@nxuss/lemma 1.33.0 → 1.35.0

package/dist/cjs/mcp/index.js.map

@@ -1 +1 @@
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package/dist/cjs/mcp/staleBuild.d.ts

@@ -10,4 +10,23 @@ export interface StaleBuildOptions {
 export declare function staleBuildNote(options?: StaleBuildOptions): string | null;
 /** Test hook: forget what was already warned about. */
 export declare function resetStaleBuildWarning(): void;
+/**
+ * staleBuildNote only speaks as a suffix on a tool result, so a user (or agent) who never calls
+ * Lemma never learns the running process lacks recent fixes. These two functions let something
+ * else — the UserPromptSubmit hook, a fresh process on every prompt — ask the question: each MCP
+ * process records which build it loaded, and the hook compares that with dist as it is now.
+ */
+export declare function mcpProcessDir(home?: string): string;
+export interface McpProcessOptions {
+    entryFile?: string | null;
+    dir?: string;
+    pid?: number;
+}
+/** Records the build this process loaded. Never throws. */
+export declare function registerMcpProcess(options?: McpProcessOptions): void;
+/**
+ * A one-line warning when a live MCP process was started from `entryFile` before its latest
+ * build, else null. Prunes records of dead processes on the way. Never throws.
+ */
+export declare function staleMcpProcessNote(entryFile: string, dir?: string, isAlive?: (pid: number) => boolean): string | null;
 //# sourceMappingURL=staleBuild.d.ts.map

package/dist/cjs/mcp/staleBuild.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"staleBuild.d.ts","sourceRoot":"","sources":["../../../src/mcp/staleBuild.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,GAAG,IAAI,CAa7E;AAED,uDAAuD;AACvD,wBAAgB,sBAAsB,IAAI,IAAI,CAE7C"}
+{"version":3,"file":"staleBuild.d.ts","sourceRoot":"","sources":["../../../src/mcp/staleBuild.ts"],"names":[],"mappings":"AAuBA,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,GAAG,IAAI,CAa7E;AAED,uDAAuD;AACvD,wBAAgB,sBAAsB,IAAI,IAAI,CAE7C;AAED;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,IAAI,GAAE,MAAqB,GAAG,MAAM,CAEjE;AAED,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,2DAA2D;AAC3D,wBAAgB,kBAAkB,CAAC,OAAO,GAAE,iBAAsB,GAAG,IAAI,CAcxE;AAWD;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,SAAS,EAAE,MAAM,EACjB,GAAG,GAAE,MAAwB,EAC7B,OAAO,GAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAkB,GAC3C,MAAM,GAAG,IAAI,CA0Bf"}

package/dist/cjs/mcp/staleBuild.js

@@ -5,8 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.staleBuildNote = staleBuildNote;
 exports.resetStaleBuildWarning = resetStaleBuildWarning;
+exports.mcpProcessDir = mcpProcessDir;
+exports.registerMcpProcess = registerMcpProcess;
+exports.staleMcpProcessNote = staleMcpProcessNote;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const os_1 = __importDefault(require("os"));
 /**
  * A running MCP process keeps the code it loaded at startup. `npm run build` rewrites dist, but
  * the host keeps talking to the old process until it reconnects, so fixes look broken (or look
@@ -52,4 +56,73 @@ function staleBuildNote(options = {}) {
 function resetStaleBuildWarning() {
     lastWarnedMtime = 0;
 }
+/**
+ * staleBuildNote only speaks as a suffix on a tool result, so a user (or agent) who never calls
+ * Lemma never learns the running process lacks recent fixes. These two functions let something
+ * else — the UserPromptSubmit hook, a fresh process on every prompt — ask the question: each MCP
+ * process records which build it loaded, and the hook compares that with dist as it is now.
+ */
+function mcpProcessDir(home = os_1.default.homedir()) {
+    return path_1.default.join(home, ".lemma", "mcp", "processes");
+}
+/** Records the build this process loaded. Never throws. */
+function registerMcpProcess(options = {}) {
+    try {
+        const entry = options.entryFile === undefined ? defaultEntryFile() : options.entryFile;
+        if (!entry || !fs_1.default.existsSync(entry))
+            return;
+        const dir = options.dir ?? mcpProcessDir();
+        fs_1.default.mkdirSync(dir, { recursive: true });
+        const pid = options.pid ?? process.pid;
+        fs_1.default.writeFileSync(path_1.default.join(dir, `${pid}.json`), JSON.stringify({ pid, entry: fs_1.default.realpathSync(entry), startedAt: STARTED_AT, loadedMtime: fs_1.default.statSync(entry).mtimeMs }));
+    }
+    catch {
+        /* a diagnostic must never be the reason the server fails to start */
+    }
+}
+function pidAlive(pid) {
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (e) {
+        return e?.code === "EPERM"; // exists, just not ours
+    }
+}
+/**
+ * A one-line warning when a live MCP process was started from `entryFile` before its latest
+ * build, else null. Prunes records of dead processes on the way. Never throws.
+ */
+function staleMcpProcessNote(entryFile, dir = mcpProcessDir(), isAlive = pidAlive) {
+    try {
+        if (!fs_1.default.existsSync(dir) || !fs_1.default.existsSync(entryFile))
+            return null;
+        const real = fs_1.default.realpathSync(entryFile);
+        const current = fs_1.default.statSync(real).mtimeMs;
+        let stale = 0;
+        for (const f of fs_1.default.readdirSync(dir)) {
+            if (!f.endsWith(".json"))
+                continue;
+            const file = path_1.default.join(dir, f);
+            try {
+                const rec = JSON.parse(fs_1.default.readFileSync(file, "utf8"));
+                if (!rec || typeof rec.pid !== "number" || !isAlive(rec.pid)) {
+                    fs_1.default.unlinkSync(file);
+                    continue;
+                }
+                if (rec.entry === real && current > Number(rec.loadedMtime) + 2000)
+                    stale++;
+            }
+            catch {
+                /* unreadable record: ignore it */
+            }
+        }
+        return stale > 0
+            ? `⚠️ Lemma: ${stale === 1 ? "the running MCP process was" : `${stale} running MCP processes were`} started before the latest build, so recent fixes are NOT active. Reconnect the server (in Claude Code: /mcp → lemma).`
+            : null;
+    }
+    catch {
+        return null;
+    }
+}
 //# sourceMappingURL=staleBuild.js.map

package/dist/cjs/mcp/staleBuild.js.map

@@ -1 +1 @@
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+{"version":3,"file":"staleBuild.js","sourceRoot":"","sources":["../../../src/mcp/staleBuild.ts"],"names":[],"mappings":";;;;;AAiCA,wCAaC;AAGD,wDAEC;AAQD,sCAEC;AASD,gDAcC;AAeD,kDA8BC;AAjID,4CAAoB;AACpB,gDAAwB;AACxB,4CAAoB;AAEpB;;;;GAIG;AACH,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;AAC9B,IAAI,eAAe,GAAG,CAAC,CAAC;AAExB,yFAAyF;AACzF,SAAS,gBAAgB;IACvB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAC5B,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,CAAC;IACtB,IAAI,CAAC;QACH,OAAO,cAAI,CAAC,IAAI,CAAC,cAAI,CAAC,OAAO,CAAC,YAAE,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,UAAU,CAAC,CAAC;IACzF,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAOD;;;;GAIG;AACH,SAAgB,cAAc,CAAC,UAA6B,EAAE;IAC5D,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,OAAO,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC;QACvF,IAAI,CAAC,KAAK,IAAI,CAAC,YAAE,CAAC,UAAU,CAAC,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;QACjD,MAAM,KAAK,GAAG,YAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;QACzC,MAAM,SAAS,GAAG,OAAO,CAAC,SAAS,IAAI,UAAU,CAAC;QAClD,oFAAoF;QACpF,IAAI,KAAK,IAAI,SAAS,GAAG,IAAI,IAAI,KAAK,IAAI,eAAe;YAAE,OAAO,IAAI,CAAC;QACvE,eAAe,GAAG,KAAK,CAAC;QACxB,OAAO,mLAAmL,CAAC;IAC7L,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,uDAAuD;AACvD,SAAgB,sBAAsB;IACpC,eAAe,GAAG,CAAC,CAAC;AACtB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,aAAa,CAAC,OAAe,YAAE,CAAC,OAAO,EAAE;IACvD,OAAO,cAAI,CAAC,IAAI,CAAC,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC;AACvD,CAAC;AAQD,2DAA2D;AAC3D,SAAgB,kBAAkB,CAAC,UAA6B,EAAE;IAChE,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,OAAO,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC;QACvF,IAAI,CAAC,KAAK,IAAI,CAAC,YAAE,CAAC,UAAU,CAAC,KAAK,CAAC;YAAE,OAAO;QAC5C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,IAAI,aAAa,EAAE,CAAC;QAC3C,YAAE,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACvC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,IAAI,OAAO,CAAC,GAAG,CAAC;QACvC,YAAE,CAAC,aAAa,CACd,cAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,GAAG,OAAO,CAAC,EAC7B,IAAI,CAAC,SAAS,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,YAAE,CAAC,YAAY,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,YAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,OAAO,EAAE,CAAC,CACvH,CAAC;IACJ,CAAC;IAAC,MAAM,CAAC;QACP,qEAAqE;IACvE,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,GAAW;IAC3B,IAAI,CAAC;QACH,OAAO,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;QACrB,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,OAAO,CAAM,EAAE,CAAC;QAChB,OAAO,CAAC,EAAE,IAAI,KAAK,OAAO,CAAC,CAAC,wBAAwB;IACtD,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,SAAgB,mBAAmB,CACjC,SAAiB,EACjB,MAAc,aAAa,EAAE,EAC7B,UAAoC,QAAQ;IAE5C,IAAI,CAAC;QACH,IAAI,CAAC,YAAE,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,YAAE,CAAC,UAAU,CAAC,SAAS,CAAC;YAAE,OAAO,IAAI,CAAC;QAClE,MAAM,IAAI,GAAG,YAAE,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC;QACxC,MAAM,OAAO,GAAG,YAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC;QAC1C,IAAI,KAAK,GAAG,CAAC,CAAC;QACd,KAAK,MAAM,CAAC,IAAI,YAAE,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC;gBAAE,SAAS;YACnC,MAAM,IAAI,GAAG,cAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;YAC/B,IAAI,CAAC;gBACH,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAE,CAAC,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC;gBACtD,IAAI,CAAC,GAAG,IAAI,OAAO,GAAG,CAAC,GAAG,KAAK,QAAQ,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC7D,YAAE,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC;oBACpB,SAAS;gBACX,CAAC;gBACD,IAAI,GAAG,CAAC,KAAK,KAAK,IAAI,IAAI,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,IAAI;oBAAE,KAAK,EAAE,CAAC;YAC9E,CAAC;YAAC,MAAM,CAAC;gBACP,kCAAkC;YACpC,CAAC;QACH,CAAC;QACD,OAAO,KAAK,GAAG,CAAC;YACd,CAAC,CAAC,aAAa,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,6BAA6B,CAAC,CAAC,CAAC,GAAG,KAAK,6BAA6B,wHAAwH;YAC1N,CAAC,CAAC,IAAI,CAAC;IACX,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC"}

package/dist/cjs/mcp/tools/memory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"memory.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/memory.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAEhE,eAAO,MAAM,uBAAuB,EAAE,cAAc,EAmVnD,CAAC;AAw1BF,eAAO,MAAM,oBAAoB,EAAE,MAAM,CAAC,MAAM,EAAE,WAAW,CAiB5D,CAAC"}
+{"version":3,"file":"memory.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/memory.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAgBH,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAShE,eAAO,MAAM,uBAAuB,EAAE,cAAc,EAqVnD,CAAC;AAu5BF,eAAO,MAAM,oBAAoB,EAAE,MAAM,CAAC,MAAM,EAAE,WAAW,CAiB5D,CAAC"}

package/dist/cjs/mcp/tools/memory.js

@@ -20,7 +20,14 @@ const utils_1 = require("../utils");
 const cognitiveMap_1 = require("../cognitiveMap");
 const SessionEvidence_1 = require("../../utils/SessionEvidence");
 const NearMiss_1 = require("../../subconscious/NearMiss");
+const ageLabel_1 = require("../../utils/ageLabel");
+const ExternalRefs_1 = require("../../subconscious/ExternalRefs");
 const TeamBrain_1 = require("../../subconscious/TeamBrain");
+const REFS_SCHEMA = {
+    type: "array",
+    items: { type: "object" },
+    description: "Non-file state it depends on: {kind:'commit',sha} or {kind:mr|issue,provider:github|gitlab,id,state:open|merged|closed} (state it asserts now); verify_memory flags a change.",
+};
 exports.MEMORY_TOOL_DEFINITIONS = [
     {
         name: "list_memories",
@@ -129,6 +136,7 @@ exports.MEMORY_TOOL_DEFINITIONS = [
                     },
                     description: "Split `response` into sub-claims, each with its own evidence, so one going stale doesn't discard the rest. Skip for a single-fact response.",
                 },
+                refs: REFS_SCHEMA,
                 domain: {
                     type: "string",
                     description: "Domain tag (e.g. 'auth') for domain-scoped search. Omitted with filePaths set: derived from the first file.",
@@ -186,6 +194,7 @@ exports.MEMORY_TOOL_DEFINITIONS = [
                     description: "Replacement sub-claims (store_memory shape); replaces the set, omit to keep.",
                 },
                 outcome: { type: "string", enum: ["confirmed", "failed"], description: "'confirmed' or 'failed' (dead end)." },
+                refs: { type: "array", items: { type: "object" }, description: "Replacement refs (store_memory shape); [] clears." },
                 domain: { type: "string", description: "Replacement domain; '' clears." },
                 derivedFrom: { type: "array", items: { type: "string" }, description: "Replacement upstream ids; [] clears." },
                 supersededBy: { type: "string", description: "Id of the memory that replaces this one; excludes it from search_memory (get_memory still works and points to the successor). Use when two memories contradict. '' un-supersedes." },
@@ -195,8 +204,8 @@ exports.MEMORY_TOOL_DEFINITIONS = [
     },
     {
         name: "verify_memory",
-        annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: false },
-        description: "Cheaply revalidate ids from a prior search_memory/store_memory result — batch hash-compare, no BM25/re-search. Each id comes back 'fresh' (every tracked file/symbol still matches), 'stale' (something changed), 'untracked' (the memory tracks nothing, so nothing was checked — this is NOT a clean bill of health), 'unverified' (evidence could not be read) or 'unknown' (purged/renamed, never reported as fresh). Accepts entry ids and claim ids together.",
+        annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+        description: "Cheaply revalidate ids from a prior search_memory/store_memory result — batch hash-compare, no BM25/re-search. Each id comes back 'fresh' (every tracked file/symbol still matches), 'stale' (something changed), 'untracked' (the memory tracks nothing, so nothing was checked — this is NOT a clean bill of health), 'unverified' (evidence could not be read) or 'unknown' (purged/renamed, never reported as fresh). Accepts entry ids and claim ids together. Memories stored with external refs (commit / MR / issue) are also checked against git and gh/glab (timeout-bounded; an unreadable state is 'unverified', never 'fresh'). 'fresh' says nothing about MR/issue state for a memory without refs.",
         inputSchema: {
             type: "object",
             properties: {
@@ -384,12 +393,20 @@ async function handleSearchMemory(args) {
             // searchHybrid already filtered anything below minSimilarity out of `results`, so the
             // near-miss check needs its own uncapped lookup — countStats:false, this must not
             // register as a second miss on top of the one searchHybrid just counted.
-            const uncapped = brain.search(query, 1, 0, { projectId: (0, TheBrainV2_1.deriveProjectId)(), domain, countStats: false });
+            const uncapped = brain.search(query, ORIENTATION_LIMIT, 0, { projectId: (0, TheBrainV2_1.deriveProjectId)(), domain, countStats: false });
             const nearMiss = (0, NearMiss_1.bucketNearMiss)(uncapped[0] ? { id: uncapped[0].id, query: uncapped[0].query, similarity: uncapped[0].similarity } : undefined, minSimilarity);
+            // A miss that says nothing cannot tell "nothing related" from "something related at 60%".
+            // These are for orientation only: below the floor, never reusable, never credited.
+            const related = uncapped
+                .filter((r) => r.similarity >= ORIENTATION_MIN)
+                .map((r) => `  - ${r.id} (${(r.similarity * 100).toFixed(0)}%, stored ${(0, ageLabel_1.ageLabel)(r.timestamp)}): ${r.query.substring(0, 100)}`);
+            const orientation = related.length > 0
+                ? `\n\nBelow the reuse floor, for orientation only (not cache hits — get_memory to read, then verify against current state before relying on any):\n${related.join("\n")}`
+                : "";
             return {
                 content: [{
                         type: "text",
-                        text: `No memory in Lemma's Brain scored at or above the ${(minSimilarity * 100).toFixed(0)}% similarity floor for this query. Investigate from scratch — there is nothing safe to reuse.${nearMiss.hint ? ` ${nearMiss.hint}` : ""}`,
+                        text: `No memory in Lemma's Brain scored at or above the ${(minSimilarity * 100).toFixed(0)}% similarity floor for this query. Investigate from scratch — there is nothing safe to reuse.${nearMiss.hint ? ` ${nearMiss.hint}` : ""}${orientation}`,
                     }],
             };
         }
@@ -408,7 +425,7 @@ async function handleSearchMemory(args) {
             const staleCount = r.claims.filter((c) => !c.fresh).length;
             return `\nClaims (${r.claims.length - staleCount}/${r.claims.length} still fresh — trust only the ✓ ones):\n${lines.join("\n")}`;
         };
-        const formatResult = (r, i) => `Result ${i + 1} (id: ${r.id}, Similarity: ${(r.similarity * 100).toFixed(1)}%)${r.outcome === "failed" ? "\n⚠️ TAGGED AS A FAILED ATTEMPT — this was tried before and did NOT work. Do not repeat it; treat this as a warning, not a suggestion." : ""}${typeof r.tokensSaved === "number" && r.tokensSaved > 0
+        const formatResult = (r, i) => `Result ${i + 1} (id: ${r.id}, Similarity: ${(r.similarity * 100).toFixed(1)}%, stored ${(0, ageLabel_1.ageLabel)(r.timestamp)})${r.outcome === "failed" ? "\n⚠️ TAGGED AS A FAILED ATTEMPT — this was tried before and did NOT work. Do not repeat it; treat this as a warning, not a suggestion." : ""}${typeof r.tokensSaved === "number" && r.tokensSaved > 0
             ? `\n💰 This memory has saved ${r.tokensSaved} tokens across ${r.hits || "?"} reuse(s) — prefer it over re-deriving.`
             : ""}\nPrompt: ${r.query.substring(0, 300)}...\nResponse: ${typeof r.response === "string" ? r.response : JSON.stringify(r.response, null, 2)}${formatClaims(r)}${Array.isArray(r.evidence) && r.evidence.length > 0
             ? `\nEvidence: ${r.evidence.map((e) => {
@@ -485,6 +502,14 @@ function relLabel(abs) {
     const rel = path_1.default.relative(process.cwd(), abs);
     return rel.startsWith("..") ? abs : rel;
 }
+/** How many below-floor candidates a miss lists, and the weakest one still worth naming. */
+const ORIENTATION_LIMIT = 3;
+const ORIENTATION_MIN = 0.3;
+/** External refs (commit / MR / issue) an entry carries, as one readable line; "" if none. */
+function refsLine(entry) {
+    const refs = Array.isArray(entry.refs) ? entry.refs : [];
+    return refs.length > 0 ? `\nExternal refs: ${refs.map(ExternalRefs_1.describeRef).join(", ")} (checked by verify_memory)` : "";
+}
 /** The files/symbols an entry is judged against, as one readable line. */
 function trackedLine(entry) {
     const files = Object.keys(entry.fileHashes || {}).map(relLabel);
@@ -493,7 +518,15 @@ function trackedLine(entry) {
         return `${relLabel(key.substring(0, sep))}::${key.substring(sep + 2)}`;
     });
     const derived = (entry.derivedFrom || []).map((id) => `derived:${id}`);
-    const all = [...files, ...symbols, ...derived];
+    // verify_memory judges each claim by its own evidence (trackedArtifactCount counts it), so
+    // this line has to name it too — otherwise an entry whose evidence lives only on its claims
+    // reads "tracks nothing" here while verify_memory reports it fresh.
+    const claimFiles = (entry.claims || []).flatMap((c) => Object.keys(c.fileHashes || {}).map(relLabel));
+    const claimSymbols = (entry.claims || []).flatMap((c) => Object.keys(c.symbolHashes || {}).map((key) => {
+        const sep = key.lastIndexOf("::");
+        return `${relLabel(key.substring(0, sep))}::${key.substring(sep + 2)}`;
+    }));
+    const all = [...new Set([...files, ...symbols, ...claimFiles, ...claimSymbols]), ...derived];
     return all.length > 0
         ? `Tracks: ${all.join(", ")}`
         : "Tracks: nothing — freshness cannot be checked for this memory, and verify_memory reports it as 'untracked' rather than 'fresh'.";
@@ -544,7 +577,7 @@ async function handleGetMemory(args) {
         return {
             content: [{
                     type: "text",
-                    text: `Memory ${entry.id} — ${status?.status ?? "unknown"}${status?.staleFiles?.length ? ` (changed: ${status.staleFiles.join(", ")})` : ""}\n${facts.join(" · ")}\n${trackedLine(entry)}${claimsBlock}${supersededNote}\n\nQuery: ${entry.query}${body}`,
+                    text: `Memory ${entry.id} — ${status?.status ?? "unknown"}${status?.staleFiles?.length ? ` (changed: ${status.staleFiles.join(", ")})` : ""}\n${facts.join(" · ")}\n${trackedLine(entry)}${refsLine(entry)}${claimsBlock}${supersededNote}\n\nQuery: ${entry.query}${body}`,
                 }],
         };
     }
@@ -572,9 +605,10 @@ async function handleUpdateMemory(args) {
         ? args.derivedFrom.filter((d) => typeof d === "string" && d)
         : undefined;
     const supersededBy = typeof args?.supersededBy === "string" ? args.supersededBy : undefined;
+    const refs = Array.isArray(args?.refs) ? (0, ExternalRefs_1.sanitizeRefs)(args.refs) : undefined;
     if (query === undefined && response === undefined && filePaths === undefined && symbols === undefined &&
         claims === undefined && outcome === undefined && domain === undefined && derivedFrom === undefined &&
-        supersededBy === undefined) {
+        supersededBy === undefined && refs === undefined) {
         return {
             content: [{
                     type: "text",
@@ -583,7 +617,16 @@ async function handleUpdateMemory(args) {
         };
     }
     try {
-        const result = (0, TheBrainV2_1.getBrain)().update(id, { query, response, filePaths, symbols, claims, outcome, domain, derivedFrom, supersededBy });
+        // Refs alone must not re-anchor the entry's file hashes (update() would): attaching "also
+        // depends on MR !1061" is not an assertion that the tracked code was re-checked.
+        const refsOnly = refs !== undefined && query === undefined && response === undefined && filePaths === undefined &&
+            symbols === undefined && claims === undefined && outcome === undefined && domain === undefined &&
+            derivedFrom === undefined && supersededBy === undefined;
+        if (refsOnly) {
+            const ok = (0, TheBrainV2_1.getBrain)().setRefs(id, refs);
+            return { content: [{ type: "text", text: ok ? `External refs on "${id}" ${refs.length > 0 ? `set to: ${refs.map(ExternalRefs_1.describeRef).join(", ")}` : "cleared"}. Nothing else was changed.` : `No entry with id "${id}" in the Brain.` }] };
+        }
+        const result = (0, TheBrainV2_1.getBrain)().update(id, { query, response, filePaths, symbols, claims, outcome, domain, derivedFrom, supersededBy, refs });
         if (!result.ok)
             return { content: [{ type: "text", text: result.message }] };
         (0, TokenReceipt_1.recordReceiptEvent)("tool_call", `update_memory: ${id}`, {
@@ -641,11 +684,14 @@ async function handleStoreMemory(args) {
     const derivedFrom = Array.isArray(args?.derivedFrom)
         ? args.derivedFrom.filter((id) => typeof id === "string" && id)
         : undefined;
+    const refs = Array.isArray(args?.refs) ? (0, ExternalRefs_1.sanitizeRefs)(args.refs) : [];
     if (!query || !responseText)
         throw new Error("Query and response are required");
     try {
         const brain = (0, TheBrainV2_1.getBrain)();
         const storeRes = brain.store(query, responseText, provider, 0.92, filePaths, undefined, outcome, symbols, claims, domain, derivedFrom, { source: "manual" });
+        if (refs.length > 0 && storeRes.id)
+            brain.setRefs(storeRes.id, refs);
         // Storing a memory saves nothing — it only creates the chance of a saving later.
         // Crediting tokens here inflated the ledger on write and then credited the same
         // answer again on every read. The saving is booked by search_memory on a fresh hit.
@@ -664,6 +710,7 @@ async function handleStoreMemory(args) {
         const domainNote = domain
             ? ` Tagged with domain '${domain}'${explicitDomain ? "" : " (auto-derived from filePaths)"} — domain-scoped searches will prefer it.`
             : "";
+        const refsNote = refs.length > 0 ? ` Also tracking external state: ${refs.map(ExternalRefs_1.describeRef).join(", ")} — verify_memory marks this stale when that changes.` : "";
         const derivedFromNote = derivedFrom && derivedFrom.length > 0
             ? ` Derived from ${derivedFrom.length} prior memor${derivedFrom.length === 1 ? "y" : "ies"} — this one goes stale too if any of those do.`
             : "";
@@ -682,7 +729,7 @@ async function handleStoreMemory(args) {
         const scrubNote = storeRes.redactions > 0
             ? ` 🛡 ${storeRes.redactions} secret(s) redacted before storage — credentials are never persisted, only their placeholders.`
             : "";
-        return { content: [{ type: "text", text: `Success: Memory stored${idNote}. ${storeRes.reason}${trackingNote}${symbolNote}${autoEvidenceNote}${outcomeNote}${claimsNote}${domainNote}${derivedFromNote}${conflictsNote}${textConflictsNote}${scrubNote}` }] };
+        return { content: [{ type: "text", text: `Success: Memory stored${idNote}. ${storeRes.reason}${trackingNote}${symbolNote}${autoEvidenceNote}${outcomeNote}${claimsNote}${domainNote}${refsNote}${derivedFromNote}${conflictsNote}${textConflictsNote}${scrubNote}` }] };
     }
     catch (e) {
         (0, utils_1.logError)("store_memory", e);
@@ -1106,7 +1153,25 @@ async function handleVerifyMemory(args) {
     if (ids.length === 0)
         throw new Error("ids is required and must be a non-empty array");
     try {
-        const results = (0, TheBrainV2_1.getBrain)().verifyByIds(ids, { semanticDiff });
+        const brain = (0, TheBrainV2_1.getBrain)();
+        // External refs (commit / MR / issue) are checked here rather than inside the Brain's
+        // freshness walk: they can shell out, and search must stay local and instant.
+        const refNotes = new Map();
+        const results = brain.verifyByIds(ids, { semanticDiff }).map((r) => {
+            const refs = (brain.getEntry(r.id)?.refs || []);
+            if (refs.length === 0 || r.status === "unknown")
+                return r;
+            const verdicts = (0, ExternalRefs_1.checkExternalRefs)(refs, process.cwd());
+            refNotes.set(r.id, verdicts.map((v) => `${v.status === "fresh" ? "✓" : v.status === "stale" ? "✗" : "?"} ${v.detail}`));
+            if (r.status === "stale")
+                return r; // already stale on files; the notes still explain
+            if (verdicts.some((v) => v.status === "stale"))
+                return { ...r, status: "stale" };
+            // Fail closed: an external state that could not be read is not a pass.
+            if (verdicts.some((v) => v.status === "unknown"))
+                return { ...r, status: "unverified" };
+            return { ...r, status: "fresh" };
+        });
         const fresh = results.filter((r) => r.status === "fresh");
         const stale = results.filter((r) => r.status === "stale");
         const unknown = results.filter((r) => r.status === "unknown");
@@ -1123,12 +1188,18 @@ async function handleVerifyMemory(args) {
             const untrackedNote = r.status === "untracked"
                 ? " — tracks no files or symbols, so nothing was verified. Not a clean bill of health: check it against the code yourself, then refresh_memory (or update_memory with filePaths/symbols) so it can be verified next time."
                 : "";
-            return `${r.id}: ${r.status}${untrackedNote}${staleNote}${cosmeticNote}${claimsNote}`;
+            const refNote = refNotes.has(r.id) ? `\n  External: ${refNotes.get(r.id).join(" | ")}` : "";
+            return `${r.id}: ${r.status}${untrackedNote}${staleNote}${cosmeticNote}${claimsNote}${refNote}`;
         };
         const summary = `${fresh.length} fresh, ${stale.length} stale, ${untracked.length} untracked, ` +
             `${unverified.length} unverified, ${unknown.length} unknown (of ${results.length} checked).`;
         const lines = results.map(formatOne).join("\n");
-        return { content: [{ type: "text", text: `${summary}\n${lines}` }] };
+        // "fresh" is about tracked files and symbols. For a status question ("is X still pending?")
+        // that is not the thing that changes, so say what the verdict does not cover.
+        const scopeNote = fresh.some((r) => !refNotes.has(r.id))
+            ? "\nNote: 'fresh' means the tracked files/symbols are unchanged. It does not cover MR/issue/branch state unless the memory carries external refs — for a status question, check that live (git / gh / glab) before answering."
+            : "";
+        return { content: [{ type: "text", text: `${summary}\n${lines}${scopeNote}` }] };
     }
     catch (e) {
         (0, utils_1.logError)("verify_memory", e);