Reorganize command line documentation

This commit reorganizes our documentation about the command line
along with several miscellaneous fixes.

In short, I moved the stuff about running mypy/managing imports
to a separate file and reorganized the command line section.

Specific major changes include:

1.  I split up information about running mypy and information
    about mypy's command line flags into two separate pages:
    "Running mypy and managing imports" and "The mypy command line".

    Rationale: I felt the current documentation on running mypy
    is very dense: it includes a lot of info on managing imports, how
    mypy discovers files, etc that I think were really only of interest
    to advanced programmers who are in the middle of trying to get mypy
    to run on a complex code base.

    I think splitting up the text into two makes it easier for
    both beginners and experts to get the info they're looking for.

2.  I rewrote the section about how mypy handles the
    `--ignore-missing-imports` and `--follow-imports` flags
    (Now located in "Running mypy..." > "How mypy handles imports").

    In particular, it more clearly distinguishes how to handle missing
    imports vs handling imports to files you didn't want type check:
    the former is applicable to everybody; the latter is only really
    applicable to people who are progressively adding type hints.

3.  I moved information about how mypy searches the file system and
    resolves imports to the bottom of the "Running mypy..." section.

    I think most people don't really need that info to start:
    running `mypy my_whole_codebase` is generally a good starting point.

4.  I reorganized the command line section to mirror how the flags
    are grouped when you run `mypy --help`.

Some minor changes:

1.  I switched to using [definition lists][0] instead of bullet points
    to document flags: I think it looks cleaner.

2.  I removed the `mypy --help` summary from the command line page:
    I don't really think anybody was reading that at all.

3.  I added documentations about the `--warn-unused-casts`,
    `-warn-unused-ignores`, `--show-error-contexts`,
    `--warn-unsed-configs`, and the different report flags.

    I did *not* document `--cache-fine-grained` and
    `--memory-xml-report` mostly because I don't actually understand
    what exactly those do.

4.  I added moved the note about integrating mypy into a separate
    page, and added a brief note about plugins to that page.

  [0]: https://sphinx-rtd-theme.readthedocs.io/en/latest/demo/lists_tables.html#definition-lists

Author: Michael0x2a