Major rewrite of doom module API

+ Fix #446, where the .local/packages.el cache was generated with
  a faulty load-path.
+ Entries in the doom-modules hash table are now plists, containing
  :flags and :path, at least.
+ Add doom-initialize-modules for loading module config.el files.
+ Add doom-module-get for accessing this plist, e.g.

    (doom-module-get :some module)         ; returns plist
    (doom-module-get :some module :flags)  ; return specific property

+ Replace doom-module-enable with doom-module-set, e.g.

    (doom-module-set :some module :flags '(+a +b +c))

+ Remove doom-module-flags (use doom-module-get instead)
+ Rename doom-module-enabled-p with doom-module-p
+ Replace doom-module-path with doom-module-find-path and
  doom-module-expand-file. The former will search for an existing module
  or file in doom-modules-dirs. The latter will expand the path from
  whatever path is stored in doom-modules.
+ Replace doom-module-paths with doom-module-load-path
+ Changed doom! to allow for nested doom! calls by delaying the loading
  of module config.el files until as late as possible.
+ Refactor doom-initialize-packages to only ihitialize package state
  (i.e. doom-packages, package-alist, and quelpa-cache), rather than its
  previous behavior of loading all Doom files (and sometimes all module
  files). This is faster and more predictable.

core/autoload/debug.el

@@ -120,7 +120,7 @@ ready to be pasted in a bug report on github."
                   if (or (not cat) (not (eq cat (car key))))
                   do (setq cat (car key)) and collect cat
                   else collect
-                  (let ((flags (doom-module-flags cat (cdr key))))
+                  (let ((flags (doom-module-get cat (cdr key) :flags)))
                     (if (equal flags '(t))
                         (cdr key)
                       (list (cdr key) flags))))