feat(indexing): add canonical core index manifest

[jorgenosberg]

• Moves Docstra indexing to a single typed core manifest, derives repository maps from that manifest, and stops loading legacy sidecar indexes or repo_map.json.
• Normalizes repo-relative file ids across ingestion and retrieval, keeps Chroma as the vector store, and fixes incremental single-file indexing plus multi-target Python import edges.
• Adds regression coverage for manifest loading, relative document ids, single-file upserts, and import resolution. closes Define the Docstra core index model #23