/substrate:orchestrate

Execute a graphed epic's bead DAG as a parallel worktree fleet. This is substrate's primary execution door — the default way to run a spec once it's graphed. /substrate:graph-spec produces the DAG; this skill runs it. It is the "orchestrator" role that references/docs-core/docs/doctrine/agents-parallel-execution-doctrine.md describes — that doctrine holds the why; this skill holds the operational loop. Read the doctrine once; do not restate its rationale here.

Orchestrated (this skill) is the primary strategy; attended (/substrate:execute) is the single-window alternative. Orchestrated = K context-budget windows, agent-coordinated, unattended. Attended = one window, one implementing agent, a human co-pilots with phase-gate pauses. Both are the same partition (§Grouping & windows) at different K; pick attended when you want to watch/adapt one window or the spec fits one window and you prefer HIL.

Arguments

• <epic-or-spec> — either an epic label epic:<slug>, a bare <slug>, or a spec path docs/tasks/ongoing/<slug>/<slug>-spec.md (its epic label is derived from the directory).
• --auto — run all waves unattended (skip the between-wave approval pause). Default is pause between waves, mirroring /substrate:execute's pause-between-phases ethos.
• --pr — review-first landing. Instead of landing one squash commit on trunk (Step 6.3), push feat/<epic-slug> after every wave (so an open PR accumulates the per-bead commits live, wave by wave) and suppress the trunk-squash entirely — the PR is the deliverable and GitHub's Squash and merge becomes the single squasher (it re-authors one clean commit, absorbing the unsigned per-bead commits). Use it when you want the epic reviewed before it reaches trunk rather than after; implies no interactive trunk landing. Composes with --auto (the two are orthogonal: --auto skips the pause, --pr changes the landing). MUST NOT be combined with the Step 6.3 trunk-squash — they are mutually exclusive by construction.

When to run

• The epic has been graphed: epic:<slug> beads exist and bash docs/scripts/bead-graph.sh --epic <slug> renders waves.
• substrate.yaml declares a gate block (the objective done-signal every bead runs).
• At least one wave is worth fanning out (multiple file-disjoint beads). A single-file or strictly-serial DAG is fine too, but the win is smaller — /substrate:execute's sequential path is equally valid there.

When to REFUSE

The dispatch seam (tool-agnostic)

The only tool-coupled seam is subagent dispatch. Everything else (git, tbd, the gate) is portable shell.

The two CC paths are behaviorally equivalent on the DAG; the Workflow fast-path adds resume/determinism, not different semantics. On OpenCode, DAG correctness is preserved even when Task calls serialize; only concurrency is optional.

Workflow — the operational loop

Step 1. Resolve <slug>

From the arg: epic:<slug> → <slug>; a bare <slug> → itself; a spec path docs/tasks/ongoing/<slug>/… → the directory name. This is the canonical epic label; it is the join key, not the parent link.

Step 2. Read the DAG (never re-derive it)

bash docs/scripts/bead-graph.sh --epic <slug>            # topological waves — the authoritative schedule

Every id in one wave is safe to run in parallel; waves run in order. Fail-fast if there are no epic:<slug> beads or the script errors — prefer the machine waves output over eyeballing wave art; a parse error aborts before any worktree is created (FMEA #7). --format mermaid is available for a visual sanity check.

Read the partition. Each bead carries a group:<window-N> label (written by /substrate:graph-spec per agents-parallel-execution-doctrine.md §Grouping & windows) — the context-budget window it belongs to. Beads in one window are file-adjacent and run sequentially in one worktree; distinct windows within a wave are file-disjoint and run in parallel. The dispatch unit is the window, not the bead. The partition is a deviatable prior: you MAY re-batch it (merge two tiny windows, split an over-full one) when runtime judgment warrants — but if you do, log the deviation: mint a run-id (<epic>-<YYYYMMDD-HHMM>) and append the reason + the planned-vs-actual windows to .substrate/runs/<epic>/<run-id>/deviation-log (gitignored). No deviation → no log entry needed. Absent group: labels (an ungraphed or pre-partition DAG) → fall back to one bead per window (the classic per-bead behavior).

Step 3. Read substrate.yaml

Read gate.{compile,test,lint}, optional gate.out-of-band, worktree-seed[], toolchain-pin.{install,env}, and optional execution.resource-envelope. Abort with an explanation if the gate block is missing — do not probe a toolchain (root CLAUDE.md policy; FMEA #2 phantom-gate mitigation depends on these keys).

Warn on an undeclared seed (no-silent-fallback). If worktree-seed is absent or empty and the repo's .gitignore names build/dependency paths the gate plausibly needs (node_modules, .venv/venv, target, dist/build, generated-client/codegen dirs, .env*), do not proceed silently: warn that a fresh worktree contains only tracked files, so the gate may fail spuriously, and that seeding will then fall to manual per-run copying. Point the user at substrate.yaml's worktree-seed[]/toolchain-pin block (populate it — /substrate:adopt can, or edit by hand) and pause for confirm-to-proceed-unseeded. This is a warning, not an abort: a repo whose gate needs no gitignored input is free to run with an empty seed.

Note the resource envelope. If execution.resource-envelope is present ({env, cores-budget, floor}), each window's gate runs with <env>=max(floor(cores-budget / K), floor) for the K windows dispatched in that wave (5c.4). Absent it, the gate runs unbounded — fine at K=1, an oversubscription at K>1 (doctrine §Supporting → A window's gate runs under a declared resource envelope).

Note the gate-coverage floor. gate.{compile,test,lint} is the minimum re-gate, not necessarily the whole suite the epic exercises. As you read the DAG (Step 2), collect the distinct per-bead Gate_i commands: any Gate_i that is not subsumed by gate.* means gate.* under-covers this epic — e.g. a frontend vitest a bead runs while gate.test only runs the backend suite, or a tsc-only bead narrower than gate.*. Do not treat gate.* alone as the composition net: the per-wave re-gate (5e) runs the union of gate.* and the per-bead gates exercised that wave. Surface this once up front so it's visible that the integrated re-gate is broader than substrate.yaml's literal gate block. (If a bead's gate is a strict subset of gate.*, /substrate:graph-spec will have tagged it gate-scope: partial — a reminder that its green is partial and only the union re-gate authorizes the merge.)

Step 4. Setup — integration branch, run-state anchor, unattended signing

git switch -c feat/<epic-slug>   # or: git switch feat/<epic-slug>   (reuse if it exists)
git config extensions.worktreeConfig true   # once, idempotent: lets each worktree carry its own config

4.1 Cut/reuse feat/<epic-slug> from trunk.

4.2 Initialise the run-state entry — before any worktree exists. Write .substrate/execution-state.json's <epic> key now:

{ "<epic>": { "run-id": "<epic>-<YYYYMMDD-HHMM>", "partition": { "window-1": ["…"] },
              "re-gates": [], "outcomes": {}, "run-log": ".substrate/runs/<epic>/<run-id>/" } }

Every later write (5c.1 dispatched, 5e re-gates[], 5f merged/verified) appends to this entry. Skip this and each of those is a write into a missing key, so an aborted run leaves no ledger at all — which is exactly what happened on the 12-window sky-journal run (2026-08-04): real merged work, a written deviation log, and no execution-state.json entry, because entry creation lived only in Step 6.1 and the run never reached it.

4.3 Signing is scoped to the worktrees, never to the repo. extensions.worktreeConfig above is the only signing-related change made to the primary checkout, and it changes no signing behaviour by itself. Do not flip repo-local commit.gpgsign false: that config is shared with the primary checkout, so a human's mid-run commit lands silently unsigned and a killed run never reaches the restore. Per-worktree unsign happens at creation (5c.2); orchestrator-authored merges pass -c commit.gpgsign=false per invocation (5d, 6.3). Nothing needs restoring at close — see doctrine §Supporting → Unattended signing.

Step 5. Per wave, in order

For each wave the DAG emits, in order:

5a. Filter to ready windows. Keep beads whose blockers are all closed or merged — tbd ready / tbd show <id>. Merge, not close, is the unblock signal (doctrine §Policy-4), so a merged-but-open Policy-4 bead still unblocks its dependents. Then group the ready beads by their group:<window-N> label — a window is dispatchable once all its beads are ready. The dispatch unit is the window.

5b. File-disjoint guard (across windows). Pairwise-intersect each ready window's Files (the union of its beads' Files). Any collision splits the colliding windows into consecutive sub-waves — merge one, re-gate, then the next branches off the new tip. This is a second net over graph-spec's partition + edges (doctrine §Supporting → File-disjoint waves; FMEA #3). Never run two windows that touch the same file in one wave. (Within a window, beads co-edit shared files by construction — that's why they share one worktree and run sequentially, not in parallel.)

5c. Dispatch — per ready window:

1. tbd update <id> --status in_progress for each bead in the window (orchestrator-only write), and stamp each bead's run-state outcome: dispatched in .substrate/execution-state.json.
2. git worktree add <path> -b <window-branch> feat/<epic-slug> — one worktree per window, off the current integration tip, so it already contains merged blockers. Never branch off stale trunk. Then immediately git -C <path> config --worktree commit.gpgsign false, so this window's commits never reach an interactive signer and the primary checkout's config stays untouched.
3. Copy every worktree-seed[] path from the primary checkout into the worktree, then run toolchain-pin.install once for the window (seeding cost is O(K windows), not O(N beads)). Seed before dispatch or the gate fails on a phantom (doctrine §Supporting → Seed …; FMEA #2). toolchain-pin.install must stay idempotent. Seed immutable inputs only — never a handle to shared mutable state (a local dev-deployment dir, a live state cache); regenerate those offline in the worktree, or route the bead to the primary checkout.
4. Compute this window's resource share from execution.resource-envelope — max(floor(cores-budget / K), floor) for the K windows in this wave — and inject it as <env>=<share> in front of the window's gate commands, alongside toolchain-pin.env.
5. Dispatch one group-runner (bead-implementer; Agent tool / Task tool / Workflow stage) with, inlined:
   • the window id and its N sequenced bead tuples — each {Goal_i, Files_i, Gate_i, spec-ref_i}, the gate fully env-resolved (toolchain-pin.env prefix + gate.* literals + any bead override), so it resolves in a worktree with no shell version-manager;
   • the window's doctrine digests — push, don't point. Union the doctrine:<id> labels across the window's beads (stamped by /substrate:graph-spec Step 4.55 from write-scope ∩ the manifest's paths:), dedupe by <id>, and inline the output of bash docs/scripts/doctrine-digest.sh <id> — that doctrine's Binding Rules block — once for the window, not once per tuple, each block labelled with its id and the beads it binds. This is the push tier: cheap, and it provably arrived, where a pointer verifies nothing (docs/doctrine/agents-doctrine.md §2.1 — the reasoning lives there; don't restate it). Escalate to the full doctrine body when a single bead's write-scope majority falls inside one doctrine's paths: — that bead sits squarely in the doctrine, so inline that whole file for its tuple in place of the digest. Bound it:
     • At most one escalation per window, the doctrine covering the most write-scope. A full body costs ~6–10× its digest (measure it: wc -l <doctrine-path> vs bash docs/scripts/doctrine-digest.sh <id> | wc -l), and a window whose beads' majorities land in different doctrines isn't squarely inside either — that's a mis-partition signal, not a licence for two full bodies.
     • Never truncate a digest, and never drop one to fit. Half-delivered binding rules are worse than a pointer: the runner acts on a subset of the MUSTs believing it has them all. If the deduped union is outsized (≳200 lines — roughly 4 digests at the 35–65 each this repo measures), drop the escalation to digest-only first; if digests alone are still outsized, the window is bound too widely — narrate it and consider re-batching per Step 2's deviatable prior. The prompt is the symptom; the partition is the fix.
     • Degrade silently. No doctrine: labels on the window's beads, or no docs/scripts/doctrine-digest.sh in the repo → inline nothing, say nothing, compose the dispatch exactly as it would be composed without this bullet. Not a warning, not an abort: most repos have never adopted paths:, and a warning would fire on every window of every one of them. A label whose id the script rejects (non-zero exit — a stale label surviving a manifest edit) is skipped, mentioned once in the wave narration, and never fatal.
   • the relevant CLAUDE.md — repo context, no longer the doctrine channel. It carries orientation and doctrine pointers; when digests are inlined above they are the binding doctrine for this window and already in the runner's context, so the pointers are the fallback for what they don't cover. In a repo that stamps no doctrine: labels, the pointer is all there is and the runner chases it as before;
   • the standing rule verbatim — "no tbd, no git push — implement each bead in sequence, run each bead's gate, report a per-bead pass/fail ledger + a diff summary."
   • for any bead carrying an out-of-band gate, say so, and ask for that bead's out-of-band checklist + the single swappable seam.

5d. Collect results (read the per-bead ledger). The group-runner returns a per-bead ledger (pass | fail | unstarted) covering every bead in the window:

• All-pass → merge <window-branch> → feat/<epic-slug> with git -c commit.gpgsign=false merge … (per-invocation, never a config flip); git worktree remove <path> and git branch -D <window-branch> (hygiene — an unchanged worktree auto-cleans; the branch does not). Newly-unblocked dependents dispatch off the updated tip.
• Stopped mid-window at bead i → the runner leaves clean per-bead commits for the pass prefix (beads 1..i-1). Merge that green prefix if the ledger shows those beads gated green; keep bead i and the unstarted remainder open, tbd update <id> --notes "<failure>". Block only the transitive dependents of the open beads — sibling windows continue (partial progress is a core DAG win; FMEA — mid-window failure). Fix or escalate the failed bead.

5e. Re-gate the integrated tip — the union gate. After the wave's merges, the orchestrator runs, once on feat/<epic-slug>, the union of gate.{compile,test,lint} and every distinct per-bead Gate_i exercised by the beads merged this wave (deduped). This union — never gate.* alone — is the sole merge-authorizing signal for the wave; the per-bead gates a group-runner ran are fast pre-checks that fail early inside a window, not the composition net. The union is what makes the re-gate sound: a per-bead gate can be narrower than gate.* (a tsc-only frontend bead), and gate.* can be narrower than the suites the wave touched (a gate.test that runs only the backend suite while a frontend vitest ran per-bead). Re-gate with gate.* alone and a whole suite the wave exercised never gets composed-checked — so a green-reported wave can sit on a red integrated tip (doctrine §Supporting → Re-run the gate on the integrated branch; FMEA #4). Two independently-green branches can still fail composed. Record the wave's re-gate into .substrate/execution-state.json as it runs — and if the <epic> entry is missing when you go to append, you skipped Step 4.2: stop and fix that rather than creating the entry late, because everything the run has already recorded went nowhere — — {wave, commands: [...], result, tip-sha} (Step 6; the file is written incrementally per wave, not only at close, so an aborted run still leaves the evidence). Red = composition failure: halt the wave transition, attach notes, fix before any dependent dispatches. A wave with no recorded re-gate entry is a protocol violation.

5f. Record outcome — defer close (two-stage gate, non-destructive). For each green, merged bead, advance its run-state outcome, do not tbd close:

• On merge → outcome: merged; after the wave's green union re-gate (5e) → outcome: verified. The bead stays open in the tracker — verified is the live done-signal a watcher renders, and the tbd close is deferred to the terminal batch (Step 6.2). Merge (not close) already unblocked its dependents, so deferring the close changes no scheduling — and no bead flips closed mid-run, so a spurious close can't drop it out of the open view.
• Out-of-band gate applies (hardware / paid service / manual) → outcome: oob-pending + tbd update <id> --notes "merged; awaiting <out-of-band> gate". It stays open; close waits for the full gate a human runs later (doctrine §Policy-4).

5f-pr. Push the integration tip (only under --pr). Immediately after the wave's union re-gate is green (5e), git push origin feat/<epic-slug>. This is what makes the PR update live, in wave-sized bursts — the per-bead commits merged this wave become visible on the PR the moment the integrated tip is authorized. On the first wave, ensure the PR exists (gh pr view feat/<epic-slug> || gh pr create -f -H feat/<epic-slug>). A red re-gate pushes nothing (halt per 5e).

5g. Pause for approval with a wave summary (beads merged / left-open / red, re-gate result, next wave preview) — unless --auto. n/pause stops cleanly so the user can inspect. Under --pr --auto (fully unattended) there is no pause; the PR is the inspection surface.

5h. The terminal doctrine-reconciliation node (final wave). The epic's last wave is always the solo kind: doctrine-reconciliation node graph-spec emitted (blocked-by every other bead, so it runs alone against the fully integrated tip). Dispatch it like any window, with two things to know:

• Its group-runner edits docs/doctrine/** in its worktree to codify the ratify-only doctrine change the epic earned. That is an ordinary working-tree change, not a tracker write — the single-writer invariant is untouched (the runner still runs no tbd, no git push; you merge and record as always). Doctrine files land inside this epic's diff, co-revertable with the feature.
• Ratify-only is enforced by the re-gate, not a bespoke lint. Its gate is the full union gate on the integrated tip (5e); since the mutation may only codify what the code already did, a green re-gate is the proof it was ratify-only. A red re-gate means the doctrine edit introduced a rule the shipped code violates — that is out of scope for this node: have the runner revert the doctrine edit (or do it yourself before merge) and note it as follow-up for /substrate:synthesize-session. There is no amendment queue to fall back on — the node either applies a green ratify-only change or reverts to a no-op.

Step 6. Epic close

1. Finalize .substrate/execution-state.json — the durable run-state. This file is written incrementally, not once at the end: stamp the run-id + chosen partition at run start, append a re-gates[] entry after every wave's union re-gate (5e), and record each bead's outcome as it merges — so a crash or an aborted run still leaves a partial, truthful ledger (and the re-gate history that makes a composition failure diagnosable after the fact). At epic close, before the squash, finalize it: under the <epic> key record the run-id, the chosen partition (window → bead-ids), any deviations from graph-spec's suggestion (with reasons, mirroring the run-log), the per-wave re-gates ([{wave, commands, result, tip-sha}] — the union-gate proof), the per-bead outcomes (status: dispatched|merged|verified|oob-pending|fail|closed + merged commit sha or null — the non-destructive lifecycle a watcher renders), and the run-log pointer (.substrate/runs/<epic>/<run-id>/). Schema in agents-parallel-execution-doctrine.md §Grouping & windows. This file stays tracked (only .substrate/runs/ is gitignored) and is committed alongside the squash.
2. Terminal batch close, then one tbd sync — orchestrator-only, at epic close (or an explicitly agreed checkpoint). Close every verified bead in a single bulk call (tbd close <id1> <id2> … --reason "gate green", stamping each outcome: closed) — this is the only tbd close in the run — then run the one tbd sync. auto_sync stays off; never sync mid-flight from a worktree (doctrine §Policy-3 → Batch sync). Beads left oob-pending stay open and close later, as their out-of-band gates pass.
3. Land the epic — two modes:
   • Default (local landing): land feat/<epic-slug> on trunk as one signed commit (including .substrate/execution-state.json): git switch <trunk> → git -c commit.gpgsign=false merge --squash feat/<epic-slug> → git commit -S -m "...". Squash keeps the unsigned bead commits out of trunk history. This is the run's single interactive-signing moment. Then reap: git branch -D feat/<epic-slug> (its content is in the squash; its history is in execution-state.json).
   • --pr mode (PR landing): do NOT touch trunk. Commit .substrate/execution-state.json onto feat/<epic-slug>, git push origin feat/<epic-slug> a final time, and ensure the PR is open (gh pr view … || gh pr create -f). The squash-to-trunk is deferred to GitHub's Squash and merge on the PR (the single squasher). The unsigned bead commits are legitimate on the PR branch; GitHub re-authors them into one commit at merge.
4. Verify signing posture — git config --local --get commit.gpgsign must still be true. This is a check, not a restore: signing was never disabled repo-wide, only per worktree, and those overrides died with their worktrees. If the check ever fails, something flipped the shared config and that is the bug (doctrine §Supporting → Unattended signing; FMEA #1).

CC Workflow fast-path (v1, optional at runtime)

On Claude Code, the per-wave dispatch MAY run as a Workflow-tool pipeline: each wave is a stage, each ready window a bead-implementer (group-runner) within it, with journaled resume and budget control over the same loop contract (steps 5a–5f). It is a performance/determinism layer, not different semantics — the portable NL floor (Agent tool, one call per window) is the default and the only path on OpenCode. Do not hardwire Workflow as the sole mechanism.

Constraints

• MUST read the DAG from bead-graph.sh --epic <slug>; MUST NOT re-derive it. Fail-fast on a parse error before any worktree exists.
• MUST abort with an explanation if substrate.yaml's gate block is missing — never probe a toolchain.
• MUST warn (not abort) before dispatch when worktree-seed is undeclared but .gitignore names build/dep paths the gate plausibly needs, and pause for confirm — never silently dispatch into worktrees that will fail the gate on an unseeded input (no-silent-fallback).
• MUST initialise the <epic> run-state entry before the first dispatch (Step 4.2). A run that appends re-gates into a missing key leaves no ledger at all.
• MUST honor the single-writer invariant: only the orchestrator runs tbd update/close/sync or git push. Subagents receive Goal/Files/Gate inlined and return a result.
• MUST push the window's deduped doctrine:<id> digests into the dispatch prompt when its beads carry those labels (5c.5) — once per window, escalating to at most one full doctrine body — and MUST NOT truncate a digest to fit. MUST degrade to today's composition silently when there are no labels or no doctrine-digest.sh: no digest block, no warning, no abort.
• MUST branch each bead worktree off the current integration tip, merge-on-green, and re-gate the integrated tip each wave with the union of gate.* and every per-bead gate exercised that wave — the union re-gate (never gate.* alone) is the sole merge-authorizing signal, and each wave's {wave, commands, result, tip-sha} MUST be recorded incrementally in .substrate/execution-state.json. A wave with no recorded re-gate entry is a protocol violation.
• MUST inject each window's execution.resource-envelope share into its gate when the repo declares one.
• MUST enforce file-disjoint waves (pairwise-Files guard) beyond graph-spec's edges.
• MUST apply the two-stage gate non-destructively: headless-green → merge + unblock dependents + advance run-state outcome (merged → verified); defer every tbd close to the single terminal batch (Step 6.2) so no bead flips closed mid-run; out-of-band proof → oob-pending, left open + noted until a human runs it. verified (not a mid-run close) is the live done-signal a watcher renders.
• MUST scope unattended signing to the worktrees (extensions.worktreeConfig + per-worktree commit.gpgsign false, -c commit.gpgsign=false for orchestrator-authored merges) and MUST NOT flip the shared repo-local config. Land trunk as one signed squash commit; at close, verify the primary is still signing rather than restoring it.
• MUST reap debris: window branches on merge, feat/<epic-slug> after the squash lands.
• MUST pause between waves unless --auto. Never silently fan out beyond the DAG.
• MUST, under --pr, push feat/<epic-slug> after each green wave re-gate and suppress the Step 6.3 trunk-squash — the two are mutually exclusive. The PR (squash-merged on GitHub) is the sole landing; the orchestrator MUST NOT create a trunk commit in --pr mode. Signing stays disabled during the run and is restored unconditionally at close exactly as in the default mode.
• MUST stay tool-agnostic — Agent↔Task is the only seam. The CC Workflow fast-path is additive, not required.
• MUST keep this body under ~500 lines — link to the doctrine for rationale, don't restate it.
• SHOULD narrate each wave (dispatched beads, gate results, merges) so the user sees liveness on long epics.