Backport bits of CLI rewrite

The rewrite for Doom's CLI is taking a while, so I've backported a few
important changes in order to ease the transition and fix a couple bugs
sooner.

Fixes #2802, #2737, #2386

The big highlights are:

- Fix #2802: We now update recipe repos *before* updating/installing any
  new packages. No more "Could not find package X in recipe repositories".

- Fix #2737: An edge case where straight couldn't reach a pinned
  commit (particularly with agda).

- Doom is now smarter about what option it recommends when straight
  prompts you to make a choice.

- Introduces a new init path for Doom. The old way:
  - Launch in "minimal" CLI mode in non-interactive sessions
  - Launch a "full" interactive mode otherwise.
  The new way
  - Launch in "minimal" CLI mode *only* for bin/doom
  - Launch is a simple mode for non-interactive sessions that still need
    access to your interactive config (like async org export/babel).
  - Launch a "full" interactive mode otherwise.

  This should fix compatibility issues with plugins that use the
  async.el library or spawn child Emacs processes to fake
  parallelization (like org's async export and babel functionality).

- Your private init.el is now loaded more reliably when running any
  bin/doom command. This gives you an opportunity to configure its
  settings.

- Added doom-first-{input,buffer,file}-hook hooks, which we use to queue
  deferred activation of a number of packages. Users can remove these
  modes from these hooks; altogether preventing them from loading,
  rather than waiting for them to load to then disable them,
  e.g. (after! smartparens (smartparens-global-mode -1)) -> (remove-hook
  'doom-first-buffer #'smartparens-global-mode)

  Hooks added to doom-first-*-hook variables will be removed once they
  run.

  This should also indirectly fix #2386, by preventing interactive modes
  from running in non-interactive session.

- Added `doom/bump-*` commands to make bumping modules and packages
  easier, and `doom/bumpify-*` commands for converting package!
  statements into user/repo@sha1hash format for bump commits.

- straight.el is now commit-pinned, like all other packages. We also
  more reliably install straight.el by cloning it ourselves, rather than
  relying on its bootstrap.el.

  This should prevent infinite "straight has diverged from master"
  prompts whenever we change branches (though, you might have to put up
  with it one more after this update -- see #2937 for workaround).

All the other minor changes:

- Moved core/autoload/cli.el to core/autoload/process.el
- The package manager will log attempts to check out pinned commits
- If package state is incomplete while rebuilding packages, emit a
  simpler error message instead of an obscure one!
- Added -u switch to 'doom sync' to make it run 'doom update' afterwards
- Added -p switch to 'doom sync' to make it run 'doom purge' afterwards
- Replace doom-modules function with doom-modules-list
- The `with-plist!` macro was removed, since `cl-destructuring-bind`
  already serves that purpose well enough.
- core/autoload/packages.el was moved into core-packages.el
- bin/doom will no longer die if DOOMDIR or DOOMLOCALDIR don't have a
  trailing slash
- Introduces doom-debug-variables; a list of variables to toggle on
  doom/toggle-debug-mode.
- The sandbox has been updated to reflect the above changes, also:
  1. Child instances will no longer inherit the process environment of
     the host instance,
  2. It will no longer produce an auto-save-list directory in ~/.emacs.d

core/core-modules.el

@@ -71,6 +71,13 @@ before the user's private module.")
 ;;
 ;;; Bootstrap API
 
+(defun doom-initialize-core-modules ()
+  "Load Doom's core files for an interactive session."
+  (require 'core-keybinds)
+  (require 'core-ui)
+  (require 'core-projects)
+  (require 'core-editor))
+
 (defun doom-initialize-modules (&optional force-p)
   "Loads the init.el in `doom-private-dir' and sets up hooks for a healthy
 session of Dooming. Will noop if used more than once, unless FORCE-P is
@@ -78,16 +85,18 @@ non-nil."
   (when (or force-p (not doom-init-modules-p))
     (setq doom-init-modules-p t
           doom-modules nil)
-    (load custom-file 'noerror 'nomessage)
-    (when (load! "init" doom-private-dir t)
-      (when doom-modules
-        (maphash (lambda (key plist)
-                   (let ((doom--current-module key)
-                         (doom--current-flags (plist-get plist :flags)))
-                     (load! "init" (plist-get plist :path) t)))
-                 doom-modules))
-      (run-hook-wrapped 'doom-before-init-modules-hook #'doom-try-run-hook)
-      (when doom-interactive-mode
+    (with-temp-buffer
+      (doom-log "Initializing core modules")
+      (doom-initialize-core-modules)
+      (when-let (init-p (load! "init" doom-private-dir t))
+        (doom-log "Initializing user config")
+        (when doom-modules
+          (maphash (lambda (key plist)
+                     (let ((doom--current-module key)
+                           (doom--current-flags (plist-get plist :flags)))
+                       (load! "init" (plist-get plist :path) t)))
+                   doom-modules))
+        (run-hook-wrapped 'doom-before-init-modules-hook #'doom-try-run-hook)
         (when doom-modules
           (maphash (lambda (key plist)
                      (let ((doom--current-module key)
@@ -95,7 +104,8 @@ non-nil."
                        (load! "config" (plist-get plist :path) t)))
                    doom-modules))
         (run-hook-wrapped 'doom-init-modules-hook #'doom-try-run-hook)
-        (load! "config" doom-private-dir t)))))
+        (load! "config" doom-private-dir t)
+        (load custom-file 'noerror (not doom-debug-mode))))))
 
 
 ;;
@@ -122,15 +132,17 @@ non-nil."
 of PROPERTY and VALUEs.
 
 \(fn CATEGORY MODULE PROPERTY VALUE &rest [PROPERTY VALUE [...]])"
-  (if-let (old-plist (doom-module-get category module))
-      (progn
-        (when plist
-          (when (cl-oddp (length plist))
-            (signal 'wrong-number-of-arguments (list (length plist))))
-          (while plist
-            (plist-put old-plist (pop plist) (pop plist))))
-        (puthash (cons category module) old-plist doom-modules))
-    (puthash (cons category module) plist doom-modules)))
+  (puthash (cons category module)
+           (if-let (old-plist (doom-module-get category module))
+               (if (null plist)
+                   old-plist
+                 (when (cl-oddp (length plist))
+                   (signal 'wrong-number-of-arguments (list (length plist))))
+                 (while plist
+                   (plist-put old-plist (pop plist) (pop plist)))
+                 old-plist)
+             plist)
+           doom-modules))
 
 (defun doom-module-set (category module &rest plist)
   "Enables a module by adding it to `doom-modules'.
@@ -223,18 +235,21 @@ those directories. The first returned path is always `doom-private-dir'."
                      collect (plist-get plist :path)))
           nil))
 
-(defun doom-modules (&optional refresh-p)
+(defun doom-module-list (&optional all-p)
   "Minimally initialize `doom-modules' (a hash table) and return it.
 This value is cached. If REFRESH-P, then don't use the cached value."
-  (or (unless refresh-p doom-modules)
-      (let (doom-interactive-mode
-            doom-modules
-            doom-init-modules-p)
-        (load! "init" doom-private-dir t)
-        (or doom-modules
-            (make-hash-table :test 'equal
-                             :size 20
-                             :rehash-threshold 1.0)))))
+  (if all-p
+      (cl-loop for path in (cdr (doom-module-load-path 'all))
+               collect (doom-module-from-path path))
+    (or doom-modules
+        (let (doom-interactive-mode
+              doom-modules
+              doom-init-modules-p)
+          (load! "init" doom-private-dir t)
+          (or doom-modules
+              (make-hash-table :test 'equal
+                               :size 20
+                               :rehash-threshold 1.0))))))
 
 
 ;;
@@ -375,8 +390,8 @@ for a list of all recognized module trees. Order defines precedence (from most
 to least)."
   `(let ((modules
           ,@(if (keywordp (car modules))
-               (list (list 'quote modules))
-             modules)))
+                (list (list 'quote modules))
+              modules)))
      (unless doom-modules
        (setq doom-modules
              (make-hash-table :test 'equal