ answer on when is code safe to call
Integrating feedback on final documents. Removing under construction warnings
Subedited emrun document.