fix: deep-dive round 2 — backbone rule flipped, pre-upgrade paths routed, flow bugs closed

[leeovery]

Round-2 deep dive over the whole stack (design log: #504; base: #512), per Lee: multiple agents, logic + conventions, catch bugs before going live. Six slices: three literal-executor walkthroughs (planning; scoping+review; discovery+spec-entry), textual forensics over the full diff, a dual-authority rules audit (CONVENTIONS.md + CLAUDE.md), and a mutation-check proving every round-1 engine guard is load-bearing.

Majors fixed

• Planning backbone Hard Rule Restructure skills to align with skill-creator guidelines #2 still commanded raw-git-never-scoped-helper for exactly the three operations the stack moved onto --plan — an always-loaded backbone rule contradicting every reference it governs. Flipped to the shipped reality, with restart cleanup named as the one surviving raw-git case.
• Pre-upgrade plans hit unrouted mid-session throws: three resume paths (planning continue, scoping adjust-continue, review-actions F) reached their first --plan commit with storage_paths never backfilled — an engine error mid-flow with mutations already applied. Each path now carries a routed guard at entry: subtree shows no storage_paths → record it from the format's Storage Pathspecs before anything commits.

Also fixed

• resolve-dependencies D never iterated past the first unresolved dependency (pre-existing on main; improve-doctrine) — per-dependency loop-back added, ops example shows both op shapes.
• display-groupings unify gains the anchor-collision guard (reconcile step 6's invariant — an anchor keyed unified could be silently demoted).
• confirm-and-persist restores the synthesis sourcing note the batch swap dropped; description optional, never invented.
• brief-synthesis C skips on zero regenerations; author-tasks drop-list covers task= on last-in-phase; review-findings shows the delete-op shape; absent storage_paths treated like [] at restart; knowledge-store staging exists-guarded; dangling (D7) token and spacing tidied.

Verified clean

Textual forensics (47 files: no escape artifacts, balanced fences, valid JSON templates, resolving cross-refs); the never-list rule tree-wide; mutation-check: every round-1 guard's test goes red if its guard is deleted; suites 1568/1568 · lint 27/27 · typecheck.

🤖 Generated with Claude Code

Stack

1. feat(engine): discovery-map add-batch — the harvest persists in one call (D7) #505
2. feat(engine): manifest apply — batched set/delete across one work unit (D7) #506
3. refactor(prose): task-map family folds onto existing batch forms (D7, stage 3) #507
4. feat(engine): manifest set — two grammars, never mixed #508
5. refactor(prose): dump/read folds — subtree gets replace per-topic loops (D7, stage 5) #509
6. feat(engine): commit --plan — plan storage stages from recorded state (D7, stage 6) #510
7. fix: batching-stack review round — re-resolve rewired, guards symmetric, hardening pinned #512
8. fix: deep-dive round 2 — backbone rule flipped, pre-upgrade paths routed, flow bugs closed #513 👈 current
9. fix(review-r3): engine hardening + crash-resume seams #514
10. feat(scoping): promotion routes through first-phase choice + bridge #515
11. fix(spec): pin the bugfix source name to the topic #516
12. fix(skills): gate-skip sentence accurate in gate-less phases #517
13. fix(review-entry): name the real upstream — specification and plan #518
14. fix(shared): strip triage-landing's unreachable superseded-research arm #519
15. feat(engine): refuse work-unit-level fields that shadow the phases tree #520
16. fix(discovery): first-written briefs join the full brief lifecycle #521
17. test(sim): pipeline simulation — engine driven end-to-end as a black box #522
18. fix(round-4): review findings — backfill keying, ratchet evasion, pull guard #523