Don't complain about unmatched '('s if there was a fatal error

On fatal errors, TeX often aborts without closing the file stack.
Suppress latexrun's internal balancing check when this happens.
Fix handling of recorder file with LuaTeX

Unlike pdfTeX and XeTeX, LuaTeX (at least as of 0.76.0) does not
include the output directory in the logged job or output file names.
Detect this and add the output directory name if necessary.