- Add pulsar-config script that sets up a directory with server.ini
   file describing web process and app.yml describing Pulsar
   configuration..
 - Move run.sh into scripts and rename to just 'pulsar', modify behavior
   to target configuration files in current working directory or directory
   specified by -c/--config or PULSAR_CONFIG_DIR.
 - Add a new mode `--mode webless` to pulsar/run.sh that acts as an
   entry point into pulsar.main and starts pulsar without a webserver
   for MQ operation.
 - Move test/check.py into pulsar/clint/test/check.py so it is installed
   with pip. Add entry point so 'pulsar-check' is available after installing
   pulsar via pip/setup.py.

 - Add a version.
 - Add a HISTORY.rst file.
 - Outline a setup.py.
 - Update .gitignore for build artifacts.

Mostly derived from trying to get the sphinx build to build without warnings.

Bring in update to plugin_config.py from Galaxy.

 - No longer needs to act as a daemon so the old name didn't make sense.
 - A bunch of scripts depend on importing this - so the new name makes those imports less confusing as well.

Based on lessons learned doing the same thing with Galaxy.

 - Polish by providing more command-line options.
 - Don't require daemonize by default - just run it as a normal process.
 - Better handling of app_loop.

Learning from planemo's cookiecutter template here.

 - Add Makefile at top-level.
 - Auto-generate modules, etc...
 - Place docs right in docs/ instead of docs/source.

flake8 calls it internally anyway.

 - Imports must come before everything else now.
 - Cannot assign lambda to vars - boo!

Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted).

update link to job managers documentation

Should make pulsar.readthedocs.org significantly prettier (all changes stolen from planemo which was generated from cookiecutter).

Replace all LWR references with Pulsar references

Refactored to check if SSH key exists, in the rare event that it has stopped existing sometime during the transfer

Handle unlinking of SSH key instead of relying on tempfile

Perhaps it's a version/environment difference, but relying on tempfile to
unlink the file when done seems to not be working. I imagine it is because
tempfile unlinks the handle when I called f.close(), so we're just going to
handle unlinking ourselves and solve that problem permanently. This has the
added benefit of us knowing that the file will be removed as soon as the
transfer is complete. RSA keys on disk for a smaller amount of time "feels"
better.

Typo of pubkey PreferredAuth options