Exiting with exception now gives non-zero exit codes
Change the standard try/catch block such that exceptions cause the
program to exit with a non-zero exit code. As a consequence, (properly
written) integration tests will now correctly show when program exits
cleanly, or when it errors out. Update app_exception_handling to test
that applications exit with non-zero error codes when passed bogus options.
I somewhat arbitrarily picked "-1" as a general "something wrong's
happening here, what it is ain't exactly clear" code. This can certainly
be changed if anyone is so inclined. (One possibility is to embed the
exit code to use in the exception itself, in case we want to use it to
pass signals up the chain.)
Also, fix some dos-mode line endings issues.
** Integration test changes expected:
app_exception_handling - different command file.
jrelax - was erroring out with a bad option. Now fixed.
The following integration tests have errors, and should now continue to
fail until those errors are fixed:
swa_rna_gagu_20_append_floating_base_by_jump
swa_rna_gagu_17_append_floating_base
swa_rna_erraser
erraser_minimize
swm_nickedhelix