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.

README.md

@@ -138,8 +138,6 @@ commands you should know about:
 + `doom env` to dump a snapshot of your shell environment to a file that Doom
   will load at startup. This allows Emacs to inherit your `PATH`, among other
   things.
-+ `doom build` to recompile all installed packages (use this if you up/downgrade
-  Emacs).
 
 
 # Roadmap