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`.

etc/spack/defaults/modules.yaml

@@ -35,13 +35,10 @@ modules:
 
   # These are configurations for the module set named "default"
   default:
-    # These values are defaulted in the code. They are not defaulted here so
-    # that we can enable backwards compatibility with the old syntax more
-    # easily (old value is in the config yaml, config:module_roots)
     # Where to install modules
-    # roots:
-    #  tcl:    $spack/share/spack/modules
-    #  lmod:   $spack/share/spack/lmod
+    roots:
+     tcl:    $spack/share/spack/modules
+     lmod:   $spack/share/spack/lmod
     # What type of modules to use
     enable:
       - tcl