Add JSON search, JSON-RPC bridge, and repo-scoped vector partitions to ccc

[faysou]

Summary

• Adds a --json option to ccc search.
• Adds ccc bridge --jsonrpc as a long-running stdin/stdout bridge for external tools.
• Adds --repo-key and repo_keys search filtering for workspace indexes containing multiple repositories.
• Stores repo_key on indexed chunks and makes it a sqlite-vec partition key alongside language.
• Derives repo_key from the nearest .git root relative to the CocoIndex project root, so nested repos such as ADK/a2a-samples are scoped exactly.
• Preserves compatibility with existing indexes that do not have repo_key by falling back to the previous path-glob scan.

Design decisions

• The JSON formatter is separate from the existing human formatter to avoid changing terminal output.
• The bridge uses newline-delimited JSON-RPC 2.0 on stdin/stdout so a parent process can keep one Python runtime alive across many requests.
• The bridge currently supports ping, search, and shutdown; bridge errors are returned as JSON-RPC error objects rather than printed to stdout.
• repo_key is a stored partition key so new workspace indexes can use fast KNN search with repo-level filtering instead of a full vector scan.
• Existing indexes are not broken: if code_chunks_vec has no repo_key column, repo_keys=["nautilus_trader"] is translated to file_path GLOB "nautilus_trader/*".

Files changed

• src/cocoindex_code/cli.py.
• src/cocoindex_code/client.py.
• src/cocoindex_code/daemon.py.
• src/cocoindex_code/indexer.py.
• src/cocoindex_code/project.py.
• src/cocoindex_code/protocol.py.
• src/cocoindex_code/query.py.
• src/cocoindex_code/schema.py.
• src/cocoindex_code/server.py.
• src/cocoindex_code/shared.py.
• tests/test_cli_helpers.py.
• tests/test_indexer_helpers.py.
• tests/test_protocol.py.

Validation

• Passed uv run pytest.
• Passed uv run ruff check ... on the touched source and test files.
• Passed uv run mypy.
• Passed uv run prek run --all-files --verbose --show-diff-on-failure --skip pytest.
• Smoke-tested ccc search --json --repo-key nautilus_trader --limit 1 streamwriter against the existing Nautilus workspace index and validated JSON output.

[faysou]

Fyi, I've done this PR to be able to integrate ccc with gitnexus for the semantic search part, and it works for me locally. Gitnexus works at single repo level but I use one index to index all my repos at the same time. The repo key is useful so gitnexus can filter ccc results on a single result, else a query was taking 25 seconds instead of half a second.