Reformat and reorganize the config file docs (#5595)

This PR cleans up the config file docs.

Here are a list of notable changes made:

1.  I moved the example to come before we list the options, not after.

    I feel this makes the first section of the page more digestible: we
    have a big block of text, but at least now we can see some of that
    information in practice immediately after.

2.  I combined the two examples into one (and rewrote the explanations
    in list form, to help mitigate the increase in complexity).

3.  I swapped the global-only and per-module sections.

    After auditing the options, it seemed to me that the global-only options
    were generally less useful then the per-module options. I also think
    it makes sense to present the more flexible options first, rather
    then last.

4.  I organized the options into the same categories I introduced when
    organizing mypy's command line interface.

    Thankfully, most categories were entirely per-module or entirely
    global-only, with a few exceptions.

5.  I switched to using the same definition list format we use in the
    command line docs for consistency.

6.  I removed the `dump_type_stats`, `dump_inference_stats`,
    `debug_cache`, and the `strict_boolean` options.

    These are all options we have either suppressed or deprecated.

7.  I added in documentation for the `python_executable`,
    `no_site_packages`, and `disallow_untyped_decorators` options.

8.  I renamed some links/deleted some now-unnecessary links.

One change I made that was unrelated to the config file was adding docs
about the `mypy_path` and the per-module `ignore_missing_imports`
options to the "Running mypy" page.

Some interesting inconsistencies I noticed (but took no action on, in a
probably-futile attempt to keep this diff small):

1.  The `warn_redundant_casts` section is global-only, not per-module
    like the other warning options.

    I left this option in the global misc section for now.

2.  There does not appear to be any way of writing a config file that
    does the same thing as `--no-site-packages`.

    I think we should either add an option for this or allow expressions
    like `python_executable = None`. (Currently, we try parsing `None`
    as a string -- this makes mypy promptly crash with a
    FileNotFoundError).

Final note: I mostly kept the descriptions the same/minimal, apart from some
minor wording tweaks here and there -- I wanted to have the command line
docs act as the main source of truth.

Author: Michael0x2a

docs/source/command_line.rst

@@ -126,6 +126,8 @@ imports.
     compliant packages. Adding this flag will disable this behavior.
 
 
+.. _platform-configuration:
+
 Platform configuration
 **********************
 
@@ -169,12 +171,15 @@ For more information on how to use these flags, see :ref:`version_and_platform_c
     compile-time constants that are always false.  This flag may
     be repeated.
 
-.. _disallow-any:
+.. _disallow-dynamic-typing:
+
+Disallow dynamic typing
+***********************
 
-Disallow Any 
-************
+The ``Any`` type is used represent a value that has a :ref:`dynamic type <dynamic-typing>`.
+The ``--disallow-any`` family of flags will disallow various uses of the ``Any`` type in
+a module -- this lets us strategically disallow the use of dynamic typing in a controlled way.
 
-The ``--disallow-any`` family of flags disallows various types of ``Any`` in a module.
 The following options are available:
 
 ``--disallow-any-unimported``
@@ -208,8 +213,6 @@ The following options are available:
     ``dict``) become disallowed as you should use their aliases from the typing
     module (such as ``List[int]`` and ``Dict[str, str]``).
 
-.. _disallow-subclassing-any:
-
 ``--disallow-subclassing-any`` 
     This flag reports an error whenever a class subclasses a value of 
     type ``Any``.  This may occur when the base class is imported from 
@@ -239,8 +242,6 @@ definitions or calls.
     This flag reports an error whenever it encounters a function definition
     without type annotations.
 
-.. _disallow-incomplete-defs:
-
 ``--disallow-incomplete-defs`` 
     This flag reports an error whenever it encounters a partly annotated
     function definition.
@@ -258,6 +259,7 @@ definitions or calls.
     This flag reports an error whenever a function with type annotations
     is decorated with a decorator without annotations.
 
+.. _none-and-optional-handling:
 
 None and Optional handling
 **************************
@@ -299,6 +301,7 @@ For more details, see :ref:`no_strict_optional`.
     mypy 0.600, and in previous versions it had to be explicitly enabled
     using ``--strict-optional`` (which is still accepted).
 
+.. _configuring-warnings:
 
 Configuring warnings
 ********************
@@ -353,6 +356,8 @@ of the above sections.
     Note: the exact list of flags enabled by running ``--strict`` may change
     over time.
 
+.. _configuring-error-messages:
+
 Configuring error messages
 **************************
 
@@ -440,6 +445,8 @@ beyond what incremental mode can offer, try running mypy in
     We recommend that you try using the :ref:`mypy_daemon` before
     attempting to use this feature.
 
+.. _advanced-flags:
+
 Advanced flags
 **************