@rafinery/cli 0.4.1 → 0.6.0

package/lib/gate/verify-citations.mjs

@@ -1,6 +1,8 @@
 // Deterministic citation checker for the atlas scan output. Lives INSIDE
 // @rafinery/cli (blueprint split, 0.4.0) — run as `rafa verify-citations`.
-// Three gates:
+// Five gates (checker v2 — the 2026-06-08 ratchet: prism's two recommended
+// checks mechanized, per the disposition protocol "every prism catch gets
+// mechanized | eval-cased | judgment"):
 //
 //  RESOLUTION (B1)   — every cite `- <file>:<line>[-<end>] :: <token>` points at a line
 //                      that actually contains <token>. Catches off-by-N / wrong-file.
@@ -11,18 +13,48 @@
 //                      or `anchor: none` for composition/ordering contracts that don't grep
 //                      as one token. So completeness can't be silently skipped (closes F1:
 //                      the guarantee is mandatory, not opt-in; exemptions are explicit).
+//  ABSENCE (B3)      — a note may declare `absent: <token>` (repeatable, anchor-style):
+//                      "this token appears NOWHERE in code." The checker re-greps every
+//                      declared absence and FAILS if it now matches (docs/.md excluded).
+//                      Mechanizes the 2026-06-08 blocker class: a false absence-claim
+//                      (the note said stubbed; the code had grown the real thing).
+//  INVENTORY         — coverage.md may declare `inventory:` entries
+//                      `- <name> :: <glob> :: <count>`; the checker recomputes each via
+//                      `git ls-files ':(glob)<glob>'` and FAILS on drift. Mechanizes the
+//                      route-inventory diff (coverage claiming N surface files vs reality).
 //
-// Writes a generated report to <root>/citation-check.md (don't hand-paste it).
+// Plus a non-failing heuristic: notes whose title/summary reads existence-shaped
+// ("does not exist", "stubbed", "not implemented"…) without declaring `absent:` are
+// listed as WARNs — prism's worklist, never a gate failure (a heuristic that fails
+// the gate would be an assumed value).
+//
+// Writes a generated report to <root>/citation-check.md (don't hand-paste it) and a
+// machine record to <root>/citation-check.json ({ checkerVersion, pass, gates … }) —
+// `rafa compile` folds that record into manifest.citations so the platform knows
+// which gate level a brain actually passed (recorded run, never assumed).
 // Returns exit code 1 on any failure. Run from repo root:  rafa verify-citations
 
-import { readFileSync, writeFileSync, readdirSync, statSync, existsSync, mkdtempSync, rmSync } from "node:fs";
+import { readFileSync, writeFileSync, readdirSync, statSync, existsSync, mkdtempSync, rmSync, mkdirSync } from "node:fs";
 import { execSync } from "node:child_process";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 
+export const CHECKER_VERSION = 2; // v1 = the 3-gate era (resolution/completeness/policy)
+
 const CITE = /^\s*-\s+(.+?):(\d+)(?:-(\d+))?\s*::\s*(.+?)\s*$/; // - file:start[-end] :: token
 const ANCHOR = /^anchor:\s*(.+?)\s*$/;
+const ABSENT = /^absent:\s*(.+?)\s*$/;
 const TYPE = /^type:\s*(.+?)\s*$/;
+const TITLE = /^title:\s*(.+?)\s*$/;
+const SUMMARY = /^summary:\s*(.+?)\s*$/;
+const INV_ENTRY = /^(.+?)\s*::\s*(.+?)\s*::\s*(\d+)$/; // name :: glob :: count
+
+// Existence-shaped phrases (title/summary only — the machine surface; the body is
+// never parsed). Deliberately narrow: policy claims ("never hardcode") must not hit.
+const ABSENCE_HEURISTIC =
+  /(does\s?n[o']?t exist|do not exist|no longer exists?|nowhere in|not (yet )?(implemented|built|wired|created|present)|only a stub|stubbed|unbuilt|unimplemented|nothing (reads|writes|calls|imports|consumes)|absent from)/i;
+
+const strip = (s) => s.replace(/\s+#.*$/, "").replace(/^["']|["']$/g, "").trim();
 
 function walk(dir) {
   if (!existsSync(dir)) return [];
@@ -32,19 +64,33 @@ function walk(dir) {
   });
 }
 
-function gitGrep(token) {
+function gitGrep(token, cwd = process.cwd()) {
   try {
-    const out = execSync(`git grep -nF -e ${JSON.stringify(token)}`, { encoding: "utf8" });
+    const out = execSync(`git grep -nF -e ${JSON.stringify(token)}`, { encoding: "utf8", cwd });
     return out.split("\n").filter(Boolean).map((l) => {
       const m = l.match(/^(.+?):(\d+):/);
       return m ? { file: m[1], line: +m[2] } : null;
-    }).filter(Boolean);
+    }).filter(Boolean)
+      // The brain is never "code": exclude .rafa/** categorically so the checker
+      // can't self-collide with manifests/notes if .rafa is (accidentally) tracked.
+      .filter((h) => !h.file.startsWith(".rafa/"));
   } catch (e) {
     if (e.status === 1) return []; // git grep: no matches
     throw e;
   }
 }
 
+// Tracked files matching a glob — deterministic inventory ground truth.
+// `:(glob)` pathspec magic makes `**` match across directories.
+function gitLsGlob(glob, cwd = process.cwd()) {
+  try {
+    const out = execSync(`git ls-files -- ${JSON.stringify(`:(glob)${glob}`)}`, { encoding: "utf8", cwd });
+    return out.split("\n").filter(Boolean);
+  } catch {
+    return null; // bad pathspec → caller reports it as a failure, never guesses 0
+  }
+}
+
 function citeResolves(file, start, end, token) {
   if (!existsSync(file)) return { ok: false, reason: "file missing" };
   const src = readFileSync(file, "utf8").split("\n");
@@ -53,28 +99,81 @@ function citeResolves(file, start, end, token) {
   return { ok: false, reason: `token not on ${start}${end !== start ? "-" + end : ""}` };
 }
 
+// coverage.md frontmatter `inventory:` block list → [{ name, glob, count }] + malformed lines.
+function parseCoverageInventory(path) {
+  const entries = [];
+  const malformed = [];
+  if (!existsSync(path)) return { entries, malformed };
+  const lines = readFileSync(path, "utf8").split("\n");
+  let fence = 0;
+  let inBlock = false;
+  for (const line of lines) {
+    if (line.trim() === "---") { fence++; if (fence >= 2) break; continue; }
+    if (fence !== 1) continue;
+    if (/^inventory:\s*$/.test(line)) { inBlock = true; continue; }
+    if (inBlock) {
+      const item = line.match(/^\s+-\s+(.+?)\s*$/);
+      if (item) {
+        const m = strip(item[1]).match(INV_ENTRY);
+        if (m) entries.push({ name: m[1].trim(), glob: m[2].trim(), count: +m[3] });
+        else malformed.push(item[1]);
+        continue;
+      }
+      if (/^\S/.test(line)) inBlock = false; // next top-level key ends the block
+    }
+  }
+  return { entries, malformed };
+}
+
 export function runVerifyCitations(argv = []) {
   const arg = (k, d) => { const m = argv.find((a) => a.startsWith(`--${k}=`)); return m ? m.slice(k.length + 3) : d; };
   const ROOT = arg("root", ".rafa/brain");                                      // --root=.rafa/improve for the improve ledger
   const NOTE_DIRS = arg("dirs", "rules,playbooks").split(",").filter(Boolean);  // --dirs=improvements
 
-  // --selftest: prove the resolution logic fails on a bad cite and passes a good one, on a
-  // throwaway temp file (no brain/repo pollution). prism runs this as its mutation probe —
-  // re-running the checker is not proof it still works; this is.
+  // --selftest: prove each gate's logic on throwaway fixtures (no brain/repo pollution).
+  // prism runs this as its mutation probe — re-running the checker is not proof it still
+  // works; this is. Covers: resolution (good+bad cite) · absence (present token must
+  // flag, missing token must pass) · inventory (count drift must flag, exact must pass).
   if (argv.includes("--selftest")) {
-    const dir = mkdtempSync(join(tmpdir(), "vc-selftest-"));
-    const f = join(dir, "sample.txt");
-    writeFileSync(f, "alpha\nTOKEN beta\ngamma\n");
-    const good = citeResolves(f, 2, 2, "TOKEN").ok; // expect true
-    const bad = citeResolves(f, 1, 1, "TOKEN").ok;  // expect false (off-by-one)
-    rmSync(dir, { recursive: true, force: true });
-    const sane = good === true && bad === false;
-    console.log(`checker self-test: ${sane ? "PASS" : "FAIL"} — good cite=${good} (expect true), bad cite=${bad} (expect false)`);
+    const results = [];
+    // resolution — pure file logic
+    {
+      const dir = mkdtempSync(join(tmpdir(), "vc-selftest-"));
+      const f = join(dir, "sample.txt");
+      writeFileSync(f, "alpha\nTOKEN beta\ngamma\n");
+      results.push(["resolution good cite", citeResolves(f, 2, 2, "TOKEN").ok === true]);
+      results.push(["resolution bad cite", citeResolves(f, 1, 1, "TOKEN").ok === false]);
+      rmSync(dir, { recursive: true, force: true });
+    }
+    // absence + inventory — need a real (temp) git index
+    {
+      const dir = mkdtempSync(join(tmpdir(), "vc-selftest-git-"));
+      try {
+        execSync("git init -q", { cwd: dir });
+        mkdirSync(join(dir, "app", "x"), { recursive: true });
+        writeFileSync(join(dir, "app", "x", "page.tsx"), "export default function X() { return SELFTEST_PRESENT; }\n");
+        writeFileSync(join(dir, "app", "readme.md"), "SELFTEST_PRESENT in docs must not count\n");
+        execSync("git add -A", { cwd: dir });
+        const present = gitGrep("SELFTEST_PRESENT", dir).filter((h) => !h.file.endsWith(".md"));
+        const gone = gitGrep("SELFTEST_TRULY_ABSENT", dir).filter((h) => !h.file.endsWith(".md"));
+        results.push(["absence flags a present token", present.length === 1]); // code hit only, .md excluded
+        results.push(["absence passes a truly absent token", gone.length === 0]);
+        const found = gitLsGlob("app/**/page.tsx", dir);
+        results.push(["inventory exact count passes", (found ?? []).length === 1]);
+        results.push(["inventory drift flags", (found ?? []).length !== 2]);
+      } finally {
+        rmSync(dir, { recursive: true, force: true });
+      }
+    }
+    const sane = results.every(([, ok]) => ok);
+    for (const [name, ok] of results) console.log(`  ${ok ? "✓" : "✗"} ${name}`);
+    console.log(`checker self-test (v${CHECKER_VERSION}): ${sane ? "PASS" : "FAIL"}`);
     return sane ? 0 : 1;
   }
 
   const notes = NOTE_DIRS.flatMap((d) => walk(join(ROOT, d)));
-  if (notes.length === 0) {
+  const coveragePath = join(ROOT, "coverage.md");
+  if (notes.length === 0 && !existsSync(coveragePath)) {
     console.log(`No notes under ${ROOT}/{${NOTE_DIRS.join(",")}}/ — run a scan first.`);
     return 0;
   }
@@ -82,13 +181,19 @@ export function runVerifyCitations(argv = []) {
   const resolution = []; // { note, loc, token, ok, reason }
   const completeness = []; // { note, anchor, site, ok, reason }
   const policy = []; // { note, ok, reason }
+  const absence = []; // { note, token, site, ok, reason }
+  const inventory = []; // { name, glob, declared, found, ok, reason, paths }
+  const warns = []; // { note, phrase }  — heuristic, never fails the gate
 
   for (const note of notes) {
     const rel = note.replace(ROOT + "/", "");
     const lines = readFileSync(note, "utf8").split("\n");
     const cites = [];
     const anchors = [];
+    const absents = [];
     let noteType = "";
+    let title = "";
+    let summary = "";
     let fence = 0;
     for (const line of lines) {
       if (line.trim() === "---") { fence++; if (fence >= 2) break; continue; }
@@ -96,9 +201,15 @@ export function runVerifyCitations(argv = []) {
       const c = line.match(CITE);
       if (c) { cites.push({ file: c[1], start: +c[2], end: c[3] ? +c[3] : +c[2], token: c[4] }); continue; }
       const a = line.match(ANCHOR);
-      if (a) { anchors.push(a[1].replace(/\s+#.*$/, "").replace(/^["']|["']$/g, "").trim()); continue; }
+      if (a) { anchors.push(strip(a[1])); continue; }
+      const ab = line.match(ABSENT);
+      if (ab) { absents.push(strip(ab[1])); continue; }
       const t = line.match(TYPE);
-      if (t) noteType = t[1].replace(/\s+#.*$/, "").trim();
+      if (t) { noteType = strip(t[1]); continue; }
+      const ti = line.match(TITLE);
+      if (ti) { title = strip(ti[1]); continue; }
+      const s = line.match(SUMMARY);
+      if (s) summary = strip(s[1]);
     }
 
     // POLICY — every contract must declare an anchor (token or explicit `none`)
@@ -126,15 +237,56 @@ export function runVerifyCitations(argv = []) {
         completeness.push({ note: rel, anchor, site: `${h.file}:${h.line}`, ok: covered, reason: covered ? "" : "grep hit not cited — site omitted" });
       }
     }
+
+    // ABSENCE (B3) — a declared absence must still be absent
+    for (const token of absents) {
+      if (token.toLowerCase() === "none") continue;
+      const hits = gitGrep(token).filter((h) => !h.file.endsWith(".md")); // docs excluded, same rule as completeness
+      if (hits.length === 0) {
+        absence.push({ note: rel, token, site: "(nowhere — as claimed)", ok: true, reason: "" });
+      } else {
+        for (const h of hits) {
+          absence.push({ note: rel, token, site: `${h.file}:${h.line}`, ok: false, reason: "claimed absent but exists — the claim went stale" });
+        }
+      }
+    }
+
+    // WARN heuristic — existence-shaped claim with no declared `absent:` token
+    if (absents.length === 0) {
+      const m = (title + " · " + summary).match(ABSENCE_HEURISTIC);
+      if (m) warns.push({ note: rel, phrase: m[0] });
+    }
+  }
+
+  // INVENTORY — coverage.md declared counts vs tracked reality
+  {
+    const { entries, malformed } = parseCoverageInventory(coveragePath);
+    for (const bad of malformed)
+      inventory.push({ name: "(malformed)", glob: bad, declared: NaN, found: NaN, ok: false, reason: "entry must be `<name> :: <glob> :: <count>`", paths: [] });
+    for (const e of entries) {
+      const paths = gitLsGlob(e.glob);
+      if (paths === null) {
+        inventory.push({ name: e.name, glob: e.glob, declared: e.count, found: NaN, ok: false, reason: "glob is not a valid git pathspec", paths: [] });
+        continue;
+      }
+      const ok = paths.length === e.count;
+      inventory.push({
+        name: e.name, glob: e.glob, declared: e.count, found: paths.length, ok,
+        reason: ok ? "" : `declared ${e.count}, found ${paths.length} — coverage is stale (refresh the scan)`,
+        paths: ok ? [] : paths.slice(0, 20),
+      });
+    }
   }
 
   const rFail = resolution.filter((r) => !r.ok);
   const cFail = completeness.filter((r) => !r.ok);
   const pFail = policy.filter((r) => !r.ok);
-  const fail = rFail.length + cFail.length + pFail.length;
+  const aFail = absence.filter((r) => !r.ok);
+  const iFail = inventory.filter((r) => !r.ok);
+  const fail = rFail.length + cFail.length + pFail.length + aFail.length + iFail.length;
 
   const md = [
-    "# Citation check (generated — do not hand-edit)",
+    `# Citation check (generated — do not hand-edit) · checker v${CHECKER_VERSION}`,
     "",
     `## Resolution (B1): ${resolution.length - rFail.length}/${resolution.length} ✓`,
     ...resolution.map((r) => `${r.ok ? "✓" : "✗"} ${r.loc} :: ${r.token}${r.ok ? "" : "  — " + r.reason + " [" + r.note + "]"}`),
@@ -145,12 +297,51 @@ export function runVerifyCitations(argv = []) {
     `## Policy (contract → anchor declared): ${policy.length - pFail.length}/${policy.length} ✓`,
     ...policy.map((r) => `${r.ok ? "✓" : "✗"} ${r.note}${r.ok ? "" : "  — " + r.reason}`),
     "",
+    `## Absence (B3, declared \`absent:\` re-grepped): ${absence.length - aFail.length}/${absence.length} ✓`,
+    ...absence.map((r) => `${r.ok ? "✓" : "✗"} absent '${r.token}' → ${r.site}${r.ok ? "" : "  — " + r.reason + " [" + r.note + "]"}`),
+    "",
+    `## Inventory (coverage declared vs \`git ls-files\`): ${inventory.length - iFail.length}/${inventory.length} ✓`,
+    ...inventory.flatMap((r) => [
+      `${r.ok ? "✓" : "✗"} ${r.name} '${r.glob}' declared ${r.declared} · found ${r.found}${r.ok ? "" : "  — " + r.reason}`,
+      ...r.paths.map((p) => `    · ${p}`),
+    ]),
+    "",
+    `## Warns (heuristic, non-failing — existence-shaped title/summary with no \`absent:\` declared): ${warns.length}`,
+    ...warns.map((w) => `⚠ ${w.note} — reads as an absence claim ("${w.phrase}") — declare \`absent: <token>\` so the gate can re-grep it, or reword`),
+    "",
     fail ? `**${fail} FAILED.**` : "**All pass.**",
     "",
   ].join("\n");
   writeFileSync(join(ROOT, "citation-check.md"), md);
 
+  // Machine record of THIS run — compile folds it into manifest.citations so the
+  // platform knows the gate level a brain passed. Recorded, never assumed.
+  writeFileSync(
+    join(ROOT, "citation-check.json"),
+    JSON.stringify(
+      {
+        checkerVersion: CHECKER_VERSION,
+        at: new Date().toISOString(),
+        pass: fail === 0,
+        gates: {
+          resolution: { pass: resolution.length - rFail.length, total: resolution.length },
+          completeness: { pass: completeness.length - cFail.length, total: completeness.length },
+          policy: { pass: policy.length - pFail.length, total: policy.length },
+          absence: { pass: absence.length - aFail.length, total: absence.length },
+          inventory: { pass: inventory.length - iFail.length, total: inventory.length },
+        },
+        warns: warns.length,
+      },
+      null,
+      2,
+    ) + "\n",
+  );
+
   console.log(md);
-  console.log(`resolution ${resolution.length - rFail.length}/${resolution.length} · completeness ${completeness.length - cFail.length}/${completeness.length} · policy ${policy.length - pFail.length}/${policy.length}` + (fail ? ` · ${fail} FAILED` : " · all pass"));
+  console.log(
+    `resolution ${resolution.length - rFail.length}/${resolution.length} · completeness ${completeness.length - cFail.length}/${completeness.length} · policy ${policy.length - pFail.length}/${policy.length} · absence ${absence.length - aFail.length}/${absence.length} · inventory ${inventory.length - iFail.length}/${inventory.length}` +
+      (warns.length ? ` · ${warns.length} warn(s)` : "") +
+      (fail ? ` · ${fail} FAILED` : " · all pass"),
+  );
   return fail ? 1 : 0;
 }

package/lib/githook.mjs

@@ -0,0 +1,54 @@
+// The git pre-push hook installer — M5 sensor #3 (the deterministic checkpoint
+// boundary). `git push` of the code branch is a ratified natural checkpoint
+// moment; this hook makes it MECHANICAL instead of SOP-remembered.
+//
+// .git/hooks is per-clone (git never versions it), so this runs at init AND
+// pull (the teammate path) AND update — every working copy gets the sensor.
+// Never clobbers a foreign hook: ours is recognized by its marker line; anything
+// else is respected and the chain-line printed for the dev to add themselves.
+
+import { chmodSync, copyFileSync, existsSync, readFileSync } from "node:fs";
+import { execSync } from "node:child_process";
+import { join } from "node:path";
+
+const MARKER = "rafa pre-push hook";
+const CHAIN_LINE = "npx -y @rafinery/cli checkpoint || true";
+
+export function installPrePush(targetDir) {
+  const src = join(targetDir, ".claude", "rafa", "hooks", "pre-push");
+  if (!existsSync(src)) return { skipped: "no vendored hook template (run `rafa update`)" };
+
+  let hooksDir;
+  try {
+    // --git-path resolves worktrees/submodules correctly; never assume .git is a dir.
+    hooksDir = execSync("git rev-parse --git-path hooks", { cwd: targetDir, encoding: "utf8" }).trim();
+    hooksDir = join(targetDir, hooksDir);
+  } catch {
+    return { skipped: "not a git repo" };
+  }
+
+  const dst = join(hooksDir, "pre-push");
+  if (existsSync(dst)) {
+    const body = readFileSync(dst, "utf8");
+    if (!body.includes(MARKER)) {
+      return {
+        skipped:
+          "a pre-push hook already exists (not rafa's) — to chain the checkpoint boundary, " +
+          `add this line to it yourself:  ${CHAIN_LINE}`,
+      };
+    }
+    // ours → refresh in place (idempotent update)
+    copyFileSync(src, dst);
+    chmodSync(dst, 0o755);
+    return { updated: true };
+  }
+  copyFileSync(src, dst);
+  chmodSync(dst, 0o755);
+  return { installed: true };
+}
+
+export function reportGitHook(r) {
+  if (r.installed) console.log("  ✓ git pre-push hook → checkpoint runs at every code push (non-blocking)");
+  else if (r.updated) console.log("  ✓ git pre-push hook refreshed");
+  else if (r.skipped) console.log(`  ! git pre-push hook not installed — ${r.skipped}`);
+}

package/lib/init.mjs

@@ -105,6 +105,31 @@ export default async function init(args) {
   );
   // Grant rafa's tools their permissions (merge, never overwrite).
   reportSettings(TARGET);
+  // Wire the M5 sensor hooks (SessionStart digest + PostToolUse dirty-marker)
+  // into .claude/settings.json — merge, never clobber the dev's own hooks.
+  {
+    const { mergeClaudeHooks, mergeStatusLine } = await import("./claude-config.mjs");
+    const h = mergeClaudeHooks(TARGET);
+    if (h.skipped) console.log(`  ! hooks untouched — ${h.skipped}`);
+    else if (h.added?.length) console.log(`  ✓ sensor hooks → .claude/settings.json (${h.added.join(", ")})`);
+    else console.log("  ✓ sensor hooks already wired");
+    const sl = mergeStatusLine(TARGET);
+    if (sl.skipped) console.log(`  ! statusline untouched — ${sl.skipped}`);
+    else if (sl.added?.length) console.log("  ✓ loop-state statusline → .claude/settings.json");
+    else console.log("  ✓ loop-state statusline already wired");
+  }
+  // The pre-push checkpoint boundary is per-clone (.git/hooks is never committed).
+  {
+    const { installPrePush, reportGitHook } = await import("./githook.mjs");
+    reportGitHook(installPrePush(TARGET));
+  }
+  // Wire the repo's own MCP servers into the (owned) agent cards so subagents
+  // can actually reach them (zero-command orchestration, 2026-07-12).
+  {
+    const { mergeRepoMcpsIntoCards } = await import("./claude-config.mjs");
+    const r = mergeRepoMcpsIntoCards(TARGET);
+    for (const u of r.updated) console.log(`  ✓ repo MCPs → ${u}`);
+  }
 
   // Keep the brain out of the code repo's diffs; keep the per-dev MCP key out of git.
   const ensureIgnored = (line, label) => {
@@ -151,6 +176,26 @@ export default async function init(args) {
     );
   }
 
+  // CI reconciliation — OPT-IN at provisioning (owner feedback #5): the workflow
+  // runs on the ORG's own secrets (their LLM key never touches our platform), so
+  // it is offered, never silently installed. Non-TTY (CI/agent shells) skips the
+  // question entirely — explicit `rafa ci-setup` remains the path there.
+  if (isInteractive()) {
+    const a = await ask(
+      "  • Wire CI reconciliation now? (GitHub Actions: mechanical fold on branch merges,\n" +
+        "    distillation on merge-to-main — runs on YOUR CI secrets) [y/N] ",
+    );
+    if (a === "y" || a === "yes") {
+      const { default: ciSetup } = await import("./ci-setup.mjs");
+      await ciSetup([]);
+    } else {
+      console.log(
+        "  • skipped — wire it anytime with `rafa ci-setup`. Until then, the next dev\n" +
+          "    session offers the same reconciliation after each merge (nothing is lost).",
+      );
+    }
+  }
+
   // Stamp the versions this repo was provisioned at — the compat anchor `update`/`migrate`
   // diff against. Carries platform identity too when provisioned via a setup URL.
   stampCurrent(

package/lib/leverage.mjs

@@ -3,12 +3,23 @@
 // only: it reads, ranks, and reports — it changes nothing. Run from your repo root.
 
 import { advise } from "./leverage/engine.mjs";
-import { PLANNED } from "./leverage/adapters/index.mjs";
+import { adapters, PLANNED } from "./leverage/adapters/index.mjs";
 
-export default async function leverage() {
+export default async function leverage(args = []) {
   const cwd = process.cwd();
   const { detected, tips } = advise(cwd);
 
+  // --json: the DETERMINISTIC toolbox inventory (ratified 2026-07-12) — what
+  // the conductor loads at bootstrap and atlas consults during scan's toolbox
+  // pass. Machine truth: only what is actually installed, never inferred.
+  if (args.includes("--json")) {
+    const inventory = {};
+    for (const a of adapters)
+      if (a.detect(cwd)) inventory[a.id] = a.inspect(cwd);
+    console.log(JSON.stringify({ detected, inventory, tips }, null, 2));
+    return;
+  }
+
   if (detected.length === 0) {
     console.log(
       "No supported agent toolchain detected here.\n" +

package/lib/migrations/index.mjs

@@ -28,7 +28,7 @@
 //     run: (cwd) => backfillPlanField(cwd, "owner", ownerOf(cwd)),
 //   };
 
-import { existsSync, rmSync } from "node:fs";
+import { existsSync, readFileSync, readdirSync, rmSync, statSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { cmpSemver } from "../releases.mjs";
 
@@ -66,7 +66,62 @@ const blueprint_split_0_4_0 = {
   },
 };
 
-export const MIGRATIONS = [blueprint_split_0_4_0];
+// plans v2 (contract §7 v2, ratified 2026-07-12): the work-item tree. Mechanical
+// half: kind parent→epic, child→task (rank semantics unchanged for flat v1 plans),
+// stored `status: blocked` → `status: todo` + a blocked_reason note (blocked is
+// DERIVED in v2). Only frontmatter lines are touched; bodies never.
+const plans_v1_to_v2 = {
+  id: "plans-v1-to-v2-work-item-tree",
+  kind: "plans",
+  mode: "mechanical",
+  summary:
+    "plans become a work-item tree (epic|task|subtask); blocked becomes derived " +
+    "(kind parent→epic, child→task; status blocked→todo + blocked_reason)",
+  appliesTo: (from, to) => from.plans < 2 && to.plans >= 2,
+  run: (cwd) => {
+    const changed = [];
+    const notes = [];
+    const dir = join(cwd, ".rafa", "plans");
+    const walk = (d) => {
+      if (!existsSync(d)) return [];
+      return readdirSync(d).flatMap((e) => {
+        const p = join(d, e);
+        return statSync(p).isDirectory() ? walk(p) : e.endsWith(".md") ? [p] : [];
+      });
+    };
+    for (const file of walk(dir)) {
+      const text = readFileSync(file, "utf8");
+      if (!text.startsWith("---")) continue;
+      const end = text.indexOf("\n---", 3);
+      if (end === -1) continue;
+      let fm = text.slice(0, end);
+      const body = text.slice(end);
+      const before = fm;
+      fm = fm.replace(/^kind:\s*parent\s*$/m, "kind: epic");
+      fm = fm.replace(/^kind:\s*child\s*$/m, "kind: task");
+      if (/^status:\s*blocked\s*$/m.test(fm)) {
+        fm = fm.replace(/^status:\s*blocked\s*$/m, "status: todo");
+        if (!/^blocked_reason:/m.test(fm))
+          fm += `\nblocked_reason: "(migrated) was 'blocked' in plans v1 — re-state the real blocker"`;
+        notes.push(`${file.slice(cwd.length + 1)}: blocked → todo + blocked_reason (re-state the real blocker)`);
+      }
+      if (fm !== before) {
+        writeFileSync(file, fm + body);
+        changed.push(file.slice(cwd.length + 1));
+      }
+    }
+    return {
+      changed,
+      notes: changed.length
+        ? notes.length
+          ? notes
+          : ["kinds re-ranked (parent→epic, child→task); review the diff"]
+        : ["no v1 plan files found — nothing to migrate"],
+    };
+  },
+};
+
+export const MIGRATIONS = [blueprint_split_0_4_0, plans_v1_to_v2];
 
 // The migrations that apply to a given move (stamped `from` → shipped `to`), in order.
 export function pendingMigrations(from, to) {

package/lib/pull.mjs

@@ -32,6 +32,13 @@ export default async function pull(args = []) {
   const inRafa = inDir(rafaDir);
   if (bootstrapped) console.log(`• bootstrapped lazy .rafa/ from rafa.json (remote: ${remote})`);
 
+  // Every working copy gets the M5 checkpoint boundary (.git/hooks is per-clone —
+  // pull IS the teammate path, so this is where a fresh clone gains the sensor).
+  {
+    const { installPrePush, reportGitHook } = await import("./githook.mjs");
+    reportGitHook(installPrePush(ROOT));
+  }
+
   // Reachability + default branch — loud if the remote can't be reached.
   let branch = "main";
   try {

package/lib/push.mjs

@@ -13,6 +13,7 @@ import { execSync } from "node:child_process";
 import { existsSync, readFileSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { runCompile } from "./gate/compile.mjs";
+import { runVerifyCitations } from "./gate/verify-citations.mjs";
 import { ensureBrainRepo, remoteDefaultBranch, inDir, die } from "./brain-repo.mjs";
 import { CLI_VERSION } from "./releases.mjs";
 
@@ -39,6 +40,26 @@ export default async function push(args = []) {
     /* no origin — manifest.repo stays "" */
   }
 
+  // ── citation gate (in-process) ──
+  // Re-run the checker HERE so the record that rides the push is the record of
+  // THIS push — a stale/hand-stamped citation-check.json can never ship
+  // (mechanized 2026-07-13 from prism's live-run recommendation: the stale-record
+  // class dies at the transport layer, not in review).
+  console.log("• rafa verify-citations — re-grounding every cite/absence/inventory …");
+  if (runVerifyCitations([]) !== 0)
+    die(
+      "citations failed the checker (see report above). Fix the notes against the " +
+        "code (or have atlas repair them), then re-push.",
+    );
+  if (
+    existsSync(join(ROOT, ".rafa", "improve", "improvements")) &&
+    runVerifyCitations(["--root=.rafa/improve", "--dirs=improvements"]) !== 0
+  )
+    die(
+      "improvement citations failed the checker (see report above). Fix the ledger " +
+        "files against the code (or have bloom correct them), then re-push.",
+    );
+
   // ── contract gate (in-process) ──
   // Compile + validate the brain. A schema-invalid brain NEVER leaves the machine —
   // the platform ingests JSON, so what we push must already conform to the contract.