Partial indexes and recovery

Codira commits successful file analyses even when another selected file fails. A ready generation with at least one successfully indexed file is queryable. Every CLI index-dependent response warns on stderr when source analysis is partial. JSON responses include index_coverage; MCP responses include the same object under provenance.index_coverage, plus partial_index_warning. Context JSON uses the MCP envelope. Metadata reports usable/partial/complete, indexed/attempted/failed counts and failed paths. Complete refers only to the selected analyzer-supported scope. Repository-wide completeness is never implied. In particular, empty references or impact results cannot prove that omitted files contain no references or dependents. Static analysis also cannot prove dynamic completeness, even after all selected files succeed.

Generation schema 2 retains relative failed paths, hashes of the attempted source, analyzer identity and original diagnostics, and a digest of effective configuration. Unchanged failures are reused during automatic freshness refreshes. Changed failed source, analyzer identity or configuration triggers another attempt on CLI freshness refresh or daemon reconciliation. MCP stays read-only; use the CLI or daemon to refresh it. Ordinary codira index and codira index --full explicitly retry failures. A legacy partial generation without snapshots is refreshed once to establish the ledger. Missing indexes retain automatic initialization; existing corrupt, failed/updating or zero-file indexes remain fatal for queries and require explicit recovery.

From the repository with its configured environment:

uv run codira index --json
uv run codira sym NAME --json
uv run codira cov --json

For registered isolated state, use --workspace WORKSPACE on each command. Correct the failed source before indexing, or explicitly configure analyzer exclusions and coverage exclusions where appropriate; exclusions change the selected scope and must never be described as analysis of the excluded source. Strict --require-full-coverage rejects source failures as well as coverage gaps. Structural readiness is independent of embedding readiness. Deferred/pending embeddings require codira index --embeddings-only --json before measurements that require those vectors. This does not retry structural analysis failures.

The core generation format advances from 1 to 2. Backend DDL and plugin runtime versions are unchanged because failure snapshots belong to the core publication contract; existing independent analyzer fixes and official bundle pins are retained.

Family queries require --allow-partial (MCP allow_partial: true) to include usable partial members. Their generation vector preserves each member's coverage. Strict family indexing still returns a nonzero status for a member analysis failure.