Indexing lifecycle: incremental indexing + schema migration

[toddysm]

Part of #168 (gap analysis: indexing lifecycle).

Problem

Startup full-rebuild indexing, idempotent MERGE, and diagnostics exist, but there is no incremental indexing or schema migration behavior as called for by #168's design-work checklist.

Scope

• Incremental indexing of changed source files (avoid full rebuild where possible).
• Schema/version migration behavior for the derived database.

Acceptance criteria

• Incremental index path with tests.
• Documented schema-migration/versioning behavior.