Refresh stored embedding rows when store or metadata changes

[dpersek]

Summary

• Refresh stored content, content_blob, and metadata when repeat embedding calls target an existing row with the same ID and content hash
• Avoid recalculating embeddings for exact existing rows while preserving normal insert/replace behavior for new IDs or changed content
• Add regression coverage for store/metadata refresh, binary content, duplicate-content rows, new IDs sharing content, and changed-content batch cases

Why

Fixes #224.

The existing embed() and embed_multi_with_metadata() paths can notice that a content_hash is already present and skip work before updating stored content or metadata. That makes rerunning embed / embed-multi with --store or new metadata leave the stored columns stale.

Tests

• uv run --group dev pytest tests/test_embed.py -k "updates_store_and_metadata_for_existing_hash or updates_content_blob_for_existing_hash or embed_inserts_new_id_for_existing_hash or existing_hash_refresh_only_updates_matching_id or embed_multi_inserts_new_id_for_existing_hash or embed_multi_updates_changed_id_when_old_hash_is_in_batch": 7 passed, 15 deselected
• uv run --group dev pytest tests/test_embed.py: 22 passed
• uv run --group dev pytest tests/test_embed_cli.py: 91 passed
• uv run --group dev ruff check llm/embeddings.py tests/test_embed.py: passed
• uv run --group dev black --target-version py312 --check llm/embeddings.py tests/test_embed.py: 2 files unchanged
• git diff --check: passed
• uv run --group dev pytest: 789 passed

Scope

• Same-collection, same-ID refresh of stored content/blob/metadata for already embedded content
• Preserves new-ID insertion and changed-content replacement behavior
• Does not implement cross-collection or cross-model embedding reuse
• Does not close embed_multi_with_metadata() compares item IDs against row IDs instead of content hashes, breaking deduplication #1397 / fix: deduplicate embed_multi_with_metadata by content hash #1405's broader duplicate-content-under-new-ID deduplication behavior