Fix CI rebase: stash everything before pull, pop with --index

git pull --rebase refuses to run with either staged OR unstaged changes.
--keep-index only stashed the unstaged side, leaving staged changes in
the index which caused 'Your index contains uncommitted changes'.

Switch to plain git stash (stashes everything) so the tree is fully
clean for the rebase, then git stash pop --index to restore both the
working tree changes and the staged index state.

Author: Guangzhen-Jin

.github/workflows/rebuild_on_module_tools_change.yml

@@ -49,17 +49,16 @@ jobs:
           # Stage files we want to commit
           git add ../docs/software/apps_md ../docs/software/app_catalog.md ../docs/software/index.md apps_descriptions.json ../docs/software/ngc_md ../docs/software/ngc_catalog.md ../docs/software/rocm_md ../docs/software/rocm_catalog.md || true
 
-          # Stash remaining unstaged changes (make generates many files we don't commit)
-          # --keep-index leaves the staged files untouched
-          git stash --keep-index || true
+          # Stash everything (staged + unstaged) so rebase sees a fully clean tree
+          git stash || true
 
-          # Pull and rebase cleanly now that working tree is clean
+          # Pull and rebase cleanly
           git pull origin ${{ github.ref_name }} --rebase
 
-          # Restore stashed files (not committed, just put back for cleanliness)
-          git stash pop || true
+          # Restore stash and reinstate the index (staged) state
+          git stash pop --index || true
 
-          # Re-stage in case rebase touched our files
+          # Re-stage as a safety net in case pop --index couldn't restore the index
           git add ../docs/software/apps_md ../docs/software/app_catalog.md ../docs/software/index.md apps_descriptions.json ../docs/software/ngc_md ../docs/software/ngc_catalog.md ../docs/software/rocm_md ../docs/software/rocm_catalog.md || true
           
           git diff --cached --quiet && echo "No changes to commit" && exit 0