use "git add -u" in merge script

"git add -A" stages all untracked content, including stray
cloned repositories that happen to exist in the worktree.
These get recorded as orphaned gitlinks, which break ArgoCD
sync because the referenced submodule commits do not exist
in the remote.

"git add -u" limits staging to already-tracked files, which
is the correct intent during conflict resolution.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: ktdreyer

scripts/rebase-main-to-alpha.sh

@@ -64,7 +64,7 @@ if [ "${REBASE_EXIT}" -ne 0 ]; then
   log "Rebase encountered conflicts. Collecting conflict state..."
 
   # Stage all files — conflict markers will be preserved in working tree
-  git add -A || true
+  git add -u || true
 
   CONFLICT_FILES="$(git diff --name-only --diff-filter=U HEAD 2>/dev/null || git status --short | grep '^UU' | awk '{print $2}' || echo "(see git status)")"
 
@@ -84,7 +84,7 @@ ${CONFLICT_FILES}
 Please resolve conflicts and merge this PR manually.
 Generated by scripts/rebase-main-to-alpha.sh on ${TIMESTAMP}." || {
     # Merge also has conflicts — stage everything and commit with markers
-    git add -A
+    git add -u
     git commit --no-verify -m "chore: best-effort merge main into alpha (conflicts present)
 
 Automated merge of upstream/main into upstream/alpha.