feat(wave14): 5 bio-inspired primitives + phase2 cleanup + substrate dogfood
## Wave 14 — 5 new primitives (44 crates total, 713 tests green)
All specs written as task.toml → passed through kei-agent-runtime prepare
→ composed prompts via capability fragments → Agent tool invocation.
First fully-dogfooded wave.
- kei-prune (9 tests): biological pruning. `candidates(idle_days)` +
`mark_retired(id)` on sidecar `prune_retirements` table (agents.status
CHECK precluded 'retired' value).
- kei-discover (8 tests): federated marketplace discovery stub. UNIQUE
slug via custom migration + FTS5 on slug+description. Engine-native
via kei-entity-store. Typed DuplicateSlug error.
- kei-brain-view (6-8 tests): stdout visualizer for ledger taxonomy
graph + agent lineage. Tree / stats / lineage subcommands. NO_COLOR
env respected. No kei-entity-store dep (direct rusqlite).
- kei-hibernate (6 tests): whole-brain tar.zst export/import. Manifest
with sha256 per-file, version gate, safe_join on extract, dry-run
mode. tar 0.4 + zstd 0.13.
- kei-ledger-sign (7 tests): ed25519 creator attestation. keygen / sign /
verify CLI. Canonical message `dna|spec_sha|creator_id` with pipe
rejection. chmod 600 on key storage (unix). Tamper-detection on load
via pubkey re-derivation.
## Phase 2 cleanup shipped in same commit
- LOC splits: walk.rs 221→91 (path_safety.rs + wikilink.rs extracted),
prepare.rs 228→199 (dead build_ledger_row removed, fn helpers split).
- Clippy pass: 6 warnings fixed (derivable_impls, manual_contains,
type_complexity x2, doc_overindented_list_items x2) in
kei-entity-store, kei-ledger, kei-spawn.
- DNA eprintln removed from kei-agent-runtime/src/dna.rs (stderr
pollution from library parse).
- kei-pipe integrations: hot_reload.rs (kei-watch wrapper, sync API,
50ms debounce) + scheduler_bridge.rs (kei-scheduler executor, shell
exec documented). +6 tests.
- Workspace [workspace.dependencies] centralised: rusqlite/chrono/
anyhow/thiserror/tempfile/toml — future crates opt in via
`.workspace = true`. Existing pins preserved.
## Substrate dogfood verified
task.toml → `kei-agent-runtime prepare` → DNA + composed prompt from
capability fragments → Agent tool invocation. kei-spawn also tested
end-to-end (prompt.md written to tasks/<agent-id>/, ledger row created).
Verified: cargo check --workspace clean, 713 tests passing,
substrate_integration.sh ✓, hook_wiring_integration.sh ✓.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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