fix(cli): rewrite 'doom sync'; deprecate 'doom build'

This changes 'doom sync' to be smarter about responding to changed
package recipes/pins, changes in Emacs version, or instances where the user
has copied a config to a new system.

In all these cases, the user would formerly have to know about a
specific combination of 'doom sync -u' and 'doom build' to ensure Doom
is in a good state. With this change, 'doom sync' handles all these
cases.

Also, 'doom build' is now deprecated (and 'doom sync' now has a
--rebuild option to mimic its old behavior).

Also also, sometimes, a package may silently fail when cloned (which
used to result in an empty repo). Now, if this is detected, cloning will
be re-attempted up to 3 times before aborting with much more visible
error.

Note: these are stopgap solutions, until v3 is finished.

lisp/cli/upgrade.el

@@ -32,7 +32,7 @@ following shell commands:
     doom clean
     doom sync -u"
   (let* ((force? (doom-cli-context-suppress-prompts-p context))
-         (sync-cmd (append '("sync" "-u") (if jobs `("-j" ,num)))))
+         (sync-cmd (append '("sync" "-u" "-B") (if jobs `("-j" ,num)))))
     (cond
      (packages?
       ;; HACK It's messy to use straight to upgrade straight, due to the