index_personal_documents walked the whole tree with no pruning, so
pointing RAG at a real-world folder silently swept in .obsidian/ plugin
JS, .git/ internals, node_modules/, and __pycache__/ — multiplying
indexing time and polluting retrieval with junk chunks.
Prune hidden directories and well-known junk directories from the walk,
and skip hidden files. The explicitly passed root is exempt, so a user
who deliberately indexes a hidden directory still gets its contents.
