refactor: use doom-module-*-file variables; add two

- Adds doom-module-packages-file and doom-module-metadata-file.
- Uses them and the other doom-module-*-file variables where they were
  previously hardcoded.
- Add .el extension to doom-module-{init,config}-file; it is now the
  consumer's responsibility to strip/change/keep the extension as they
  see fit.

lisp/doom-packages.el

@@ -455,7 +455,7 @@ also be a list of module keys."
                            ((symbolp module-list) (doom-module-list 'all))
                            (module-list)))
         ;; TODO: doom-module-context + doom-context
-        (packages-file "packages.el")
+        (packages-file doom-module-packages-file)
         doom-disabled-packages
         doom-packages)
     (when (assq :user module-list)