fix: use git add -u in merge script to avoid orphaned gitlinks (#1133)

## Summary

- Replace `git add -A` with `git add -u` in
`scripts/rebase-main-to-alpha.sh` (both occurrences on lines 67 and 87)
- `git add -A` stages all untracked content, including stray cloned
repositories in the worktree, which get recorded as orphaned gitlinks
that break ArgoCD sync
- `git add -u` only stages changes to already-tracked files, which is
the correct behavior during conflict resolution

Fixes #1131

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.