@ionivetech/mugiwara 0.6.6 → 0.7.0

package/.claude-plugin/marketplace.json

@@ -5,13 +5,13 @@
   },
   "metadata": {
     "description": "The Straw Hat crew for AI agents",
-    "version": "0.6.6"
+    "version": "0.7.0"
   },
   "plugins": [
     {
       "name": "mugiwara",
       "description": "The Straw Hat crew of AI agents and skills: brainstorm, plan, execute, checkpoint, quality, gates, review, security, healing.",
-      "version": "0.6.6",
+      "version": "0.7.0",
       "source": "./"
     }
   ]

package/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "mugiwara",
   "displayName": "Mugiwara",
-  "version": "0.6.6",
+  "version": "0.7.0",
   "description": "The Straw Hat crew of AI agents and skills: brainstorm, plan, execute, checkpoint, quality, gates, review, security, healing.",
   "author": {
     "name": "ionivetech"
@@ -33,12 +33,10 @@
       "memory-keeper"
     ],
     "skills": [
-      "mugiwara-agent-security",
       "mugiwara-backend",
       "mugiwara-brainstorm",
       "mugiwara-checkpoint",
       "mugiwara-claim-audit",
-      "mugiwara-context-budget",
       "mugiwara-contract-first",
       "mugiwara-execution",
       "mugiwara-frontend",
@@ -48,17 +46,14 @@
       "mugiwara-lessons",
       "mugiwara-orchestration",
       "mugiwara-planning",
-      "mugiwara-pr",
       "mugiwara-quality",
       "mugiwara-resume",
       "mugiwara-review",
       "mugiwara-root-cause",
       "mugiwara-security",
       "mugiwara-ship",
-      "mugiwara-sunset",
       "mugiwara-testcases",
-      "mugiwara-workflow",
-      "using-mugiwara"
+      "mugiwara-workflow"
     ]
   }
 }

package/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "mugiwara",
-  "version": "0.6.6",
+  "version": "0.7.0",
   "description": "The Straw Hat crew of AI agents and skills: brainstorm, plan, execute, checkpoint, quality, gates, review, security, healing.",
   "author": {
     "name": "ionivetech"
@@ -17,12 +17,10 @@
   "skills": "./content/skills/",
   "metadata": {
     "skills": [
-      "mugiwara-agent-security",
       "mugiwara-backend",
       "mugiwara-brainstorm",
       "mugiwara-checkpoint",
       "mugiwara-claim-audit",
-      "mugiwara-context-budget",
       "mugiwara-contract-first",
       "mugiwara-execution",
       "mugiwara-frontend",
@@ -32,17 +30,14 @@
       "mugiwara-lessons",
       "mugiwara-orchestration",
       "mugiwara-planning",
-      "mugiwara-pr",
       "mugiwara-quality",
       "mugiwara-resume",
       "mugiwara-review",
       "mugiwara-root-cause",
       "mugiwara-security",
       "mugiwara-ship",
-      "mugiwara-sunset",
       "mugiwara-testcases",
-      "mugiwara-workflow",
-      "using-mugiwara"
+      "mugiwara-workflow"
     ],
     "agents": [
       "brook-healing",

package/.cursor-plugin/plugin.json

@@ -2,7 +2,7 @@
   "name": "mugiwara",
   "displayName": "Mugiwara",
   "description": "The Straw Hat crew of AI agents and skills: brainstorm, plan, execute, checkpoint, quality, gates, review, security, healing.",
-  "version": "0.6.6",
+  "version": "0.7.0",
   "author": {
     "name": "ionivetech"
   },
@@ -18,12 +18,10 @@
   "skills": "./content/skills/",
   "metadata": {
     "skills": [
-      "mugiwara-agent-security",
       "mugiwara-backend",
       "mugiwara-brainstorm",
       "mugiwara-checkpoint",
       "mugiwara-claim-audit",
-      "mugiwara-context-budget",
       "mugiwara-contract-first",
       "mugiwara-execution",
       "mugiwara-frontend",
@@ -33,17 +31,14 @@
       "mugiwara-lessons",
       "mugiwara-orchestration",
       "mugiwara-planning",
-      "mugiwara-pr",
       "mugiwara-quality",
       "mugiwara-resume",
       "mugiwara-review",
       "mugiwara-root-cause",
       "mugiwara-security",
       "mugiwara-ship",
-      "mugiwara-sunset",
       "mugiwara-testcases",
-      "mugiwara-workflow",
-      "using-mugiwara"
+      "mugiwara-workflow"
     ],
     "agents": [
       "brook-healing",

package/.kimi-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "mugiwara",
-  "version": "0.6.6",
+  "version": "0.7.0",
   "description": "The Straw Hat crew of AI agents and skills: brainstorm, plan, execute, checkpoint, quality, gates, review, security, healing.",
   "author": {
     "name": "ionivetech"
@@ -17,12 +17,10 @@
   "skills": "./content/skills/",
   "metadata": {
     "skills": [
-      "mugiwara-agent-security",
       "mugiwara-backend",
       "mugiwara-brainstorm",
       "mugiwara-checkpoint",
       "mugiwara-claim-audit",
-      "mugiwara-context-budget",
       "mugiwara-contract-first",
       "mugiwara-execution",
       "mugiwara-frontend",
@@ -32,17 +30,14 @@
       "mugiwara-lessons",
       "mugiwara-orchestration",
       "mugiwara-planning",
-      "mugiwara-pr",
       "mugiwara-quality",
       "mugiwara-resume",
       "mugiwara-review",
       "mugiwara-root-cause",
       "mugiwara-security",
       "mugiwara-ship",
-      "mugiwara-sunset",
       "mugiwara-testcases",
-      "mugiwara-workflow",
-      "using-mugiwara"
+      "mugiwara-workflow"
     ],
     "agents": [
       "brook-healing",

package/.opencode/plugins/mugiwara.mjs

@@ -1,8 +1,9 @@
 // mugiwara — OpenCode plugin.
 //
 // Registers skills/agents via config hook (superpowers pattern: one plugin,
-// zero file-copy), announces the crew at session start, and handles runtime
-// mode switching. Helpers live in mugiwara-helpers.mjs — this module has a
+// zero file-copy) and handles runtime mode switching. Deliberately silent at
+// session start: mugiwara activates only when its skills/agents are used.
+// Helpers live in mugiwara-helpers.mjs — this module has a
 // single export because OpenCode's legacy loader calls every exported function
 // as a plugin (same constraint ponytail documents).
 //
@@ -65,9 +66,6 @@ function readBannerColors() {
   }
 }
 
-const ANNOUNCE =
-  "Mugiwara crew available. The workflow auto-activates for non-trivial requests — no need to call `/using-mugiwara` at session start (it is an optional router). Run the crew pipeline inline in the main conversation: embody ONE crew role at a time using its skill, wait for its report, then move to the next. Never Task-dispatch a crew member — the crew runs in the main thread; subagents only for [PARALLEL] task batches, concurrent review/security, and independent re-run checks. Progress shows as checkpoint reports at wave/stage boundaries, pausing on failure or risk. Every wave opens with a banner `===== ⚔️ WAVE N — CREW (ROLE) =====` and closes with a handoff `→ Wave N+1 — Crew (Role)`; Zoro shows per-task progress `[task N/M]` with each task's evidence. Switch mode with `/mugiwara` (guided|semi|auto). See skills/mugiwara-workflow.";
-
 function parseFrontmatter(text) {
   const m = text.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n?/);
   if (!m) throw new Error('Missing frontmatter fence (---)');
@@ -172,17 +170,4 @@ export default async () => ({
       }
     }
   },
-
-  'experimental.chat.system.transform': async (_input, output) => {
-    if (!output?.system || !Array.isArray(output.system)) return;
-    if (!output.system.some((s) => s.includes('Mugiwara crew available'))) {
-      if (output.system.length > 0) {
-        output.system[output.system.length - 1] += '\n\n' + ANNOUNCE;
-      } else {
-        output.system.push(ANNOUNCE);
-      }
-    }
-    const active = `Active mode: ${readMode()} (guided|semi|auto; flip applies next wave).`;
-    if (!output.system.some((s) => s.includes('Active mode:'))) output.system.push(active);
-  },
 });

package/AGENTS.md

@@ -9,8 +9,9 @@ exceptions. Comments in source code should be English. This conversation is the
 only place Indonesian is acceptable.
 
 **`.mugiwara/` artifacts are English too.** Every file the crew writes —
-`plans/`, `logs/`, `results/`, `reports/`, `spec/`, `state/`, `continue/`,
-`issues/`, `review/` — is written in English, one language only. A mission
+Every `.mugiwara/missions/<mission>/` artifact — `plan.md`, `flows/*`,
+`report.md`, `spec.md`, `decisions.md`, `blockers.md`, `review.md`,
+state and continue JSON — is written in English, one language only. A mission
 artifact in any other language is a defect, not a style choice. The audit
 trail is read by the whole team and by future sessions; it must not depend on
 the author's conversational language.
@@ -184,7 +185,7 @@ mention every agent file. Enforced by `--check-docs`.
 
 ## Skill count
 
-26 is the ceiling. A new skill replaces an old one — never add to grow.
+21 is the ceiling. A new skill replaces an old one — never add to grow.
 
 ## Commit style
 
@@ -193,7 +194,7 @@ Conventional Commits: `feat:`, `fix:`, `refactor:`, `docs:`, `chore:`.
 ## Directory map
 
 ```
-content/skills/    — 26 skill dirs, each with SKILL.md + optional references/
+content/skills/    — 21 skill dirs, each with SKILL.md + optional references/
 content/agents/    — 14 agent .md files (11 user-facing + 3 internal)
 references/         — shared reference files (definition-of-done, source-grounding, etc.)
 docs/               — user-facing documentation

package/GEMINI.md

@@ -1,12 +1,12 @@
 # Mugiwara
 
 The Straw Hat crew of AI agents and skills. 11 specialist agents — Luffy
-orchestrates, Nami plans, Zoro executes, Chopper audits, Brook heals — plus 26
+orchestrates, Nami plans, Zoro executes, Chopper audits, Brook heals — plus 21
 skills covering brainstorming, planning, execution, checkpointing, quality,
 gates, review, security, and self-healing.
 
-Start any non-trivial mission by loading the `using-mugiwara` skill (or ask "how do I
-use mugiwara?") — it routes you to the right crew member. See
+Start any non-trivial mission by loading the `mugiwara-orchestration` skill —
+it is the gatekeeper: classify, route, check-in, close. See
 `content/skills/mugiwara-workflow/SKILL.md` for the full pipeline.
 
 For development standards when working on mugiwara itself, see `AGENTS.md`.

package/README.md

@@ -27,8 +27,7 @@ every agent, every skill, every rule is static markdown.
 
 ## See the evidence
 
-A closed mission leaves a report you can actually read. This is the exact
-format `mugiwara run mission-report.sh` produces:
+A closed mission leaves a report you can actually read — and after `mugiwara archive <mission>`, the whole trail folds INTO it. This is the shape of `.mugiwara/missions/<mission>/report.md`:
 
     # Mission: invitation-accepted-flow . 2026-08-11
 
@@ -43,16 +42,16 @@ format `mugiwara run mission-report.sh` produces:
 
     | Flow stage | Artifact | Verdict |
     |------|----------|---------|
-    | Execute (Flow 3) | `01-execution.md` | PASS |
-    | Checkpoint (Flow 4) | `02-audit.md` | PASS |
-    | Quality (Flow 5) | `03-quality.md` | PASS |
-    | Gates (Flow 6) | `04-gates.md` | PASS |
-    | Healing (Flow 8) | `05-healing.md` | PASS |
-    | Closure (Flow 9) | `06-closure.md` | GO |
+    | Execute (Flow 3) | `flows/01-execution.md` | PASS |
+    | Checkpoint (Flow 4) | `flows/02-audit.md` | PASS |
+    | Quality (Flow 5) | `flows/03-quality.md` | PASS |
+    | Gates (Flow 6) | `flows/04-gates.md` | PASS |
+    | Healing (Flow 8) | `flows/05-healing.md` | PASS |
+    | Closure (Flow 9) | `flows/06-closure.md` | GO |
 
     ## Review & blockers
 
-    Review + security files: invitation-accepted-flow-review.md, invitation-accepted-flow-security.md
+    Review + security findings: review.md, security.md
     Findings: 3
     Blocker ledger rows: 1
 
@@ -78,7 +77,7 @@ all nine flow stages. Mugiwara itself is free; token usage depends on the lane:
 | Standard (feature)  |  5–7  |      ~13k      | 25k    |
 | Full (architecture) | 9–11  |      ~23k      | 50k    |
 
-Usage tracked in `.mugiwara/state/<mission>/[member].json` per mission. Budget warns at 1.5×,
+Usage tracked in `.mugiwara/missions/<mission>/[member].json` per mission. Budget warns at 1.5×,
 pauses at 3×. Lane bases are measured from the skills/agents loaded per lane
 by `scripts/lane-base.ts` — the constants fail CI if they drift from content
 load.
@@ -98,7 +97,7 @@ load.
 npx @ionivetech/mugiwara@latest install --target all --yes
 ```
 
-First run: run `mugiwara onboard` in your terminal for guided setup (zero-LLM wizard). Then ask something non-trivial:
+First run: install writes `.mugiwara/config` with defaults — edit it anytime (mode, coverage, depths). Then ask something non-trivial:
 
 ```
 > add role-based access control: admin, editor, viewer
@@ -117,14 +116,14 @@ pipeline config to write.**
 | You say                                        | What happens                                                                                                                                                                             |
 | ---------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `add search bar to products page`              | Luffy triages → Nami plans 3 tasks → Zoro executes TDD → Chopper audits → Sanji runs quality → Franky gates → Robin reviews → code pushed, PR summary ready                              |
-| `split payment system: gateway, ledger, fraud` | Nami interviews team → writes initiative plan with sub-missions + assignees → each dev works in own branch → the plan's sub-mission table shows progress → all done → initiative closure |
+| `split payment system: gateway, ledger, fraud` | Nami interviews → writes one plan split into sub-missions, each with its own branch and done-criteria → each dev resumes only their own sub-mission → all mergeable at the end |
 | `Brook, fix the failing login test`            | Healer reads failure ledger, root-cause fixes, proves fix ≤3 cycles                                                                                                                      |
 | `Jinbe, audit auth middleware`                 | STRIDE + OWASP + dependency audit. Read-only — never touches code                                                                                                                        |
 | `/mugiwara auto`                               | Switches to full autonomy — all flow stages run without asking, from the next flow stage |
 
 - **Full pipeline** when the task is big or direction is unclear
 - **Direct agent** when you know exactly what you need — say the name
-- **Slash commands** when you want to drive: `/mugiwara-plan`, `/mugiwara-review`, `/mugiwara-security`, `/mugiwara-ship`, `/mugiwara onboard`
+- **Slash commands** when you want to drive: `/mugiwara`, `/mugiwara-continue`, `/mugiwara-review`, `/mugiwara-security`
 
 → [Full walkthrough](docs/getting-started.md) · [Full workflow walkthrough](docs/concepts/workflow.md)
 
@@ -132,16 +131,37 @@ pipeline config to write.**
 
 ### All features
 
+**Every day, on every repo:**
+
 | Feature                  | What you get                                                                                    |
 | ------------------------ | ----------------------------------------------------------------------------------------------- |
 | **Lane sizing**          | Work auto-sized from `git diff`. Typo = instant fix. Auth migration = full pipeline.            |
 | **Evidence trail**       | `.mugiwara/` workspace: plans, audit reports, quality reports, review findings, blocker ledger. |
-| **Team collaboration**   | One shared plan, per-(mission, member) state + resume. Any number of engineers, zero collisions. |
+| **Closure integrity**    | Archive fails on dangling links, secrets in the trail, or missing evidence.                     |
+| **Provenance**           | Per-commit attribution — agent, model, lane, evidence. `mugiwara blame`.                        |
+| **Rollback map**         | Executable `rollback.sh` per mission: exact revert commands. Human runs it. Under squash merges the diff is collapsed — `rollback.sh` contains `UNRESOLVED` guidance with `git log --grep="<mission>"` and `exit 1` instead of a silent "nothing to revert" (measured caveat). |
+| **Review routing**       | Ranked reading order in every report: sensitive paths first, scaffolding last.                  |
+| **Staleness guard**      | Resume warns when main moved past the mission's base.                                           |
+
+**When a team scales it up:**
+
+| Feature                  | What you get                                                                                    |
+| ------------------------ | ----------------------------------------------------------------------------------------------- |
+| **Policy as code**       | `mugiwara.policy.yml`: force lanes up, raise coverage gates, flag paths for human approval.     |
+| **Signed attestation**   | Optional minisign signing of the report — evidence that cannot be edited after the fact.        |
+| **Handoff**              | `mugiwara handoff`: engineer-to-engineer report from computed state.                            |
+| **Context budget**       | Trail size measured at closure; optional ceiling fails the archive like a test.                 |
+| **Team collaboration**   | One shared plan, per-(mission, member) state + resume. Zero collisions.                         |
+
+**Always on, under the surface:**
+
+| Feature                  | What you get                                                                                    |
+| ------------------------ | ----------------------------------------------------------------------------------------------- |
 | **Self-healing**         | Brook reads all failures at once, fixes root causes, re-runs verification. ≤3 cycles.           |
-| **Resume from anywhere** | Session lost? Rebuilds from `.mugiwara/state/<mission>/` + machine-written `continue/<mission>/`. Continues, never restarts. Auto surfaces in-flight work (lists when ambiguous). |
+| **Resume from anywhere** | Rebuilds from `.mugiwara/` state. Continues, never restarts.                                    |
 | **12 platforms**         | Claude Code, opencode, Copilot, Gemini, Codex, Cursor, Kimi, Pi, Antigravity + CLI.             |
 
-→ All 28 features, with how-to-use + scenarios: [Every feature](docs/concepts/features.md) · [Team collaboration](docs/concepts/collaboration.md) · [Full pipeline](docs/concepts/workflow.md) · [Lanes](docs/concepts/lanes.md) · [Modes](docs/concepts/modes.md) · [Config](docs/concepts/config.md) · [Audit trail](docs/concepts/audit-trail.md) · [Cost](docs/concepts/cost.md)
+→ All features, with how-to-use + scenarios: [Every feature](docs/concepts/features.md) · [Full pipeline](docs/concepts/workflow.md) · [Lanes](docs/concepts/lanes.md) · [Modes](docs/concepts/modes.md) · [Config](docs/concepts/config.md) · [Audit trail](docs/concepts/audit-trail.md) · [Cost](docs/concepts/cost.md) · [Provenance](docs/concepts/provenance.md) · [Policy](docs/concepts/policy-as-code.md) · [Closure tools](docs/concepts/closure-tools.md) · [Permissions](docs/concepts/permissions.md)
 
 ## The pipeline
 
@@ -161,32 +181,11 @@ flowchart TB
 
 ## The crew
 
-11 agents (+3 internal). Each has role boundaries — auditors
-and reviewers are read-only. Call them by name or let the pipeline auto-route.
-
-| Agent                | Role                                                                                    |  Permission   |
-| -------------------- | --------------------------------------------------------------------------------------- | :-----------: |
-| `luffy-orchestrator` | Captain — triage, check-ins, closure                                                    |       —       |
-| `usopp-brainstorm`   | Critical friend — interrogates, researches, recommends                                  |       —       |
-| `nami-planner`       | Planner — interviews, full scan, scaled plans, team initiatives                         |       —       |
-| `zoro-execution`     | Executor — TDD per task, evidence per commit                                            |       —       |
-| `chopper-checkpoint` | Auditor — re-runs criteria, failure ledger                                              | **read-only** |
-| `sanji-quality`      | Quality — format, lint, test, duplication, complexity, maintainability, code attributes |       —       |
-| `franky-gates`       | Gates — coverage, build, DoD, per-condition sonar gate                                  |       —       |
-| `robin-reviewer`     | Reviewer — breaking-change map, reliability rating, code attribute deep review          | **read-only** |
-| `jinbe-security`     | Security — STRIDE, OWASP, hotspots, SCA license, secret scan, responsibility            | **read-only** |
-| `brook-healing`      | Healer — reads ledger, root-cause fixes ≤3 cycles                                       |       —       |
-| `resume-coordinator` | Resumer — rebuilds state from `.mugiwara/`, continues never restarts                    |       —       |
-
-**Internal agents** (dispatch-only):
-
-| Agent              | Role                                                  | Used by                        |
-| ------------------ | ----------------------------------------------------- | ------------------------------ |
-| `skeptic-verifier` | Adversarial verifier — doubts every claim             | Flow 4.5, high-stakes missions |
-| `eval-runner`      | Harness tester — task suites, judge rubric            | `bun scripts/run-evals.ts`     |
-| `memory-keeper`    | Lessons ledger — surface at start, capture at closure | Flow 0 (read), Flow 9 (write)  |
-
-→ [Agent details: summoning, boundaries, parameters](docs/concepts/agents.md)
+11 agents (+3 internal), one specialist per role — auditors and reviewers are
+read-only by declared tool scope. Full table, summoning syntax, and boundary
+rules live in one place:
+
+→ [Agent details: roles, scopes, summoning, boundaries](docs/concepts/agents.md)
 
 ## Team collaboration
 
@@ -196,36 +195,34 @@ colliding, and one engineer can juggle several missions.
 
 ```
 .mugiwara/
-├── state/<mission>/state.json        # solo state
-├── state/<mission>/<member>.json     # your team member state
-├── continue/<mission>/state.json     # solo resume point
-├── continue/<mission>/<member>.json  # your resume point
-└── plans/<mission>.md                # ONE shared plan (source of truth)
+└── missions/<mission>/
+    ├── plan.md                  # ONE shared plan (source of truth)
+    ├── state.json               # solo state
+    ├── <member>.json            # per-member state
+    ├── continue.json            # solo resume point
+    └── continue-<member>.json   # per-member resume point
 ```
 
 Quick start for a team:
 
 ```bash
-# Nami writes one plan with a ## Sub-missions table (assignee + branch per member)
-/mugiwara-plan                          # guided/semi asks "Solo or team?"
+# Nami writes one plan; very-large scopes get a ## Mission split with a
+# sub-mission per part, each with its own branch and done-criteria.
 
-# Each member works on their own branch, resume only their own work
+# Each member works on their own branch, resumes only their own work
 /mugiwara continue                      # list every in-flight mission for YOU
 /mugiwara continue payment-gateway      # solo → resume; team → list members
 /mugiwara continue payment-gateway patty # resume exactly patty's work
 
 # Coordination radar
-mugiwara initiative status plans/<mission>.md          # who's where
-mugiwara initiative conflict-check plans/<mission>.md  # shared-file overlap
-# In an installed project: read the sub-mission table in the plan doc, and
-# `mugiwara status` for computed per-mission position.
+mugiwara status   # computed per-mission position: flow stage, tasks, lane, blockers
 ```
 
 Auto mode runs every flow stage autonomously — and never downgrades to guided
 mid-mission. In a team plan, auto covers **your member scope only**: resuming
 your sub-mission runs it to ship, never the other members'.
 
-→ [Full collaboration guide with a worked example](docs/concepts/collaboration.md) · [Multi-actor reference](references/multi-actor.md)
+→ [Multi-actor reference](references/multi-actor.md)
 
 ## When not to use Mugiwara
 
@@ -251,11 +248,12 @@ Switch mode any time: `/mugiwara guided | semi | auto`. Or edit `.mugiwara/confi
 | `coverage_modified` | 80                              | Coverage threshold for modified files (%)      |
 | `review_depth`      | full                            | full / standard / quick — Robin's review depth |
 | `quality_depth`     | full                            | full / standard / quick — Sanji's check depth  |
+| `verify_merged`     | off                             | on merges Flow 5+6 into one verify pass (never Lane 3) |
 | `delegate_threshold`| 60                              | % of token budget at which remaining tasks dispatch to workers |
 | `heal_max_cycles`   | 3                               | Max heal-loop cycles before human escalation    |
 | `verbosity`         | normal                          | normal / full — how much the crew echoes. `normal` hides investigation steps (reads, greps) and file contents; edits, results, decisions stay visible. `full` echoes everything. Never suppresses decisions, questions, blockers, or lane rises |
 
-Set via `mugiwara onboard` or edit directly. Unknown keys ignored. Project
+Set via edit directly (`.mugiwara/config`). Unknown keys ignored. Project
 config (`.mugiwara/config`) overrides global (`~/.mugiwara/config`).
 
 **How much does the crew ask you?**
@@ -276,14 +274,12 @@ mid-mission. Only a genuine blocker or the heal halt pauses.
 
 | Need                    | Command / Doc                            |
 | ----------------------- | ---------------------------------------- |
-| First-time setup        | `mugiwara onboard` (terminal) or `/mugiwara onboard` |
-| Plan a feature          | `/mugiwara-plan` or just describe it     |
 | Review a PR diff        | `/mugiwara-review` or "review this PR"   |
 | Security audit          | `/mugiwara-security` or "Jinbe, audit X" |
-| Ship gate check         | `/mugiwara-ship`                         |
-| See initiative progress | `mugiwara initiative status <plan>` |
 | Resume a mission        | `/mugiwara continue <mission> [member]` or "where were we?" |
 | See mission position    | `mugiwara status` (flow stage, tasks, lane, blockers, budget) |
+| Close out a mission     | `mugiwara archive <mission>` — folds the trail into report.md |
+| Tidy closed missions    | `mugiwara clean` (batch; `--all --force` includes in-flight) |
 | Switch mode             | `/mugiwara guided\|semi\|auto`           |
 | Check gate locally      | `bun run gate`                           |
 | All docs                | [docs/](docs/)                           |
@@ -418,7 +414,7 @@ Uninstall: `mugiwara uninstall`
 
 </details>
 
-All platforms get the full crew — 11 agents (+3 internal), 26 skills.
+All platforms get the full crew — 11 agents (+3 internal), 21 skills.
 Enforcement depth varies by harness; see the [harness matrix](docs/reference/harness-matrix.md).
 
 → [How the skills stay small: three-layer disclosure](docs/reference/skill-anatomy.md)
@@ -453,6 +449,13 @@ mugiwara update --target <id> --yes           # overwrite to latest
 mugiwara uninstall                            # remove installed files
 mugiwara list                                 # show installations
 mugiwara list --check                         # health check
+mugiwara status                               # computed mission state
+mugiwara continue [mission] [member]          # resume / list in-flight
+mugiwara archive <mission>                    # fold the trail into report.md (integrity-gated)
+mugiwara clean [--all] [--before <date>]      # batch-archive closed missions
+mugiwara blame <path>                         # provenance note on the last commit touching path
+mugiwara handoff <mission>                    # engineer-to-engineer handoff report
+mugiwara sign <mission> [--verify]            # optional minisign attestation of report.md
 mugiwara reset --keep-logs                    # wipe state, keep lessons
 ```
 
@@ -460,7 +463,9 @@ mugiwara reset --keep-logs                    # wipe state, keep lessons
 
 **Start here:** [Getting started](docs/getting-started.md) · [What mugiwara replaces](docs/concepts/comparison.md)
 
-**Concepts:** [Workflow](docs/concepts/workflow.md) · [Lanes](docs/concepts/lanes.md) · [Modes](docs/concepts/modes.md) · [Execution model](docs/concepts/execution-model.md) · [Git strategy](docs/concepts/git-strategy.md) · [Config](docs/concepts/config.md) · [Cost](docs/concepts/cost.md) · [Audit trail](docs/concepts/audit-trail.md) · [Security](docs/concepts/security.md)
+**Concepts:** [Workflow](docs/concepts/workflow.md) · [Lanes](docs/concepts/lanes.md) · [Modes](docs/concepts/modes.md) · [Execution model](docs/concepts/execution-model.md) · [Git strategy](docs/concepts/git-strategy.md) · [Config](docs/concepts/config.md) · [Cost](docs/concepts/cost.md) · [Audit trail](docs/concepts/audit-trail.md) · [Security](docs/concepts/security.md) · [Provenance](docs/concepts/provenance.md) · [Policy as code](docs/concepts/policy-as-code.md) · [Closure tools](docs/concepts/closure-tools.md) · [Permissions](docs/concepts/permissions.md)
+
+**Adopt:** [Adoption guide](docs/reference/adoption-guide.md) · [Adoption kit](docs/adoption.md)
 
 **Crew:** [Agents](docs/concepts/agents.md) · [Skills](docs/concepts/skills.md)
 
@@ -476,8 +481,9 @@ mugiwara reset --keep-logs                    # wipe state, keep lessons
 
 | Claim | Status |
 |---|---|
-| Retrieval routing rank-1 | **93.5%**, 181 probes, offline, in CI |
+| Retrieval routing rank-1 | **94.3%**, 150 probes, offline, in CI |
 | Reference pointers resolve | **66/66**, 3 tiers, in CI |
+| Index size published vs measured | **doc-gated** — validator fails on drift, in CI |
 | Lane constants match content load | **verified**, in CI |
 | Write-scope enforcement | **opencode only** — rules-based elsewhere |
 | Cross-harness mission behavior | **12/12 platforms** — 9 rules-dir installs + 3 marketplace manifests, in CI |

package/content/agents/brook-healing.md

@@ -1,7 +1,7 @@
 ---
 name: brook-healing
 description: Persona for mugiwara-healing. Root-cause healer: reads blocker ledger, triages failures, spawns parallel heal workers, max 3 cycles.
-skills: mugiwara-healing, mugiwara-git, mugiwara-sunset, mugiwara-root-cause, mugiwara-orchestration
+skills: mugiwara-healing, mugiwara-git, mugiwara-root-cause, mugiwara-orchestration
 write-scope: source
 ---
 
@@ -9,7 +9,7 @@ write-scope: source
 
 ## Before you start
 
-1. Read the mission state (`.mugiwara/state/<mission>/[member].json`) for this member.
+1. Read the mission state (`.mugiwara/missions/<mission>/state.json | <member>.json`) for this member.
 2. Full entry protocol: `_shared/references/agent-protocol.md` — 4 checks; run in order.
 3. Announce `→ Flow N — <crew>`. **If triage routed elsewhere, say so and stop.** Being summoned is not authorisation to do another crew member's job.
 
@@ -17,6 +17,10 @@ write-scope: source
 
 Self-healing: repairs what failed in earlier flow stages, minimally, and proves each fix. Reads the failure ledger and works it down.
 
+## Tool scope
+
+Read + write inside the repo + shell for tests and builds. No network access — healing never reaches outside the checkout (no package downloads, no API calls); a fix that needs a new dependency escalates to Luffy instead. Enforced where the harness supports it (docs/concepts/permissions.md); on tier 2/3 this section is the contract, not enforcement.
+
 ## Experience
 
 Surgeon who fixes root causes, not symptoms. Abilities: triage matrix, minimal-diff discipline, rollback prep before risky fixes, proving each fix by re-running the failed check.
@@ -28,7 +32,7 @@ Flow 8 of `mugiwara-workflow`, with failure inputs from Chopper/Sanji/Franky/Rob
 ## Rules
 
 1. Follow `mugiwara-healing` exactly (triage matrix, root-cause rule, cycle counter).
-2. Read `.mugiwara/issues/YYYY-MM-DD-<mission>-blockers.md` and work each row; mark rows fixed as you clear them.
+2. Read `.mugiwara/missions/<mission>/blockers.md` and work each row; mark rows fixed as you clear them.
 3. Never weaken or delete tests/configs to silence a failure.
 4. Apply `mugiwara-git` for fixes: atomic commits, save-points before a risky fix, rollback plan prepared for risky ones.
 5. Same failure after 3 heal cycles → stop and escalate to Luffy with full history.
@@ -38,7 +42,7 @@ Flow 8 of `mugiwara-workflow`, with failure inputs from Chopper/Sanji/Franky/Rob
 
 ## Output
 
-Fixed list + escalated list in `.mugiwara/results/<mission>/05-healing.md` → summarized inline → back to Flow 4 (Chopper) for re-audit.
+Fixed list + escalated list in `.mugiwara/missions/<mission>/flows/05-healing.md` → summarized inline → back to Flow 4 (Chopper) for re-audit.
 
 ## Return to Luffy
 

package/content/agents/chopper-checkpoint.md

@@ -10,7 +10,7 @@ write-scope: artifacts
 
 ## Before you start
 
-1. Read the mission state (`.mugiwara/state/<mission>/[member].json`) for this member.
+1. Read the mission state (`.mugiwara/missions/<mission>/state.json | <member>.json`) for this member.
 2. Full entry protocol: `_shared/references/agent-protocol.md` — 4 checks; run in order.
 3. Announce `→ Flow N — <crew>`. **If triage routed elsewhere, say so and stop.** Being summoned is not authorisation to do another crew member's job.
 
@@ -18,6 +18,10 @@ write-scope: artifacts
 
 Audits execution against the plan. Trusts nothing; re-verifies everything — efficiently. Does not fix — findings only.
 
+## Tool scope
+
+Read + shell (inspection commands only: `git show/log/diff`, test re-runs). Never Write/Edit a source file; the only permitted writes are mission artifacts under `.mugiwara/`. An auditor that can edit code is not an auditor — enforced where the harness supports it (see docs/concepts/permissions.md); on tier 2/3 this section is the contract, not enforcement.
+
 ## Experience
 
 QA lead who has caught "works on my machine" for 20 years. Abilities: re-running every claim, commit forensics (`git show --stat`), parallel-file conflict detection, honest code-vs-env classification, zero tolerance for borrowed evidence.
@@ -34,7 +38,7 @@ Flow 4 of `mugiwara-workflow`, with the plan doc and Zoro's execution report.
 4. Commit hygiene: `git log --stat <flow-base>..HEAD` once — only declared files per task commit.
 5. Parallel-conflict check: `git diff --name-only` across parallel task commits — no shared file.
 6. Classify failures honestly (code vs env); never file a code failure as `env`.
-7. Append each failing criterion to `.mugiwara/issues/YYYY-MM-DD-<mission>-blockers.md` in the `| flow stage | task | symptom | attempted | help-needed |` format with the right category.
+7. Append each failing criterion to `.mugiwara/missions/<mission>/blockers.md` in the `| flow stage | task | symptom | attempted | help-needed |` format with the right category.
 8. DoD check: verdict per axis — correctness, quality, integration, docs, ship-readiness — then one flow-stage verdict.
 9. Never edit code; never fix a finding yourself.
 10. Issue the verdict only after the audit is complete.
@@ -42,7 +46,7 @@ Flow 4 of `mugiwara-workflow`, with the plan doc and Zoro's execution report.
 
 ## Output
 
-Audit report to `.mugiwara/results/<mission>/02-audit.md` + failure ledger rows in `.mugiwara/issues/` → summarized inline in the conversation (Luffy on PASS, Brook on FAIL).
+Audit report to `.mugiwara/missions/<mission>/flows/02-audit.md` + failure ledger rows in `.mugiwara/missions/<mission>/blockers.md` → summarized inline in the conversation (Luffy on PASS, Brook on FAIL).
 
 ## Return to Luffy