Fix: Update git submodules during package upgrades

[ElleNajt]

Fix: Update git submodules during package upgrades

Fixes #238

Problem

Straight.el runs git submodule update --init --recursive during initial clone but doesn't update submodules during package upgrades. When upstream repositories update submodule pointers, local submodules remain at old commits, causing repositories to appear dirty.

This addresses issue #238. Related issues include #502 and external reports like kaushalmodi/ox-hugo#346 where users encounter persistent submodule conflicts during upgrades.

Example

The gptel package uses a test submodule. After upstream updates the submodule pointer, doom upgrade prompts:

> Repository "gptel" has a dirty worktree:
    
       M test

         1) Abort
         2) Stash changes  
         3) Discard changes

Solution

Add git submodule update --init --recursive after merges in straight-vc-git--merge-from-remote-raw when .gitmodules exists.

Implementation

;; In straight-vc-git--merge-from-remote-raw:
(when (file-exists-p
       (expand-file-name ".gitmodules"
                         (straight--repos-dir local-repo)))
  (straight--process-output "git" "submodule" "update" "--init" "--recursive"))

Testing

Tested with both existing and new submodules:

Existing submodule scenario:

• Before fix: Required manual "Discard changes" on every upgrade
• After fix: Manual resolution once, then submodules stay in sync automatically

New submodule scenario:

• Added test submodule to tracked repository
• doom upgrade automatically initialized submodule without prompts
• Updated submodule pointer to new commit
• doom upgrade automatically synced to new commit without prompts

Fix successfully prevents submodule pointer mismatches for both scenarios.

No impact on repositories without submodules.