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Cycle 5 — Parallel Lanes Orchestration

Drafted 2026-05-20 for two Claude Code terminal sessions running concurrently in the B.I.B.L.E repo. This document is both the coordination protocol AND the boot prompt for the second session. If you are a Claude Code session that Tyler just opened and pointed at this file: read this file fully, then act as the chem/bio/phys lane orchestrator described in §3.

The math-lane session (started 2026-05-19) shipped Cycle 4 and the structural-cleanup pass; the second (chem/bio/phys) session is opening Cycle 5 on the chem/bio/phys axis. Both run agentically — each session is itself an orchestrator that dispatches sub-agents per the §6 dispatch protocol.

§1 Project orientation (assume nothing — read in full)

You are working on the B.I.B.L.E project (Codex curriculum framework). Project root: /Users/tyler/Documents/Code Projects/B.I.B.L.E/. The project is a tiered, multi-domain mathematical-knowledge framework — every unit ships with Beginner / Intermediate / Master tiers, anchored to canonical textbooks, validated against a 27-point structural rubric (scripts/validate_unit.py), and (for math/theoretical-physics) accompanied by a Lean 4 formalization.

Before doing any work, read in this order:

  1. docs/plans/AGENT_PRODUCTION_PLAYBOOK.md (the canonical playbook — tier definitions, 7-section template, no-compromise quality contract, dispatch protocol, sub-agent rules, validator gates).
  2. docs/plans/CYCLE_4_STYLE_PARITY_PLAN.md (the math-style contract — note §2 revised: bio/chem/applied-physics is prose-first, Lean optional, 6000+ words, multi-section Master).
  3. docs/plans/PRODUCTION_RUNBOOK.md (operational checklist for producing a unit end-to-end).
  4. manifests/orchestrator_status.md (most recent cycle returns — start of session orientation).
  5. manifests/skipped_units.md (T1-only backlog — important for the math lane; less so for chem/bio/phys but still worth knowing).
  6. manifests/pending_approvals.md (mostly historical; resolved 2026-05-20 bulk-mark).

The math-style contract for your lane (chem/bio/phys, §2 revised):

  • 7-section Beginner/Intermediate template present.
  • Lean optional. Declare lean_status: none + lean_mathlib_gap rationale + human_reviewer: Tyler (pending external <domain> reviewer). Add Lean only when it formalizes a substantive claim (e.g., a Wright-Fisher u(p) inequality, a kinetic ODE existence). Do NOT shoehorn category theory into a chem unit.
  • Master tier with ≥ 3 named H2 sub-sections, each substantively developed prose. This is the primary style-parity lift — single-sub-section Master is the existing gap you're closing.
  • Word count ≥ 6000 for new production; ≥ 8000 for deepening.
  • validate_unit.py returns 27/27 (exit 0).
  • Bio/chem/applied-physics units are prose-first: words convey the mechanism, equations and Lean appear where they add explanatory force, not as decoration.

§2 Current state of the corpus (verified 2026-05-20)

  • Total shipped units: 376+ (last logged in plan.json; corpus has grown since).
  • All 58 Fast Track books audited (books_unaudited: []).
  • Cycle 4 just shipped 6 units at 27/27 across math/bio/chem (KR-theory, φ⁴, natural selection deepened, hydrogen QM deepened, Wright-Fisher new, MAPK new).
  • Pass-W after Cycle 4 stitched 11 reciprocal cross-links with no regressions.
  • Layer-A cleanup (2026-05-20) done: deps.json pending list backfilled, CONCEPT_CATALOG.md missing entries added, 17.07.01 reference flag fixed, 19/19 verified units pass 27/27.

Structural collisions still open (math-lane will handle, do not touch):

  • 12-quantum/02-formalism/12.02.01-*.md vs 12-quantum/02-hilbert-formalism/12.02.01-*.md (duplicate ID, same topic, different lengths).
  • 12-quantum/03-time-evolution/12.03.01-*.md vs 12-quantum/03-fock-spaces/12.03.01-*.md (duplicate ID, different topics).
  • 09-quantum-theory/ (2 units, math-track Woit-style QM) shares Chapter 9 with 09-classical-mech/.
  • 11-thermodynamics/ (1 unit Souriau-Gibbs) shares Chapter 11 with 11-stat-mech-physics/.

Math-lane session owns these fixes. Chem/bio/phys lane: avoid editing files in 12-quantum/02-formalism/, 12-quantum/02-hilbert-formalism/, 12-quantum/03-fock-spaces/, 12-quantum/03-time-evolution/, 09-quantum-theory/, 11-thermodynamics/ until math-lane signals the cleanup commit has landed.

§3 Lane ownership

Lane Owner Content sections Exemptions
Math Session A (math-lane orchestrator) content/00-precalc/ through content/07-representation-theory/ All structural-cleanup files in §2
Chem/Bio/Phys Session B (you, if you're reading this as a freshly-opened terminal) content/08-stat-mech/, 09-classical-mech/, 10-em-sr/, 11-stat-mech-physics/, 12-quantum/ (except the §2 collision files), 13-gr-cosmology/, 14-genchem-pchem/, 15-orgchem/, 16-inorgchem/, 17-mol-cell-bio/, 18-organismal-bio/, 19-eco-evo-bio/, 20-philosophy/ Files explicitly excluded in §2

Lean modules follow content: math units' Lean lives in lean/Codex/Foundations/, lean/Codex/Analysis/, etc.; physics units in lean/Codex/Quantum/, lean/Codex/ClassicalMech/, etc. The Lean namespace Codex.* is the project's Lean library name and stays globally consistent.

Shared files (both lanes append, conflicts resolved on commit-then-pull-rebase):

  • docs/catalogs/CONCEPT_CATALOG.md — append entries for new concepts; both lanes add their entries.
  • manifests/deps.json — append IDs to pending and shipped lists; let scripts/integrate_unit.py reconcile.
  • manifests/skipped_units.md — append-only; strike-through when an item is produced (per playbook §18.4).
  • manifests/weaving_report.md — append Pass-W reports per cycle.
  • manifests/orchestrator_status.md — append cycle reports per lane; tag with "Math lane Cycle N" or "Chem/Bio/Phys lane Cycle N".
  • docs/catalogs/FASTTRACK_BOOKLIST.md — read-only unless a booklist edit is needed.

§4 Coordination protocol

4.1 Commit / pull / push cadence

  • Pull before starting a cycle. git pull --rebase origin main before dispatching any agents.
  • Commit after each cycle. A "cycle" = one batch dispatch (4–6 units) + their validator passes + Pass-W stitching.
  • Push immediately after commit. Don't let local diverge from remote by more than one cycle.
  • If pull-rebase hits a conflict, do NOT auto-resolve. Pause and ping Tyler with a short message naming the conflicting files. Conflicts will almost always be in the shared files (§3) — they're benign (both sides appended), but human review is faster than scripted reconciliation.

4.2 Shared-file editing rules

  • deps.json: append IDs only; never reorder existing entries. JSON keys preserved.
  • CONCEPT_CATALOG.md: append ### namespace.id blocks at the end of the file. Don't insert mid-file (avoids merge conflicts).
  • skipped_units.md: append session-headed sections at the end. Strike-through line edits OK for items your lane produces.
  • weaving_report.md: append per-cycle entry at end.
  • orchestrator_status.md: append per-cycle entry at end with lane tag.

4.3 Cross-lane stitching

Pass-W cross-links across lanes (e.g., a Math-lane unit citing a Chem-lane unit, or vice versa) are sometimes necessary. Rules:

  • If your cycle's unit cites a unit in the other lane, that's fine — frontmatter prerequisites: or in-prose [citation] references are one-way and don't require touching the cited file.
  • If your cycle's unit needs reciprocal outbound stitching from a unit in the other lane (i.e., the other-lane unit should add an "and see [your unit]" entry in its Connections section), include it in your Pass-W agent's brief but flag the cross-lane edit in the report. Wait to commit until you've verified the other-lane unit's owner has the latest pull.
  • Or simpler: add the outbound stitch IF the file is unambiguously stable (no recent edits from the other lane), AND tag the commit with cross-lane stitch so the other lane reviews.

4.4 Naming new sub-chapters

If your lane needs to open a new sub-chapter (e.g., 19-eco-evo-bio/11-population-ecology/), check first whether it already exists with a different slug. Use ls content/<section>/ to scan. Avoid the structural collisions in §2.

§5 Boot brief: what to do in your first Cycle 5 dispatch

If you are Session B opening Cycle 5 chem/bio/phys, here's the recommended slate. Dispatch all 4-6 in a single parallel-Agent message after orientation:

5.1 Track B — deepenings (existing thin units → math-style depth)

Unit Current state Target
19.01.01 Hardy-Weinberg (check current state — likely 3000–4500w, Master single section) 8000w, 3+ Master sub-sections (selection coupling, drift in finite populations, multi-locus extension, connection to Wright-Fisher 19.02.05)
17.02.01 Cell membranes structure (similar state) 8000w, 3+ Master sub-sections (membrane proteins as 7TM/single-pass classes, lipid rafts and microdomains, mechanotransduction, membrane biogenesis)
15.04.02 SN1 vs SN2 (already a sibling unit at 3500w-ish) Single Master section 8000w, 4 Master sub-sections (carbocation rearrangements, solvent effects in detail, neighboring-group participation, asymmetric variants with chiral auxiliaries)

5.2 Track C — new production at math-style depth

Unit Where it lives Why
16.04.01 Coordination compounds (or next gap) 16-inorgchem/04-coordination/ Inorganic chem is the thinnest chapter family (8 units in 7 sub-chapters). Coordination chemistry is high-leverage — connects to crystal-field, bioinorganic, organometallic.
18.05.01 Action potentials and the Hodgkin-Huxley model 18-organismal-bio/05-nervous-system/ Organismal bio has 8 units across 7 chapters — gaps everywhere. Hodgkin-Huxley is the highest cross-domain-density topic (ODE + ion electrochem + bio mechanism).
12.07.02 Time-dependent perturbation theory and Fermi's golden rule 12-quantum/07-perturbation/ 12.07.01 (time-independent) shipped; the time-dependent companion is the natural deepening + standard QM textbook content.

5.3 Dispatch each agent with the §5.1 contract from CYCLE_4

Each agent brief should include:

  • Working dir: /Users/tyler/Documents/Code Projects/B.I.B.L.E/
  • Required reading: docs/plans/AGENT_PRODUCTION_PLAYBOOK.md §1–§4, docs/plans/CYCLE_4_STYLE_PARITY_PLAN.md §2 + §5.1
  • Sibling-unit style reference (a 27/27-passing same-chapter unit)
  • The hard requirements (7-section template, Lean optional per §2, ≥3 Master sub-sections, 6000+ words, 27/27 validator, prose-first)
  • Run python3 scripts/validate_unit.py <path> until 27/27 before returning
  • Report word count, validator status, Master sub-section list, catalog edits, Lean decision

5.4 After dispatch: re-validate, then Pass-W, then commit

  1. Independent re-validation. Don't trust agent self-reports — run validator yourself on every returned file. If any fails 27/27, re-dispatch that agent with the specific failure.
  2. Pass-W. Dispatch one Pass-W agent with the cross-stitch list you've identified. Cross-lane stitches per §4.3.
  3. Commit with a structured message naming the cycle and units.
  4. Push to Forgejo origin/main.

§6 Dispatch protocol (sub-agent template)

The math-lane session uses this template; copy and adapt:

You are producing a single Codex unit for the B.I.B.L.E project. Cycle 5, Track B/C, lane chem-bio-phys.

Working directory: /Users/tyler/Documents/Code Projects/B.I.B.L.E/

Required reading:
1. docs/plans/AGENT_PRODUCTION_PLAYBOOK.md §1-§4
2. docs/plans/CYCLE_4_STYLE_PARITY_PLAN.md §2 (note bio/chem prose-first) and §5.1
3. [sibling-unit style reference, full path]

Target unit:
- ID: NN.NN.NN
- Title: [title]
- Path: content/[section]/[chapter]/NN.NN.NN-[slug].md
- Section: [section], chapter: [chapter]
- Concept catalog ID: [namespace.id] (add to docs/catalogs/CONCEPT_CATALOG.md if missing — validator gate overrides "don't edit catalog" rule)

Topic anchor: [primary textbook references with chapter/page citations]

Hard requirements (failure = re-do, not partial accept):
1. 7-section Beginner/Intermediate template (Intuition → Visual → Worked example → Check your understanding → Formal definition → Key theorem with proof → Exercises).
2. Lean section: OPTIONAL for this lane. Default to `lean_status: none` with substantive `lean_mathlib_gap` + `human_reviewer: Tyler (pending external [domain] reviewer)`. Only add Lean if it formalizes a substantive claim non-decoratively.
3. Master tier with ≥ 3 named H2 sub-sections, prose-first.
4. Word count ≥ 6000 (new) or ≥ 8000 (deepening).
5. python3 scripts/validate_unit.py <path> returns 27/27 (exit 0). Fix in-loop, don't return until clean.
6. No emojis, no prohibited phrasings (obviously, clearly, trivially, simply, non-trivial, etc.), paragraphs ≤ 250w, Beginner paragraphs ≤ 120w with no proof language / no advanced formal notation, ≥1 image/diagram reference in Beginner.
7. Frontmatter mirrors [sibling-unit].

Workflow:
1. Read all required materials.
2. Draft unit at target path.
3. Add catalog entry if needed (append at end of CONCEPT_CATALOG.md).
4. Run validator until 27/27.
5. Return short report (word count, validator status, Master sub-section list, catalog edits, Lean decision).

Do NOT return until 27/27. Do NOT pad for length.

§7 What success looks like for Cycle 5 (chem/bio/phys lane)

After this cycle ships:

  • 3 thin bio/chem units brought to math-style depth (deepenings: 19.01.01, 17.02.01, 15.04.02 or substitutes).
  • 3 new bio/chem/phys units shipped at full 6000+ word depth (16.04.01, 18.05.01, 12.07.02 or substitutes).
  • Bio Master-sub-section depth: median 1 → 3+ across the lane (style-parity contract scaling).
  • Chem 15-orgchem / 16-inorgchem coverage starts closing.
  • Forgejo origin/main accepts the push cleanly with no cross-lane conflicts.
  • Pass-W cross-stitches recorded in weaving_report.md.

If any agent returns with quality below the §5.1 contract, re-dispatch that specific unit with the failure noted — do NOT accept a half-depth ship. Quality contract beats throughput.

§8 Session B boot script (copy into your terminal if you are Session B)

Read docs/plans/CYCLE_5_PARALLEL_LANES.md fully. You own the chem/bio/phys lane (§08-20).
Pull origin/main, run dashboard to check current state, then dispatch your Cycle 5 batch per §5.
Validate everything 27/27 yourself before returning. Pass-W after. Commit + push when clean.
Don't touch the structural-cleanup files listed in §2 — math-lane handles those.

Tyler can paste that script into the second terminal and the session boots into the chem/bio/phys orchestrator role.

§9 Math-lane (Session A) next steps

For reference, Session A will be working on:

  • Layer A structural cleanup (12.02.01 dedupe; 12.03.01 renumber; 09-quantum-theory rename; 11-thermodynamics merge).
  • Layer C math production: Cycle 5 math batch — characteristic-classes T1 cluster (03.06.07 Chern-Simons, 03.06.10 Stiefel-Whitney/Pontryagin numbers, 03.06.11 Hirzebruch signature, 03.06.12 unoriented bordism, 03.06.14 Steenrod squares).

Math-lane runs Pass-W on its own batch separately. Cross-lane stitches per §4.3.

§10 Quality contract reminder

Per AGENTIC_EXECUTION_PLAN.md §8 (the no-compromise contract): never compromise quality for throughput. If an agent returns at 23/27 or with a missing Master sub-section, re-dispatch. If a cycle takes 60 minutes instead of 40 because two agents needed re-dispatch, that's the correct outcome. If you're moving "fast" but units come back partial — slow down.

Tyler 2026-05-20: "make sure we cover all these subjects in the style and fashion of math … faster while maintaining quality or improving it." The "or improving it" is load-bearing.