refactor(yaad): split sqlite.go into nodes, edges, and tx files

Mechanically split storage/sqlite.go (2015 LOC) into four same-package
files for readability, moving code verbatim with no behavior, API, or
exported-symbol changes:

- sqlite.go: shared infra (schema, busy-retry, stmt cache, sessions,
  file-watch, scan helpers)
- sqlite_nodes.go: node, version, metadata, signature, access-log ops
- sqlite_edges.go: edge, graph-stats, cycle-check ops
- sqlite_tx.go: WithTx/txStore plus version rollback/diff

Verified with go build, go vet, go test, and golangci-lint (0 issues).

Author: Patel230