feat(validation): persist eligible_files.json for post-index validation

[Dead-Bytes]

Summary

• Adds writeEligibleFiles to the flat-folder strategy: persists .bytebell/eligible_files.json (knowledgeId, commitHash, sorted file list, affected folders) to the source layer between scan-and-classify and the parallel analyse-small / analyse-big phases.
• Writes to local disk when source.localRepoDir is set and to archiveSink when configured; hard-fails if neither target is available. Read back by @bytebell/knowledge-validation to cross-check that every file the analyzer was asked to process landed in Neo4j.
• Brings pre-release up to current main: drops the retired db, db-core, graph-db, graph-core, and sqlite packages, consolidates @bytebell/config schema into a single file, removes the mongo / neo4j provider.ts shims and the DbProgressReporter, and prunes unused exports under @bytebell/types (analysis, config, database, graph).
• Server, MCP, and queue packages updated for the new import surfaces; dependency lists trimmed accordingly.

Test plan

• bun run typecheck is clean.
• Run a GitHub ingestion end-to-end against a small repo; confirm .bytebell/eligible_files.json appears under source.localRepoDir before any small/big file analysis log line.
• Run the same ingestion with only archiveSink configured (no local repo dir); confirm the artifact is pushed through the sink and analysis proceeds.
• Run with neither target available; confirm the strategy fails fast with the expected error rather than producing an un-validatable knowledge.
• Smoke-test @bytebell/knowledge-validation against a freshly-indexed knowledge and confirm it reads the artifact and reports parity.
• Boot @bytebell/server and hit /health, /repos, /stats, /mcp-stats to confirm the package removals did not break route wiring.