Merge branch 'next' into feat/1173-wire-agent-converters-descriptor

docs/CLI-TOOLS.md

@@ -477,6 +477,9 @@ node gsd-tools.cjs current-timestamp [full|date|filename]
 # Count and list pending todos
 node gsd-tools.cjs list-todos [area]
 
+# List captured seeds (optionally filter by status: dormant|active|triggered)
+node gsd-tools.cjs list-seeds [status]
+
 # Check file/directory existence
 node gsd-tools.cjs verify-path-exists <path>
 
@@ -546,6 +549,20 @@ node gsd-tools.cjs worktree set-baseref
 
 **`worktree set-baseref`** applies a no-clobber write of `worktree.baseRef:"head"` to `.claude/settings.local.json`. If the file already contains an explicit `baseRef` value other than `"head"`, the existing value is preserved and `skipped:"explicit-other"` is returned. Malformed JSON causes an error rather than a silent overwrite. Both fresh installs and upgrades of GSD Core run this automatically when `workflow.use_worktrees` is enabled (the default); the command is also available for manual use — for example, to apply the setting when worktrees were toggled on after installation, or to re-apply it after a settings change.
 
+### Wave-manifest recording
+
+The execute-phase orchestrator records each spawned executor's worktree identity into a wave cleanup manifest so the matching `cleanup-wave` reader can later merge and remove exactly those worktrees.
+
+```bash
+# Append a validated per-agent entry to the wave cleanup manifest.
+# Returns JSON: { ok, reason, entry, manifest_path } (exit 0), or
+#   { ok:false, reason, hint } with a non-zero exit on a rejected entry.
+node gsd-tools.cjs worktree record-agent \
+  --manifest <path> --agent-id <id> --path <worktree> --branch <branch> --base <sha>
+```
+
+**`worktree record-agent`** appends one `{agent_id, worktree_path, branch, expected_base}` entry to an already-initialized manifest, validating every field **at write time using the same rules the `cleanup-wave` reader enforces** — `--branch` must match the disposable `^worktree-agent-[A-Za-z0-9._/-]+$` namespace, and `--path`/`--branch`/`--base` must be non-empty. `--agent-id` is required (write-strict), even though the reader treats it as optional. A missing or garbled field — or a duplicate `(worktree_path, branch)` the reader would dedup away — fails loudly with a recovery hint and a non-zero exit **without** writing, instead of appending an under-populated or silently-dropped entry. Whitespace-only `--path`/`--base` are rejected (values are trimmed). The on-disk manifest shape is unchanged (the reader re-derives `allowed_bases`); the orchestrator still initializes the empty `{orchestrator_root, worktrees: []}` shell inline before any agent is recorded.
+
 ---
 
 ## Graphify

docs/COMMANDS.md

@@ -1370,6 +1370,8 @@ Execute a trivial task inline — no subagents, no planning overhead. For typo f
 
 Cross-AI peer review of phase plans from external AI CLIs.
 
+Reviewers are prompted to verify the plan's claims against the actual repository source — opening the referenced files and citing `file:line` evidence with the mechanism — rather than reviewing the plan text in isolation. A reviewer that has no file access flags what it cannot verify instead of asserting it, and `file:line`-grounded findings are weighted more heavily during consensus synthesis.
+
 | Argument | Required | Description |
 |----------|----------|-------------|
 | `--phase N` | **Yes** | Phase number to review |
@@ -1485,10 +1487,11 @@ Capture ideas, tasks, notes, and seeds to their appropriate destination. Default
 | `--backlog <description>` | Add to the backlog parking lot using 999.x numbering |
 | `--seed [idea summary]` | Capture a forward-looking idea with trigger conditions |
 | `--list` | List pending todos and select one to work on |
+| `--list-seeds [status]` | List/audit captured seeds, optionally filtered by status (read-only) |
 | `--global` | Use global scope (for note operations) |
 
 **Backlog:** 999.x numbering keeps items outside the active phase sequence; phase directories are created immediately so `/gsd-discuss-phase` and `/gsd-plan-phase` work on them.
-**Seeds:** Preserve full WHY, WHEN to surface, and breadcrumbs — consumed by `/gsd-new-milestone`.
+**Seeds:** Preserve full WHY, WHEN to surface, and breadcrumbs — consumed by `/gsd-new-milestone`. Audit parked seeds anytime with `--list-seeds` (optionally `--list-seeds dormant`).
 
 **Produces:** `.planning/todos/` (default), note files (--note), ROADMAP.md backlog section (--backlog), `.planning/seeds/SEED-NNN-slug.md` (--seed)
 
@@ -1500,6 +1503,8 @@ Capture ideas, tasks, notes, and seeds to their appropriate destination. Default
 /gsd-capture --backlog "GraphQL API layer"         # Add to backlog
 /gsd-capture --seed "Add real-time collaboration when WebSocket infra is in place"
 /gsd-capture --list                                # Browse and act on todos
+/gsd-capture --list-seeds                          # Audit all captured seeds
+/gsd-capture --list-seeds dormant                  # Filter seeds by status
 ```
 
 ---

docs/FEATURES.md

@@ -1230,9 +1230,9 @@ When verification returns `human_needed`, items are persisted as a trackable HUM
 
 ### 43. Backlog Parking Lot
 
-**Commands:** `/gsd-capture --backlog <description>`, `/gsd-review-backlog`, `/gsd-capture --seed <idea>`
+**Commands:** `/gsd-capture --backlog <description>`, `/gsd-review-backlog`, `/gsd-capture --seed <idea>`, `/gsd-capture --list-seeds [status]`
 
-**Purpose:** Capture ideas that aren't ready for active planning. Backlog items use 999.x numbering to stay outside the active phase sequence. Seeds are forward-looking ideas with trigger conditions that surface automatically at the right milestone.
+**Purpose:** Capture ideas that aren't ready for active planning. Backlog items use 999.x numbering to stay outside the active phase sequence. Seeds are forward-looking ideas with trigger conditions that surface automatically at the right milestone. `--list-seeds` provides a read-only audit of all parked seeds (with optional status filter) without waiting for the next milestone.
 
 **Requirements:**
 - REQ-BACKLOG-01: Backlog items MUST use 999.x numbering to stay outside active phase sequence
@@ -1241,6 +1241,7 @@ When verification returns `human_needed`, items are persisted as a trackable HUM
 - REQ-BACKLOG-04: Promoted items MUST be renumbered into the active milestone sequence
 - REQ-SEED-01: Seeds MUST capture the full WHY and WHEN to surface conditions
 - REQ-SEED-02: `/gsd-new-milestone` MUST scan seeds and present matches
+- REQ-SEED-03: `/gsd-capture --list-seeds` MUST list seeds with status, scope, and trigger for audit, with optional status filtering
 
 **Produces:**
 | Artifact | Description |

docs/INVENTORY-MANIFEST.json

@@ -147,6 +147,7 @@
       "ingest-docs.md",
       "insert-phase.md",
       "list-phase-assumptions.md",
+      "list-seeds.md",
       "list-workspaces.md",
       "manager.md",
       "map-codebase.md",
@@ -368,6 +369,7 @@
       "roadmap-upgrade.cjs",
       "roadmap.cjs",
       "runtime-artifact-conversion.cjs",
+      "runtime-artifact-install-plan.cjs",
       "runtime-artifact-layout.cjs",
       "runtime-config-adapter-registry.cjs",
       "runtime-homes.cjs",

docs/INVENTORY.md

@@ -215,6 +215,7 @@ Full roster at `gsd-core/workflows/*.md`. Workflows are thin orchestrators that
 | `ingest-docs.md` | Scan a repo for mixed planning docs; classify, synthesize, and bootstrap or merge into `.planning/` with a conflicts report. | `/gsd-ingest-docs` |
 | `insert-phase.md` | Insert a decimal phase for urgent work discovered mid-milestone. | `/gsd-phase --insert` |
 | `list-phase-assumptions.md` | Surface Claude's assumptions about a phase before planning. | `/gsd-discuss-phase --assumptions` |
+| `list-seeds.md` | List and audit captured seeds (read-only), with optional status filter. | `/gsd-capture --list-seeds` |
 | `list-workspaces.md` | List all GSD workspaces found in `~/gsd-workspaces/` with their status. | `/gsd-workspace --list` |
 | `manager.md` | Interactive milestone command center — dashboard, inline discuss, background plan/execute. | `/gsd-manager` |
 | `map-codebase.md` | Orchestrate parallel codebase mapper agents to produce `.planning/codebase/` docs. | `/gsd-map-codebase` |
@@ -476,6 +477,7 @@ Full listing: `gsd-core/bin/lib/*.cjs`.
 | `roadmap-upgrade.cjs` | Migration tool for converting legacy `Phase N` entries to milestone-prefixed `Phase M-NN` convention; `computeMigrationPlan` + `applyMigration` with dry-run default and atomic rollback |
 | `roadmap.cjs` | ROADMAP.md parsing, phase extraction, plan progress |
 | `runtime-artifact-conversion.cjs` | Runtime artifact conversion module — projects Claude-authored commands, agents, and skills into runtime-specific artifact bodies while preserving installer compatibility exports |
+| `runtime-artifact-install-plan.cjs` | Runtime artifact install plan module — stages pre-resolved layout kinds, applies runtime body rewrites, and returns copy-plan items plus cleanup obligations |
 | `runtime-artifact-layout.cjs` | Runtime artifact layout module — resolves the artifact directory shapes (commands, agents, skills) for each supported runtime; single source of truth for per-runtime artifact placement (#3663) |
 | `runtime-config-adapter-registry.cjs` | Explicit runtime config adapter registry — resolves per-runtime config-mutation install intent (install surface, shared-settings gate, finish-phase permission writer); see ADR-58. |
 | `runtime-hooks-surface.cjs` | Runtime hooks surface module — standalone hook-surface writer functions extracted from bin/install.js (ADR-857 phase 5f-1); owns Cline/Cursor/Copilot/Codex hook artifact generation and reconciliation. |

docs/USER-GUIDE.md

@@ -334,6 +334,15 @@ Seeds are forward-looking ideas with trigger conditions. Unlike backlog items, s
 
 `/gsd-new-milestone` scans all seeds and presents matches. **Storage:** `.planning/seeds/SEED-NNN-slug.md`
 
+Once you've parked a few, audit them on demand instead of waiting for the next milestone to surface them:
+
+```bash
+/gsd-capture --list-seeds            # Review every parked seed
+/gsd-capture --list-seeds dormant    # Narrow to one status
+```
+
+This is read-only — it renders an audit table (ID, status, scope, trigger, title) and a per-status summary, and never modifies a seed. Filter by `dormant`, `active`, or `triggered` when you only want to see seeds in one state.
+
 ### Persistent Context Threads
 
 Threads are lightweight cross-session knowledge stores for work that spans multiple sessions but doesn't belong to any specific phase.

docs/adr/1508-runtime-artifact-conversion-module.md

@@ -14,7 +14,7 @@ This is the **last upward dependency from the `.cts` source tree into the hand-a
 
 ## Decision
 
-- Promote the `[Planned]` **Runtime Artifact Conversion Module** (`src/runtime-artifact-conversion.cts`) to the single owner of per-runtime **content rewriting**: the per-runtime converters (already relocated as ADR-3660's "first slice", #1099), **plus** the rewrite engine `_applyRuntimeRewrites`, the staged-content walkers, path-prefix derivation, and commit attribution. The **Runtime Artifact Layout Module** keeps owning **placement** only.
+- Promote the `[Planned]` **Runtime Artifact Conversion Module** (`src/runtime-artifact-conversion.cts`) to the single owner of per-runtime **content rewriting**: the per-runtime converters (already relocated as ADR-3660's "first slice", #1099), **plus** the rewrite engine `_applyRuntimeRewrites`, the staged-content walkers, path-prefix derivation, and commit attribution. The **Runtime Artifact Layout Module** keeps owning **placement** only. **Exception:** opencode and kilo path-prefix rewriting remains a deliberate `bin/install.js`-owned pre-conversion step (see `applyOpencodeFamilyPathPrefix`); this is intentional per #784 and is not a violation of the single-owner rule.
 - **Public seam** — two deep calls; the caller passes only what it has, the module derives the rest:
   - `rewriteStagedSkillBodies(stagedDir, { runtime, configDir, scope }, env?)` — in-place walk (skills / kimi-agents).
   - `rewriteStagedCommandBodies(stagedDir, { runtime, configDir, scope }, env?) → tempDir` — copy-to-temp (commands).

docs/adr/550-spec-phase-probe-contract.md

@@ -114,9 +114,19 @@ This addendum ratifies three contract points:
 Net effect on D4: the *guarantee* ("a `test`-tier prohibition is never a silent pass") was preserved at every step — fail-closed-now (#644), genuine-execution (#1259), and now **machine-proven fail-first (#1279)**. A `test`-tier prohibition reaches `green`/`passed` ONLY when the wired check both genuinely, non-vacuously passes AND is independently proven to fail on a violation; every miss/fail/un-provable hard-gates. The decision also lives in `src/prohibition-enforcement.cts` comments, `gsd-core/references/prohibition-probe.md`, `gsd-core/workflows/verify-phase.md`, and the #1279 changeset.
 
 **Review corrections (#1314 maintainer review) — two soundness items:**
-- **node-test fixture-existence guard (was fail-OPEN) — FIXED.** The node-test prover originally guarded only `if (!fixture)`. A missing/typo'd/stale `violationFixture` path made `GSD_PROHIB_SUBJECT` point at a non-existent file; an honest negative test then threw ENOENT *inside its callback* — a failing test named distinctly from the file — which `isNonVacuousNodeTestRed` accepted as proof, **forging a green from a setup crash** (asymmetric with the lint-rule path, which fail-CLOSES on `< 1` file result). Fixed by requiring `fs.existsSync(path.resolve(cwd, fixture))` before spawning (symmetric fail-closed; resolved against the producer's `cwd` to match the child's resolution). **Documented residual (#1346):** existence is necessary but not sufficient — a deceptive test that reds merely *because* `GSD_PROHIB_SUBJECT` is set (not because the subject's CONTENT violates) is still accepted; proving causation generically for an arbitrary author-supplied test is not possible, so it is recorded as a constraint, not implied-solved.
+- **node-test fixture-existence guard (was fail-OPEN) — FIXED.** The node-test prover originally guarded only `if (!fixture)`. A missing/typo'd/stale `violationFixture` path made `GSD_PROHIB_SUBJECT` point at a non-existent file; an honest negative test then threw ENOENT *inside its callback* — a failing test named distinctly from the file — which `isNonVacuousNodeTestRed` accepted as proof, **forging a green from a setup crash** (asymmetric with the lint-rule path, which fail-CLOSES on `< 1` file result). Fixed by requiring `fs.existsSync(path.resolve(cwd, fixture))` before spawning (symmetric fail-closed; resolved against the producer's `cwd` to match the child's resolution). **Residual (#1346) — now MITIGATED by an optional control; see the 2026-06-21 addendum below:** existence is necessary but not sufficient — a deceptive test that reds merely *because* `GSD_PROHIB_SUBJECT` is set (not because the subject's CONTENT violates) was still accepted; a generic always-on proof is impossible, so #1346 adds an **opt-in clean-subject control** that proves content-dependence when the author supplies one (and the residual remains, documented, only for checks with no control fixture).
 - **`violationFixture` projection source (#1278 ↔ #1279 now COMPOSE) — DELIVERED.** Initially `descriptorFromProjection` reconstructed only `{ kind, target, rule? }` and the projection carried no fixture, so a prohibition wired purely through the deterministic path always hard-gated. This PR threads a **fourth flat scalar `check_violation_fixture`** through `projectProhibitions` + `descriptorFromProjection` (rides both kinds; mirrors `CheckDescriptor.violationFixture`). A prohibition authored with all four scalars now **machine-proves fail-first and greens end-to-end through the projection alone** (zero hand-authoring) — the round-trip is pinned by a fast-check property + CHK-03(D) + an end-to-end COMPOSE capstone. Fail-closed is preserved: a descriptor with no `check_violation_fixture` (or a blank one) projects absent and hard-gates. The remaining work under #1346 is now just the node-test causation residual above.
 
+## Addendum (2026-06-21, #1346) — node-test causation control: prove the RED is CONTENT-caused
+
+The #1314 review left one tracked residual (above): the node-test prover confirms the violation fixture exists and that the negative test goes a non-vacuous RED, but could not prove the RED was caused by the subject's **content** rather than by `GSD_PROHIB_SUBJECT` merely being *set*. A deceptive content-independent test (`assert.ok(!process.env.GSD_PROHIB_SUBJECT)`) was still accepted. A general always-on proof is impossible for an arbitrary author-supplied test, so #1346 closes the gap with an **opt-in control** rather than a forced one.
+
+This addendum ratifies one contract point:
+
+- **(d) `CheckDescriptor.cleanFixture?` / `check_clean_fixture` — the causation control (the 5th flat scalar).** An OPTIONAL author-supplied path to a KNOWN-CLEAN control subject. When present, the node-test prover runs the SAME negative test a second time with `GSD_PROHIB_SUBJECT=<cleanFixture>` and requires it to stay a **non-vacuous GREEN**. Fail-first is then proven ONLY when the check is **RED on the violation AND GREEN on the clean subject** — i.e. the red is content-dependent. A deceptive test that reds whenever the env var is set reds on the clean subject too → the control fails → not proven (fail-closed). The scalar rides both kinds through `projectProhibitions` + `descriptorFromProjection` exactly as `check_violation_fixture` does (round-trip pinned by the fast-check property + an end-to-end COMPOSE capstone exercising both the honest and deceptive subjects).
+
+**Why opt-in, not required:** making the control mandatory would regress the #1314 zero-authoring compose path — every existing node-test prohibition (which carries no clean fixture) would suddenly hard-gate. So **absent `cleanFixture` → no control runs and behavior is byte-identical to post-#1314**; the residual remains a documented permanent constraint *only* for checks whose author did not supply a clean control. An author opts into the stronger machine guarantee by supplying one. The lint-rule kind needs no analog: its "subject" *is* the linted file (no `GSD_PROHIB_SUBJECT` indirection), so the "reds because the env var is set" gap does not exist there. Net effect on D4 is unchanged — every miss/fail/un-provable still hard-gates; this only *tightens* what counts as proven. The mechanism lives in `src/prohibition-enforcement.cts` (`defaultProveFailFirst` node-test branch + the `runNodeTestWithSubject` helper) and `src/probe-core.cts` (`projectProhibitions`), compiled by `build:lib`.
+
 ## Addendum (2026-06-15): optional `check` descriptor on the prohibition item — D3 shape extension (#1278)
 
 This ratifies the **deterministic SOURCE** for the test-tier `CheckDescriptor` that #1259 (PR #1273) left caller/verifier-supplied. #1259 shipped the PRODUCER (`check prohibition-enforcement`) that *runs* a wired check given a `{kind, target, rule?}` descriptor, but the descriptor itself was invented by the verify-phase LLM each run (the "locate" half). #1278 makes that locate half **deterministic**: an optional `check` descriptor is authored at spec-phase on the resolved `test`-tier prohibition, projected by `projectProhibitions`, and read back by verify-phase — so a wired, passing test closes the gap with **zero manual authoring**. This extends the **Decision 3 prohibition-item shape** (it adds optional keys to that item), so it is ratified here rather than rewriting D3 in place.