RAGTool does not update deleted files from cached storage

[BrandonwLii]

Whenever RAGTool is initialized, it searches through all the files matching index_path and indexes them. Files that were indexed from a previous initialization and are unchanged are skipped, which improves performance. However, RAGTool does not check for files that have been deleted between initializations, and they remain in the index. This behavior can be confusing, as RAGTool is expected to have the current files in the index whenever initialized.

This is probably best implemented through an optional parameter remove_deleted_files = True.