@milehimikey/em 1.16.1 → 1.17.0

package/dist/cli/ledgerCheck.js

@@ -12,7 +12,7 @@
 // second, divergent git plumbing.
 import { existsSync, readdirSync } from "node:fs";
 import { basename, dirname, join, resolve } from "node:path";
-import { hasUsableFrontmatter } from "../catalog/sliceDoc.js";
+import { hasUsableFrontmatter, ratifiedBody } from "../catalog/sliceDoc.js";
 import { readSliceDoc } from "../catalog/readSliceDoc.js";
 import { realGit, listSliceKeysAtRevision, resolveDocAtRevision } from "./diff-inputs.js";
 /** Slice keys currently on disk under `<baseDir>/slices/*.md` — the working-tree counterpart to
@@ -89,7 +89,10 @@ export function checkLedger(anchorFile, from, to, runGit = realGit) {
         }
         const oldVersion = oldDoc.version;
         const newVersion = newDoc.version;
-        const bodyChanged = oldDoc.body.trim() !== newDoc.body.trim();
+        // GH #253/#257: "content" is the SIGNED content — `ratifiedBody()` leaves out the `## Open
+        // Questions` heading and its `deferred to v<n>` items, so a deferral `em slice defer` wrote
+        // into a ratified doc is not a content change here either (it describes a later version).
+        const bodyChanged = ratifiedBody(oldDoc.body).trim() !== ratifiedBody(newDoc.body).trim();
         const docsLineageChanged = lineageChanged(oldDoc, newDoc);
         const contentChanged = bodyChanged || docsLineageChanged;
         let code = null;
@@ -102,19 +105,41 @@ export function checkLedger(anchorFile, from, to, runGit = realGit) {
         else if (!contentChanged && newVersion > oldVersion) {
             code = "ledger-version-without-content-change";
         }
-        if (!code)
-            continue;
-        const message = code === "ledger-version-regression"
-            ? `slice "${sliceKey}": version went backwards (v${oldVersion} -> v${newVersion})`
-            : code === "ledger-content-without-version-bump"
-                ? `slice "${sliceKey}": doc content changed but version: didn't bump (still v${oldVersion})`
-                : `slice "${sliceKey}": version: bumped (v${oldVersion} -> v${newVersion}) but doc content is unchanged`;
-        findings.push({ sliceKey, code, message, oldVersion, newVersion, bodyChanged, lineageChanged: docsLineageChanged });
+        if (code) {
+            const message = code === "ledger-version-regression"
+                ? `slice "${sliceKey}": version went backwards (v${oldVersion} -> v${newVersion})`
+                : code === "ledger-content-without-version-bump"
+                    ? `slice "${sliceKey}": doc content changed but version: didn't bump (still v${oldVersion})`
+                    : `slice "${sliceKey}": version: bumped (v${oldVersion} -> v${newVersion}) but doc content is unchanged`;
+            findings.push({ sliceKey, code, message, oldVersion, newVersion, bodyChanged, lineageChanged: docsLineageChanged });
+        }
+        // GH #257: independent of the version rule. A re-ratification writes a fresh hash (and
+        // `revise` clears it first), so "same hash, different signed body" can only be an edit that
+        // bypassed both gates — including one that bumped `version:` by hand. Docs with no hash on
+        // the old side (ratified before 1.15) have nothing to hold them to.
+        if (bodyChanged && oldDoc.ratifiedHash !== null && oldDoc.ratifiedHash === newDoc.ratifiedHash) {
+            findings.push({
+                sliceKey,
+                code: "ledger-body-changed-without-reratification",
+                message: `slice "${sliceKey}": signed body changed but ratifiedHash did not (v${oldVersion} -> v${newVersion}) — edited without re-ratification`,
+                oldVersion,
+                newVersion,
+                bodyChanged,
+                lineageChanged: docsLineageChanged,
+            });
+        }
     }
     return { findings, waived: [], skipped, checkedCount: keys.length };
 }
 /** The only finding code a waiver may excuse (MIL-185, R9) — see `WaivedLedgerFinding`. */
-const WAIVABLE_LEDGER_CODE = "ledger-content-without-version-bump";
+/** The findings a waiver may excuse: the formatting-only false positive (MIL-185) and, since GH
+ *  #257, the hash finding — a repo baselining docs edited before it started enforcing the hash
+ *  needs a way to say so, auditably. A version regression or a bump with no content change
+ *  stays unwaivable. A waiver names a slice key and excuses every waivable finding on it. */
+const WAIVABLE_LEDGER_CODES = new Set([
+    "ledger-content-without-version-bump",
+    "ledger-body-changed-without-reratification",
+]);
 // `%x00`/`%x01` are git's own pretty-format escapes for those literal bytes — git substitutes
 // them into its OUTPUT, so the argv string handed to spawnSync stays plain ASCII text (an actual
 // embedded NUL byte in an argv string throws in Node's child_process). The output bytes they
@@ -196,8 +221,9 @@ export function readLedgerWaiverTrailers(anchorFile, from, to, runGit = realGit)
 export function applyLedgerWaivers(result, flagWaivedKeys, trailerWaivers) {
     const waivableBySliceKey = new Map();
     for (const finding of result.findings) {
-        if (finding.code === WAIVABLE_LEDGER_CODE)
-            waivableBySliceKey.set(finding.sliceKey, finding);
+        if (!WAIVABLE_LEDGER_CODES.has(finding.code))
+            continue;
+        waivableBySliceKey.set(finding.sliceKey, [...(waivableBySliceKey.get(finding.sliceKey) ?? []), finding]);
     }
     const waivedSliceKeys = new Set();
     const waived = [...result.waived];
@@ -207,10 +233,11 @@ export function applyLedgerWaivers(result, flagWaivedKeys, trailerWaivers) {
         if (seenFlagKeys.has(sliceKey))
             continue;
         seenFlagKeys.add(sliceKey);
-        const finding = waivableBySliceKey.get(sliceKey);
+        const found = waivableBySliceKey.get(sliceKey);
         const source = { source: "flag" };
-        if (finding) {
-            waived.push({ ...finding, waivedBy: source });
+        if (found) {
+            for (const finding of found)
+                waived.push({ ...finding, waivedBy: source });
             waivedSliceKeys.add(sliceKey);
         }
         else {
@@ -220,10 +247,11 @@ export function applyLedgerWaivers(result, flagWaivedKeys, trailerWaivers) {
     for (const trailer of trailerWaivers) {
         if (waivedSliceKeys.has(trailer.sliceKey))
             continue; // already waived by a flag entry
-        const finding = waivableBySliceKey.get(trailer.sliceKey);
+        const found = waivableBySliceKey.get(trailer.sliceKey);
         const source = { source: "trailer", commit: trailer.commit };
-        if (finding) {
-            waived.push({ ...finding, waivedBy: source });
+        if (found) {
+            for (const finding of found)
+                waived.push({ ...finding, waivedBy: source });
             waivedSliceKeys.add(trailer.sliceKey);
         }
         else {
@@ -231,7 +259,9 @@ export function applyLedgerWaivers(result, flagWaivedKeys, trailerWaivers) {
         }
     }
     waived.sort((a, b) => a.sliceKey.localeCompare(b.sliceKey));
-    const findings = result.findings.filter((f) => !waivedSliceKeys.has(f.sliceKey));
+    // Only the waivable findings on a waived key leave `findings`; an unwaivable one (a regression)
+    // on the same key stays and still fails the run.
+    const findings = result.findings.filter((f) => !(waivedSliceKeys.has(f.sliceKey) && WAIVABLE_LEDGER_CODES.has(f.code)));
     return { result: { ...result, findings, waived }, unknownWaivers };
 }
 //# sourceMappingURL=ledgerCheck.js.map

package/dist/cli/ledgerCheck.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ledgerCheck.js","sourceRoot":"","sources":["../../src/cli/ledgerCheck.ts"],"names":[],"mappings":"AAAA,+BAA+B;AAC/B,+FAA+F;AAC/F,8FAA8F;AAC9F,6FAA6F;AAC7F,yFAAyF;AACzF,+FAA+F;AAC/F,8FAA8F;AAC9F,EAAE;AACF,+FAA+F;AAC/F,4EAA4E;AAC5E,4FAA4F;AAC5F,kCAAkC;AAElC,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AAClD,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAsB,MAAM,wBAAwB,CAAC;AAChG,OAAO,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAC;AAC1D,OAAO,EAAa,OAAO,EAAE,uBAAuB,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAoErG;4FAC4F;AAC5F,SAAS,mBAAmB,CAAC,OAAe;IAC1C,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACpC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IAChC,OAAO,WAAW,CAAC,GAAG,CAAC;SACpB,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,QAAQ,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC;AAC1C,CAAC;AAED;;uEAEuE;AACvE,SAAS,QAAQ,CAAC,CAAkB,EAAE,CAAkB;IACtD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,IAAI;QAAE,OAAO,CAAC,KAAK,CAAC,CAAC;IAC7C,OAAO,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC;AACzB,CAAC;AAED,SAAS,YAAY,CAAC,CAAa,EAAE,CAAa;IAChD,IAAI,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM;QAAE,OAAO,KAAK,CAAC;IACxC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAClD,CAAC;AAED;;8FAE8F;AAC9F,SAAS,cAAc,CAAC,MAAgB,EAAE,MAAgB;IACxD,OAAO,CACL,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,SAAS,CAAC;QAC7C,CAAC,YAAY,CAAC,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,UAAU,CAAC;QACnD,CAAC,YAAY,CAAC,MAAM,CAAC,YAAY,EAAE,MAAM,CAAC,YAAY,CAAC,CACxD,CAAC;AACJ,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,UAAkB,EAAE,IAAY,EAAE,EAAiB,EAAE,SAAoB,OAAO;IAC1G,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC;IAC7C,MAAM,OAAO,GAAG,uBAAuB,CAAC,UAAU,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC;IAClE,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,uBAAuB,CAAC,UAAU,EAAE,EAAE,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC;IACpG,MAAM,IAAI,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;IAE3D,MAAM,QAAQ,GAAoB,EAAE,CAAC;IACrC,MAAM,OAAO,GAAiB,EAAE,CAAC;IAEjC,KAAK,MAAM,QAAQ,IAAI,IAAI,EAAE,CAAC;QAC5B,MAAM,MAAM,GAAG,oBAAoB,CAAC,UAAU,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC;QACxE,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,mBAAmB,EAAE,CAAC,CAAC;YACxD,SAAS;QACX,CAAC;QACD,MAAM,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,oBAAoB,CAAC,UAAU,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;QAC7G,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;YAC9C,SAAS;QACX,CAAC;QACD,yEAAyE;QACzE,mFAAmF;QACnF,4FAA4F;QAC5F,4FAA4F;QAC5F,uFAAuF;QACvF,0FAA0F;QAC1F,IAAI,CAAC,oBAAoB,CAAC,MAAM,CAAC,IAAI,CAAC,oBAAoB,CAAC,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;YACzH,OAAO,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,qBAAqB,EAAE,CAAC,CAAC;YAC1D,SAAS;QACX,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,CAAC,OAAO,CAAC;QAClC,MAAM,UAAU,GAAG,MAAM,CAAC,OAAO,CAAC;QAClC,2FAA2F;QAC3F,4FAA4F;QAC5F,0FAA0F;QAC1F,MAAM,WAAW,GAAG,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,KAAK,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC;QAC1F,MAAM,kBAAkB,GAAG,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAC1D,MAAM,cAAc,GAAG,WAAW,IAAI,kBAAkB,CAAC;QAEzD,IAAI,IAAI,GAA6B,IAAI,CAAC;QAC1C,IAAI,UAAU,GAAG,UAAU,EAAE,CAAC;YAC5B,IAAI,GAAG,2BAA2B,CAAC;QACrC,CAAC;aAAM,IAAI,cAAc,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;YACvD,IAAI,GAAG,qCAAqC,CAAC;QAC/C,CAAC;aAAM,IAAI,CAAC,cAAc,IAAI,UAAU,GAAG,UAAU,EAAE,CAAC;YACtD,IAAI,GAAG,uCAAuC,CAAC;QACjD,CAAC;QACD,IAAI,IAAI,EAAE,CAAC;YACT,MAAM,OAAO,GACX,IAAI,KAAK,2BAA2B;gBAClC,CAAC,CAAC,UAAU,QAAQ,+BAA+B,UAAU,QAAQ,UAAU,GAAG;gBAClF,CAAC,CAAC,IAAI,KAAK,qCAAqC;oBAC9C,CAAC,CAAC,UAAU,QAAQ,2DAA2D,UAAU,GAAG;oBAC5F,CAAC,CAAC,UAAU,QAAQ,wBAAwB,UAAU,QAAQ,UAAU,gCAAgC,CAAC;YAC/G,QAAQ,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,cAAc,EAAE,kBAAkB,EAAE,CAAC,CAAC;QACtH,CAAC;QAED,uFAAuF;QACvF,4FAA4F;QAC5F,2FAA2F;QAC3F,oEAAoE;QACpE,IAAI,WAAW,IAAI,MAAM,CAAC,YAAY,KAAK,IAAI,IAAI,MAAM,CAAC,YAAY,KAAK,MAAM,CAAC,YAAY,EAAE,CAAC;YAC/F,QAAQ,CAAC,IAAI,CAAC;gBACZ,QAAQ;gBACR,IAAI,EAAE,4CAA4C;gBAClD,OAAO,EAAE,UAAU,QAAQ,qDAAqD,UAAU,QAAQ,UAAU,oCAAoC;gBAChJ,UAAU;gBACV,UAAU;gBACV,WAAW;gBACX,cAAc,EAAE,kBAAkB;aACnC,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,YAAY,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC;AACtE,CAAC;AAED,2FAA2F;AAC3F;;;6FAG6F;AAC7F,MAAM,qBAAqB,GAAmC,IAAI,GAAG,CAAoB;IACvF,qCAAqC;IACrC,4CAA4C;CAC7C,CAAC,CAAC;AASH,8FAA8F;AAC9F,iGAAiG;AACjG,6FAA6F;AAC7F,gGAAgG;AAChG,iGAAiG;AACjG,yFAAyF;AACzF,MAAM,eAAe,GAAG,MAAM,CAAC;AAC/B,MAAM,iBAAiB,GAAG,MAAM,CAAC;AACjC,MAAM,QAAQ,GAAG,MAAM,CAAC;AACxB,MAAM,UAAU,GAAG,MAAM,CAAC;AAE1B;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,wBAAwB,CAAC,UAAkB,EAAE,IAAY,EAAE,EAAiB,EAAE,SAAoB,OAAO;IACvH,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,EAAE,WAAW,EAAE,iBAAiB,CAAC,CAAC,CAAC;IAC9F,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IACrC,MAAM,QAAQ,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package/dist/cli/ratify.d.ts

@@ -104,8 +104,18 @@ export type RatifiedIdentityResult = {
  * still gives the ratified body an identity, and `--slice-ready` still checks it. Every git call
  * runs `-C baseDir` — the model's directory, never the process cwd — so a model nested in a
  * larger repository, or run from elsewhere, resolves against the right work tree.
+ *
+ * GH #255 — `noRef`: the repo's merge strategy rewrites commits (squash, rebase, merge queue),
+ * so `HEAD` of the ratification PR branch will not be reachable from the target branch once the
+ * branch is deleted; a ref recorded here would dangle, and `mark-implemented` would copy the
+ * dangling pointer into `shippedRef`. With `noRef` the identity is the hash alone — the same shape
+ * as outside git — and git is not consulted at all: the uncommitted-changes refusal exists only so
+ * the recorded ref's tree really holds the signed body, and with no ref there is nothing for it to
+ * protect (the hash is computed from the body itself).
  */
-export declare function resolveRatifiedIdentity(git: GitRunner | null, baseDir: string, docPath: string, raw: string): RatifiedIdentityResult;
+export declare function resolveRatifiedIdentity(git: GitRunner | null, baseDir: string, docPath: string, raw: string, opts?: {
+    noRef?: boolean;
+}): RatifiedIdentityResult;
 export declare function applyRatifyFrontmatter(raw: string, sliceKey: string, ratifiedBy: string, ratifiedOn: string, skipReview?: boolean, confirmation?: MeaningConfirmation | null, identity?: RatifiedIdentity | null): ApplyRatifyResult;
 export type RunRatifyResult = {
     ok: true;
@@ -125,4 +135,6 @@ export type RunRatifyResult = {
  * `--slice-ready`/`em export` use (MIL-121 cross-binding included), then reads/applies/writes
  * it. `baseDir` is the `.em` file's directory, same convention every doc/note path in `em` uses.
  */
-export declare function runRatify(model: NormalizedModel, refs: RefsResult, baseDir: string, sliceKey: string, ratifiedBy: string, ratifiedOn: string, skipReview?: boolean, confirmation?: MeaningConfirmation | null, git?: GitRunner | null): RunRatifyResult;
+export declare function runRatify(model: NormalizedModel, refs: RefsResult, baseDir: string, sliceKey: string, ratifiedBy: string, ratifiedOn: string, skipReview?: boolean, confirmation?: MeaningConfirmation | null, git?: GitRunner | null, 
+/** GH #255: record `ratifiedHash:` only — no `ratifiedRef:`, no git consulted (`--no-ref`). */
+noRef?: boolean): RunRatifyResult;

package/dist/cli/ratify.js

@@ -50,7 +50,7 @@ import { readFileSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { continuationOf } from "../model/continuation.js";
 import { resolveSliceDocJoin } from "../catalog/docJoin.js";
-import { sliceDocBodyHash } from "../catalog/sliceDoc.js";
+import { ratifiedHashScope, sliceDocBodyHash } from "../catalog/sliceDoc.js";
 import { buildModelIndex } from "../model/queryIndex.js";
 import { realGit } from "./diff-inputs.js";
 import { fieldLineRegex, fieldLineWithEolRegex, locateFrontmatterInner, normalizeFieldValue } from "./frontmatterSurgery.js";
@@ -179,10 +179,18 @@ export function upstreamUnratifiedSlices(model, refs, baseDir, sliceKey) {
  * still gives the ratified body an identity, and `--slice-ready` still checks it. Every git call
  * runs `-C baseDir` — the model's directory, never the process cwd — so a model nested in a
  * larger repository, or run from elsewhere, resolves against the right work tree.
+ *
+ * GH #255 — `noRef`: the repo's merge strategy rewrites commits (squash, rebase, merge queue),
+ * so `HEAD` of the ratification PR branch will not be reachable from the target branch once the
+ * branch is deleted; a ref recorded here would dangle, and `mark-implemented` would copy the
+ * dangling pointer into `shippedRef`. With `noRef` the identity is the hash alone — the same shape
+ * as outside git — and git is not consulted at all: the uncommitted-changes refusal exists only so
+ * the recorded ref's tree really holds the signed body, and with no ref there is nothing for it to
+ * protect (the hash is computed from the body itself).
  */
-export function resolveRatifiedIdentity(git, baseDir, docPath, raw) {
+export function resolveRatifiedIdentity(git, baseDir, docPath, raw, opts = {}) {
     const hash = sliceDocBodyHash(raw);
-    if (git === null)
+    if (git === null || opts.noRef === true)
         return { ok: true, identity: { ref: null, hash } };
     const inside = git(["-C", baseDir, "rev-parse", "--is-inside-work-tree"]);
     if (inside.status !== 0 || inside.stdout.trim() !== "true")
@@ -317,7 +325,20 @@ export function applyRatifyFrontmatter(raw, sliceKey, ratifiedBy, ratifiedOn, sk
     // else appended to the existing line's edit, ahead of the MIL-238 confirmation line.
     const refMatch = identity ? fieldLineRegex("ratifiedRef").exec(inner) : null;
     const hashMatch = identity ? fieldLineRegex("ratifiedHash").exec(inner) : null;
+    // GH #255: a ref-less identity (`--no-ref`, or outside git) must not leave an earlier
+    // `ratifiedRef:` line standing — that stale pointer is exactly what the caller asked not to
+    // record. The whole line goes, EOL included.
+    const staleRef = identity && identity.ref === null ? fieldLineWithEolRegex("ratifiedRef").exec(inner) : null;
     const identityLines = [];
+    // GH #260: when `--skip-review` is what let this ratification through, the bypass is persisted
+    // on the doc as `reviewSkipped: <status it skipped from>`, right after `ratifiedOn:` — so a
+    // later reader of the doc (or of its git history, or a CI diff) can tell a reviewed
+    // ratification from one that bypassed review. A ratification that passed the gate writes
+    // nothing. An existing line (a same-signer run completing its record) is replaced in place.
+    // `em slice revise` clears it with the other sign-off keys.
+    const skippedMatch = fieldLineRegex("reviewSkipped").exec(inner);
+    if (skippedReviewFrom !== null && !skippedMatch)
+        identityLines.push(`reviewSkipped: ${skippedReviewFrom}`);
     if (identity && identity.ref !== null && !refMatch)
         identityLines.push(`ratifiedRef: ${identity.ref}`);
     if (identity && !hashMatch)
@@ -351,6 +372,11 @@ export function applyRatifyFrontmatter(raw, sliceKey, ratifiedBy, ratifiedOn, sk
     if (identity && refMatch && identity.ref !== null) {
         edits.push({ index: refMatch.index, oldLen: refMatch[0].length, next: `${refMatch[1]}${identity.ref}` });
     }
+    if (staleRef)
+        edits.push({ index: staleRef.index, oldLen: staleRef[0].length, next: "" });
+    if (skippedReviewFrom !== null && skippedMatch) {
+        edits.push({ index: skippedMatch.index, oldLen: skippedMatch[0].length, next: `${skippedMatch[1]}${skippedReviewFrom}` });
+    }
     if (identity && hashMatch)
         edits.push({ index: hashMatch.index, oldLen: hashMatch[0].length, next: `${hashMatch[1]}${identity.hash}` });
     edits.sort((a, b) => b.index - a.index);
@@ -366,7 +392,9 @@ export function applyRatifyFrontmatter(raw, sliceKey, ratifiedBy, ratifiedOn, sk
  * `--slice-ready`/`em export` use (MIL-121 cross-binding included), then reads/applies/writes
  * it. `baseDir` is the `.em` file's directory, same convention every doc/note path in `em` uses.
  */
-export function runRatify(model, refs, baseDir, sliceKey, ratifiedBy, ratifiedOn, skipReview = false, confirmation = null, git = realGit) {
+export function runRatify(model, refs, baseDir, sliceKey, ratifiedBy, ratifiedOn, skipReview = false, confirmation = null, git = realGit, 
+/** GH #255: record `ratifiedHash:` only — no `ratifiedRef:`, no git consulted (`--no-ref`). */
+noRef = false) {
     const sliceIndex = refs.sliceKeys.indexOf(sliceKey);
     if (sliceIndex === -1) {
         return { ok: false, message: `no slice with export key "${sliceKey}" in this model` };
@@ -418,7 +446,7 @@ export function runRatify(model, refs, baseDir, sliceKey, ratifiedBy, ratifiedOn
     // ratifier is, with nothing written.
     if (!probe.changed) {
         const recorded = recordedRatifiedHash(raw);
-        if (recorded !== null && recorded !== sliceDocBodyHash(raw)) {
+        if (recorded !== null && ratifiedHashScope(raw, recorded) === "mismatch") {
             return {
                 ok: false,
                 message: `${doc.path}: body changed since ratification (no longer matches ratifiedHash) — ` +
@@ -428,7 +456,7 @@ export function runRatify(model, refs, baseDir, sliceKey, ratifiedBy, ratifiedOn
     }
     let result = probe;
     if (probe.changed) {
-        const identity = resolveRatifiedIdentity(git, baseDir, doc.path, raw);
+        const identity = resolveRatifiedIdentity(git, baseDir, doc.path, raw, { noRef });
         if (!identity.ok)
             return identity;
         const applied = applyRatifyFrontmatter(raw, sliceKey, ratifiedBy, ratifiedOn, skipReview, confirmation, identity.identity);

package/dist/cli/ratify.js.map

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package/dist/cli/refsCheck.d.ts

@@ -0,0 +1,78 @@
+import { NormalizedModel } from "../model/model.js";
+import { RefsResult } from "../model/refs.js";
+import { GitRunner } from "./diff-inputs.js";
+export type RefField = "ratifiedRef" | "shippedRef" | "conformedAt";
+export type RefStatus = "ancestor" | "not-ancestor" | "unresolved" | "undecidable";
+export interface RefResult {
+    sliceKey: string;
+    /** The doc the ref was read from, relative to the model directory (`slices/<key>.md`). */
+    path: string;
+    field: RefField;
+    ref: string;
+    status: RefStatus;
+    /** Why, when `status` is not `ancestor`: git's own words, or the shallow-clone note. */
+    detail: string | null;
+}
+/** Where a waiver came from: the repeatable `--waive <slice-key>` flag, or a line of the
+ *  `--waive-file` baseline. A waived result is still fully reported, just not counted toward
+ *  the exit code — the `em ledger` convention (MIL-185). */
+export type RefWaiveSource = {
+    source: "flag";
+} | {
+    source: "file";
+    path: string;
+};
+export interface WaivedRefResult extends RefResult {
+    waivedBy: RefWaiveSource;
+}
+/** A waiver naming a slice key with nothing to excuse — surfaced, never swallowed (a typo'd
+ *  baseline line would otherwise silently stop meaning anything). */
+export interface UnknownRefWaiver {
+    sliceKey: string;
+    source: RefWaiveSource;
+}
+export interface RefsCheckResult {
+    reachableFrom: string;
+    /** The full sha `--reachable-from` resolved to. */
+    target: string;
+    /** True when the repository is a shallow clone — every result is then `undecidable`. */
+    shallow: boolean;
+    /** Docs that carried at least one ref field. */
+    checkedDocs: number;
+    /** Every (doc, field) that was examined, waived or not. */
+    checkedRefs: number;
+    /** Active results: everything that is not `ancestor` and was not waived. `ancestor` results
+     *  are listed too (a CI log should show what WAS verified), so filter on `status` to count. */
+    results: RefResult[];
+    waived: WaivedRefResult[];
+    /** False when any active result is not `ancestor` — `undecidable` included. */
+    ok: boolean;
+}
+export type CheckRefsOutcome = {
+    ok: true;
+    result: RefsCheckResult;
+} | {
+    ok: false;
+    message: string;
+};
+/** The git-facing half, exposed for tests: classify one ref against an already-resolved target. */
+export declare function classifyRef(run: GitRunner, baseDir: string, ref: string, target: string, shallow: boolean): {
+    status: RefStatus;
+    detail: string | null;
+};
+/**
+ * Check every recorded ref on every slice doc of `model` against `reachableFrom`. `baseDir` is the
+ * `.em` file's directory (the docs' repository is located from it with `-C`, never the process
+ * cwd). Returns a message instead of a result when the directory is not in a git work tree or
+ * `reachableFrom` itself does not resolve — those are the caller's mistakes, not findings.
+ */
+export declare function checkRefs(model: NormalizedModel, refs: RefsResult, baseDir: string, reachableFrom: string, run?: GitRunner): CheckRefsOutcome;
+/** One slice key per line; blank lines and `#` comments ignored. Missing file → empty list, so a
+ *  recipe can reference a baseline before anyone has needed one. */
+export declare function readWaiveFile(path: string): string[];
+/** Excuse every non-`ancestor` result on a waived slice key — the exit code ignores them, the
+ *  report still shows them under `waived`. `ancestor` results need no excuse and stay put. */
+export declare function applyRefWaivers(result: RefsCheckResult, flagKeys: string[], fileKeys: string[], filePath: string | null): {
+    result: RefsCheckResult;
+    unknownWaivers: UnknownRefWaiver[];
+};

package/dist/cli/refsCheck.js

@@ -0,0 +1,153 @@
+// SPDX-License-Identifier: MIT
+// `em refs` (GH #258): are the commits a model's slice docs point at still real, and still on the
+// branch the docs live on? `ratifiedRef:` (MIL-284) is `HEAD` of whatever branch `em slice ratify`
+// ran on, `shippedRef:` is its copy taken at `mark-implemented`, and a bare `conformedAt:` is the
+// target-repo revision a conform sweep diffed against. Under squash or rebase merges every one of
+// them can name a commit that exists only on a deleted PR branch — unreachable from the target
+// branch, then garbage-collected — while `em validate`, `--slice-ready` and `em ledger` all keep
+// passing, because none of them resolves a ref. This command does, once, per field, per doc.
+//
+// Three outcomes per (doc, field) plus one for "I can't tell":
+//   ancestor      — resolves and is reachable from `--reachable-from` (the healthy case)
+//   not-ancestor  — resolves (still in the object store) but is NOT reachable: the squash-merge
+//                   signature before the orphaned commit is pruned
+//   unresolved    — does not resolve at all: pruned, never fetched, or a typo
+//   undecidable   — a shallow clone, or git failed in a way that is neither yes nor no; never
+//                   reported as a pass (the issue's third acceptance line)
+// Opt-in, CI-recipe tier like `em ledger`: it reads git, so it is deliberately not part of
+// `em validate` (docs/ci.md). Local object store only — no network. Pure aside from the
+// injectable GitRunner and fs reads via readSliceDoc; no process.exit, no console.
+//
+// Kinded `conformedAt:` values (`build:1234`, GH #261) are not git revisions and are skipped —
+// `parseConformedAt` decides. Docs with no ref fields are not reported.
+import { existsSync, readFileSync } from "node:fs";
+import { readSliceDoc } from "../catalog/readSliceDoc.js";
+import { hasUsableFrontmatter, parseConformedAt } from "../catalog/sliceDoc.js";
+import { realGit } from "./diff-inputs.js";
+function git(run, baseDir, args) {
+    return run(["-C", baseDir, ...args]);
+}
+/** The git-facing half, exposed for tests: classify one ref against an already-resolved target. */
+export function classifyRef(run, baseDir, ref, target, shallow) {
+    if (shallow) {
+        return { status: "undecidable", detail: "shallow clone — history is truncated, reachability cannot be decided (checkout with fetch-depth: 0)" };
+    }
+    const exists = git(run, baseDir, ["cat-file", "-e", `${ref}^{commit}`]);
+    if (exists.status !== 0) {
+        return { status: "unresolved", detail: "does not resolve to a commit in this repository (pruned after its branch was deleted, never fetched, or mistyped)" };
+    }
+    const anc = git(run, baseDir, ["merge-base", "--is-ancestor", ref, target]);
+    if (anc.status === 0)
+        return { status: "ancestor", detail: null };
+    if (anc.status === 1)
+        return { status: "not-ancestor", detail: `resolves but is not an ancestor of ${target.slice(0, 7)} — reachable only from a branch that was squash/rebase-merged and deleted` };
+    return { status: "undecidable", detail: `git merge-base failed: ${anc.stderr.trim() || `exit ${anc.status}`}` };
+}
+/**
+ * Check every recorded ref on every slice doc of `model` against `reachableFrom`. `baseDir` is the
+ * `.em` file's directory (the docs' repository is located from it with `-C`, never the process
+ * cwd). Returns a message instead of a result when the directory is not in a git work tree or
+ * `reachableFrom` itself does not resolve — those are the caller's mistakes, not findings.
+ */
+export function checkRefs(model, refs, baseDir, reachableFrom, run = realGit) {
+    const inside = git(run, baseDir, ["rev-parse", "--is-inside-work-tree"]);
+    if (inside.status !== 0 || inside.stdout.trim() !== "true") {
+        return { ok: false, message: `${baseDir} is not inside a git work tree — em refs resolves commits, so it needs one` };
+    }
+    const target = git(run, baseDir, ["rev-parse", "--verify", "--quiet", `${reachableFrom}^{commit}`]);
+    if (target.status !== 0 || !/^[0-9a-f]{40,64}$/.test(target.stdout.trim())) {
+        return { ok: false, message: `--reachable-from "${reachableFrom}" does not resolve to a commit (fetch it first? \`git fetch origin main\`)` };
+    }
+    const targetSha = target.stdout.trim();
+    const shallowProbe = git(run, baseDir, ["rev-parse", "--is-shallow-repository"]);
+    const shallow = shallowProbe.status === 0 && shallowProbe.stdout.trim() === "true";
+    const results = [];
+    const seen = new Set();
+    let checkedDocs = 0;
+    model.slices.forEach((_slice, i) => {
+        const sliceKey = refs.sliceKeys[i];
+        if (seen.has(sliceKey))
+            return;
+        seen.add(sliceKey);
+        const doc = readSliceDoc(baseDir, sliceKey);
+        if (!doc || !hasUsableFrontmatter(doc))
+            return;
+        const path = `slices/${sliceKey}.md`;
+        const fields = [
+            ["ratifiedRef", doc.ratifiedRef],
+            ["shippedRef", doc.shippedRef],
+            ["conformedAt", doc.conformedAt !== null && parseConformedAt(doc.conformedAt).kind === "git" ? doc.conformedAt : null],
+        ];
+        const present = fields.filter((f) => f[1] !== null);
+        if (present.length === 0)
+            return;
+        checkedDocs++;
+        for (const [field, ref] of present) {
+            const { status, detail } = classifyRef(run, baseDir, ref, targetSha, shallow);
+            results.push({ sliceKey, path, field, ref, status, detail });
+        }
+    });
+    return {
+        ok: true,
+        result: {
+            reachableFrom,
+            target: targetSha,
+            shallow,
+            checkedDocs,
+            checkedRefs: results.length,
+            results,
+            waived: [],
+            ok: results.every((r) => r.status === "ancestor"),
+        },
+    };
+}
+/** One slice key per line; blank lines and `#` comments ignored. Missing file → empty list, so a
+ *  recipe can reference a baseline before anyone has needed one. */
+export function readWaiveFile(path) {
+    if (!existsSync(path))
+        return [];
+    return readFileSync(path, "utf8")
+        .split(/\r?\n/)
+        .map((l) => l.replace(/#.*$/, "").trim())
+        .filter((l) => l.length > 0);
+}
+/** Excuse every non-`ancestor` result on a waived slice key — the exit code ignores them, the
+ *  report still shows them under `waived`. `ancestor` results need no excuse and stay put. */
+export function applyRefWaivers(result, flagKeys, fileKeys, filePath) {
+    const excusable = new Set(result.results.filter((r) => r.status !== "ancestor").map((r) => r.sliceKey));
+    const waivedKeys = new Map();
+    const unknownWaivers = [];
+    const noted = new Set();
+    // First mention of a key wins (flags are considered before the file); a key with nothing to
+    // excuse is noted once, whichever sources name it.
+    const consider = (keys, source) => {
+        for (const key of keys) {
+            if (waivedKeys.has(key) || noted.has(key))
+                continue;
+            if (excusable.has(key))
+                waivedKeys.set(key, source);
+            else {
+                noted.add(key);
+                unknownWaivers.push({ sliceKey: key, source });
+            }
+        }
+    };
+    consider(flagKeys, { source: "flag" });
+    if (filePath !== null)
+        consider(fileKeys, { source: "file", path: filePath });
+    const waived = [...result.waived];
+    const kept = [];
+    for (const r of result.results) {
+        const by = waivedKeys.get(r.sliceKey);
+        if (by && r.status !== "ancestor")
+            waived.push({ ...r, waivedBy: by });
+        else
+            kept.push(r);
+    }
+    waived.sort((a, b) => a.sliceKey.localeCompare(b.sliceKey) || a.field.localeCompare(b.field));
+    return {
+        result: { ...result, results: kept, waived, ok: kept.every((r) => r.status === "ancestor") },
+        unknownWaivers,
+    };
+}
+//# sourceMappingURL=refsCheck.js.map

package/dist/cli/refsCheck.js.map

@@ -0,0 +1 @@
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