Deprecate top-level module config (#28659)

* Ignore top-level module config; add auto-update

In Spack 0.17 we got module sets (modules:[name]:[prop]), and for
backwards compat modules:[prop] was short for modules:default:[prop].

But this makes it awkward to define default config for the "default"
module set.

Since 0.17 is branched off, we can now deprecate top-level module config
(that is, just ignore it with a warning).

This PR does that, and it implements `spack config update modules` to
make upgrading easy (we should have added that to 0.17 already...)

It also removes references to  `dotkit` stuff which was already
deprecated in 0.13 and could have been removed in 0.14.

Prefix inspections are the only exception, since the top-level prefix inspections
used for `spack load` and `spack env activate`.

lib/spack/docs/config_yaml.rst

@@ -72,21 +72,6 @@ used to configure module names.
    packages have been installed will prevent Spack from being
    able to find the old installation directories.
 
---------------------
-``module_roots``
---------------------
-
-Controls where Spack installs generated module files.  You can customize
-the location for each type of module.  e.g.:
-
-.. code-block:: yaml
-
-   module_roots:
-     tcl:    $spack/share/spack/modules
-     lmod:   $spack/share/spack/lmod
-
-See :ref:`modules` for details.
-
 --------------------
 ``build_stage``
 --------------------

lib/spack/docs/configuration.rst

@@ -37,8 +37,6 @@ Here is an example ``config.yaml`` file:
 
    config:
      install_tree: $spack/opt/spack
-     module_roots:
-       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir/$user/spack-stage
        - ~/.spack/stage
@@ -253,8 +251,6 @@ your configurations look like this:
 
    config:
      install_tree: $spack/opt/spack
-     module_roots:
-       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir/$user/spack-stage
        - ~/.spack/stage
@@ -278,8 +274,6 @@ command:
    $ spack config get config
    config:
      install_tree: /some/other/directory
-     module_roots:
-       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir/$user/spack-stage
        - ~/.spack/stage
@@ -345,13 +339,11 @@ higher-precedence scope is *prepended* to the defaults. ``spack config
 get config`` shows the result:
 
 .. code-block:: console
-   :emphasize-lines: 7-10
+   :emphasize-lines: 5-8
 
    $ spack config get config
    config:
      install_tree: /some/other/directory
-     module_roots:
-       lmod: $spack/share/spack/lmod
      build_stage:
        - /lustre-scratch/$user/spack
        - ~/mystage
@@ -375,13 +367,11 @@ user config looked like this:
 The merged configuration would look like this:
 
 .. code-block:: console
-   :emphasize-lines: 7-8
+   :emphasize-lines: 5-6
 
    $ spack config get config
    config:
      install_tree: /some/other/directory
-     module_roots:
-       lmod: $spack/share/spack/lmod
      build_stage:
        - /lustre-scratch/$user/spack
        - ~/mystage
@@ -502,9 +492,6 @@ account all scopes. For example, to see the fully merged
      template_dirs:
      - $spack/templates
      directory_layout: {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
-     module_roots:
-       tcl: $spack/share/spack/modules
-       lmod: $spack/share/spack/lmod
      build_stage:
      - $tempdir/$user/spack-stage
      - ~/.spack/stage
@@ -552,9 +539,6 @@ down the problem:
    /home/myuser/spack/etc/spack/defaults/config.yaml:23    template_dirs:
    /home/myuser/spack/etc/spack/defaults/config.yaml:24    - $spack/templates
    /home/myuser/spack/etc/spack/defaults/config.yaml:28    directory_layout: {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
-   /home/myuser/spack/etc/spack/defaults/config.yaml:32    module_roots:
-   /home/myuser/spack/etc/spack/defaults/config.yaml:33      tcl: $spack/share/spack/modules
-   /home/myuser/spack/etc/spack/defaults/config.yaml:34      lmod: $spack/share/spack/lmod
    /home/myuser/spack/etc/spack/defaults/config.yaml:49    build_stage:
    /home/myuser/spack/etc/spack/defaults/config.yaml:50    - $tempdir/$user/spack-stage
    /home/myuser/spack/etc/spack/defaults/config.yaml:51    - ~/.spack/stage

lib/spack/docs/module_file_support.rst

@@ -181,10 +181,7 @@ to the environment variables listed below the folder name.
 Spack modules can be configured for multiple module sets. The default
 module set is named ``default``. All Spack commands which operate on
 modules default to apply the ``default`` module set, but can be
-applied to any module set in the configuration. Settings applied at
-the root of the configuration (e.g. ``modules:enable`` rather than
-``modules:default:enable``) are applied to the default module set for
-backwards compatibility.
+applied to any module set in the configuration.
 
 """""""""""""""""""""""""
 Changing the modules root