refactor: eliminate explicit any from unlocked backend modules + lint ratchet

context-manager, logger, rag-engine, session-transcript, indexer: typed
with unknown + structural shapes for foreign JSON (transcript formats
get loose optional-field types; parse failures skip a record, never
throw). Logger now extracts message/stack when handed an Error as meta —
spreading an Error silently produced {} before, so those log calls were
dropping the error entirely.

no-explicit-any is now 'error' repo-wide with a shrink-only exemption
list for the five files mid-refactor (nerve-center, mcp-server,
atomic-file, job-board, coordination-types).