Function update_embeddings 

pub fn update_embeddings(
    store: &GraphStore,
    root: &Path,
    changed_files: &[&str],
) -> Result<usize>

Incrementally update embeddings for changed files.

Loads existing embeddings, re-embeds symbols in changed_files, removes orphans, and saves back. If changed_files is empty, treats all symbols as changed (full rebuild).