CLC-2053 Fix server-killing bugs; CLC-2088 Restore current logging behavior to most operations scripts

First commit:

When running tasks from the command line, we generally count on output to the terminal, and the scripts already specify log files to be used in preference to the application server log.

I left the torquebox and trinidad starts as they were, since otherwise the LOGGING_STDOUT env would be passed on to the application server.

Second commit:

Some critical bugs in commit https://github.com/ets-berkeley-edu/calcentral/commit/afc757e42f11b123838adaf6c5f4e70378c2532d resulted in death for "rails server", "rails console", etc. Fixed that & removed some obsolete comments that were missed.