Partial refactor of cli.py (mainly help screen and arg parsing)

[wren]

Fixes #344
Fixes #374
Fixes #520
Fixes #814
Fixes #866
Fixes #875

This is a partial refactor (another PR to come soon) cli.py, specifically focused on the
arg parsing code, and the run function. For any args that were changed, I also added
the old flag as a hidden option, so existing aliases and scripts will still work behind
the scenes.

Most of the changes are transparent to users, but will make life easier for
contributors.

Changes that affect users:

• Fixed some bugs (see above)
• Reorganized the help screen (might be too big now, so maybe it's the new man page?)
• Changed the name of some flags (old flags still work)
• Some flags operate slightly differently. Instead of taking an optional string
  immediately after the argument (e.g. --encrypt filename.txt), they now take that
  optional string from an option (e.g. --encrypt --file filename.txt). Please note
  that these additional flags are completely optional, and not giving these options has
  the same default behavior as before. The affected flags are:
  • --import (--import TYPE is now --import --format TYPE)
  • --encrypt (--encrypt FILENAME is now --encrypt --file FILENAME)
  • --decrypt (--decrypt FILENAME is now --decrypt --file FILENAME)

Changes that don't affect users, but do affect contributors:

• Standalone commands (like --list and --encrypt) are now housed in an argparse
  option, and are executed at the correct time. This makes it easier to add more
  commands later (commands.py), and reduces the amount of overhead tracking all the
  various command line options that a user can specify. You can now add a standalone
  command by simply writing a function (commands.py), and registering the function
  in the arg parser (arg_parser.py). That's it. Then jrnl --newcommand will work as
  expected.
• The multiple modes of jrnl are disappearing, and we'll be left only with searching,
  and writing. This PR starts that work (although it's not complete). After searching,
  you have the option to do various things with the search results (e.g. put them into
  editor, delete them, display them in alternate format, etc). That's already how jrnl
  works for the users, but the code will now better follow that flow.
• In this PR, more functions have gone into util.py (I know, I'm sorry). The intent is
  not for them to stay there (we already have an issue to clean that file up Pull functionality out of util.py #737). The
  functions here will be split into smaller files when that issue is dealt with.
• More tests! Mainly starting to flesh out the pytest suite, but also adding some more
  behave tests.
• Our behave now supports simulating piping data into jrnl. This was added for testing
  importing, but can be used elsewhere as needed.

Checklist

• I have read the contributing doc.
• I have included a link to the relevant issue number.
• I have tested this code locally.
• I have checked to ensure there aren't other open pull requests
  for the same issue.
• I have written new tests for these changes, as needed.
• All tests pass.

[micahellison]

Great tests, nice refactoring, and it's a delight to see these argument bugs squashed. This will be nice to build off of. Thanks for your work on this.