doc: use terms like `logs`, `STDOUT`, `STDERR`

The general term `output` may be confusing, because it can mean other
items generated by a program. Where possible, use specific terminology
for log files.
log: improve terminology.
rose date: fix offset and print_format usage

It was failing when both were used together.
Merge pull request #797 from matthewrmshin/log

doc: use terms like `logs`, `STDOUT`, `STDERR`
Merge pull request #798 from matthewrmshin/fix-rose-date-offset-print_format

rose date: fix offset and print_format usage
rose date: support more letter options

* `--parse-format=FORMAT` can now be `-p FORMAT` (for `strptime`).
* `--format=FORMAT` is now a shorthand for `--print-format=FORMAT`
  (but not `--parse-format=FORMAT`).
* `--print-format=FORMAT` can now be `-f FORMAT` (for `strftime`).

Combine `--print-format=FORMAT` and `--format=FORMAT` internally. The
effect is that `rosie lookup` and `rosie ls` will now accept
`--print-format=FORMAT`.
rose mpi-launch: don't call inner by default.

The inner wrapper may cause problems at some sites. It should not be
called as a default. The program will now make an `--inner` call only if
`ROSE_LAUNCH_ULIMIT_OPTS` is defined.
rosie ls works for other users.
Merge pull request #800 from matthewrmshin/rose-mpi-launch-inner

rose mpi-launch: don't call inner by default.
rosie-checkout: add test battery

Test all basic usages at normal verbosity.
Modify `rosie checkout -f` to return 1 on any failure.
Merge branch 'master' into rose-date-letter-opts
Merge branch 'master' into t-rosie-checkout
CLI documentation and verbose mode fix.
Merge pull request #803 from matthewrmshin/t-rosie-checkout

rosie-checkout: add test battery
Merge pull request #799 from matthewrmshin/rose-date-letter-opts

rose date: support more letter options
Fixed a missing "-c" in clock-triggered tutorial.
Merge pull request #805 from arjclark/clock-triggered-typo

rose documentation: Fix a missing "-c" in clock-triggered tutorial.
Update CHANGES.md
API doc: update.

Add new Python modules.
Add section on Bash library.
Change -U to -u and document.