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/cli/upgrade.el

@@ -154,7 +154,7 @@ following shell commands:
 
 (defun doom-upgrade--get-straight-recipe ()
   (with-temp-buffer
-    (insert-file-contents (doom-path doom-core-dir "packages.el"))
+    (insert-file-contents (doom-path doom-core-dir doom-module-packages-file))
     (when (re-search-forward "(package! straight" nil t)
       (goto-char (match-beginning 0))
       (let ((sexp (sexp-at-point)))