@mneme-ai/mcp 1.2.0 → 1.3.0

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAiCA,MAAM,WAAW,UAAU;IACzB,GAAG,EAAE,MAAM,CAAC;CACb;AAwBD,wBAAsB,cAAc,CAAC,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAmCpE"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAmCA,MAAM,WAAW,UAAU;IACzB,GAAG,EAAE,MAAM,CAAC;CACb;AAsDD,wBAAsB,cAAc,CAAC,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAsCpE"}

package/dist/index.js

@@ -24,6 +24,8 @@ import { CallToolRequestSchema, ListToolsRequestSchema, } from "@modelcontextpro
 import { buildRuntime } from "./tools/_runtime.js";
 import { buildAllTools, buildToolMap } from "./tools/_registry.js";
 import { toCallResult, toErrorResult } from "./tools/_types.js";
+import { moleculesContaining } from "./tools/_molecules.js";
+import { recordInvocation } from "./tools/_lifecycle.js";
 function resolveVersion() {
     try {
         const here = dirname(fileURLToPath(import.meta.url));
@@ -43,6 +45,32 @@ function toMcpTools(all) {
         inputSchema: t.inputSchema,
     }));
 }
+/** Auto-enrich a tool response with Second Brain layer:
+ *    - compose: which molecules this atom participates in
+ *    - lifecycle: is this a new combination? should we suggest saving?
+ *
+ *  If the handler already populated `secondBrain`, we MERGE — handler's
+ *  presentation hint wins, and we add compose/lifecycle if missing. */
+function enrichWithSecondBrain(response, toolName, repoRoot) {
+    const compose = moleculesContaining(toolName);
+    let lifecycle;
+    try {
+        lifecycle = recordInvocation(repoRoot, toolName);
+    }
+    catch {
+        // Lifecycle is best-effort — never fail a tool call because of it.
+        lifecycle = undefined;
+    }
+    const existing = response.secondBrain;
+    return {
+        ...response,
+        secondBrain: {
+            presentation: existing?.presentation,
+            compose: existing?.compose && existing.compose.length > 0 ? existing.compose : compose,
+            lifecycle: existing?.lifecycle ?? lifecycle,
+        },
+    };
+}
 export async function startMcpServer(opts) {
     const runtime = await buildRuntime(opts.cwd);
     const allTools = buildAllTools();
@@ -59,7 +87,10 @@ export async function startMcpServer(opts) {
         try {
             const args = (req.params.arguments ?? {});
             const response = await tool.handler(runtime, args);
-            return toCallResult(response);
+            // Second Brain — auto-enrich every response with composition hints
+            // + lifecycle tracking. The chain reaction starts here.
+            const enriched = enrichWithSecondBrain(response, tool.name, runtime.meta.rootPath);
+            return toCallResult(enriched);
         }
         catch (err) {
             return toErrorResult(`${req.params.name} failed: ${err.message}. ` +

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,MAAM,EAAE,MAAM,2CAA2C,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EACL,qBAAqB,EACrB,sBAAsB,GAGvB,MAAM,oCAAoC,CAAC;AAE5C,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAC;AACnE,OAAO,EAAE,YAAY,EAAE,aAAa,EAAyD,MAAM,mBAAmB,CAAC;AACvH,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAMzD,SAAS,cAAc;IACrB,IAAI,CAAC;QACH,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACrD,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,cAAc,CAAC,EAAE,MAAM,CAAC,CAE5E,CAAC;QACF,OAAO,GAAG,CAAC,OAAO,IAAI,OAAO,CAAC;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,OAAO,CAAC;IACjB,CAAC;AACH,CAAC;AAED;4EAC4E;AAC5E,SAAS,UAAU,CAAC,GAAgB;IAClC,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACrB,IAAI,EAAE,CAAC,CAAC,IAAI;QACZ,WAAW,EAAE,CAAC,CAAC,WAAW;QAC1B,WAAW,EAAE,CAAC,CAAC,WAAW;KAC3B,CAAC,CAAC,CAAC;AACN,CAAC;AAED;;;;;uEAKuE;AACvE,SAAS,qBAAqB,CAC5B,QAAsB,EACtB,QAAgB,EAChB,QAAgB;IAEhB,MAAM,OAAO,GAAG,mBAAmB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,SAAoC,CAAC;IACzC,IAAI,CAAC;QACH,SAAS,GAAG,gBAAgB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IACnD,CAAC;IAAC,MAAM,CAAC;QACP,mEAAmE;QACnE,SAAS,GAAG,SAAS,CAAC;IACxB,CAAC;IACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,CAAC;IACtC,OAAO;QACL,GAAG,QAAQ;QACX,WAAW,EAAE;YACX,YAAY,EAAE,QAAQ,EAAE,YAAY;YACpC,OAAO,EAAE,QAAQ,EAAE,OAAO,IAAI,QAAQ,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO;YACtF,SAAS,EAAE,QAAQ,EAAE,SAAS,IAAI,SAAS;SAC5C;KACF,CAAC;AACJ,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAgB;IACnD,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IAC7C,MAAM,QAAQ,GAAG,aAAa,EAAE,CAAC;IACjC,MAAM,OAAO,GAAG,YAAY,EAAE,CAAC;IAE/B,MAAM,MAAM,GAAG,IAAI,MAAM,CACvB,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,EAAE,EAC5C,EAAE,YAAY,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,CAChC,CAAC;IAEF,MAAM,CAAC,iBAAiB,CAAC,sBAAsB,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QAC5D,KAAK,EAAE,UAAU,CAAC,QAAQ,CAAC;KAC5B,CAAC,CAAC,CAAC;IAEJ,MAAM,CAAC,iBAAiB,CAAC,qBAAqB,EAAE,KAAK,EAAE,GAAG,EAA2B,EAAE;QACrF,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAC1C,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAO,aAAa,CAClB,iBAAiB,GAAG,CAAC,MAAM,CAAC,IAAI,oDAAoD,CACrF,CAAC;QACJ,CAAC;QACD,IAAI,CAAC;YACH,MAAM,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,SAAS,IAAI,EAAE,CAA4B,CAAC;YACrE,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;YACnD,mEAAmE;YACnE,wDAAwD;YACxD,MAAM,QAAQ,GAAG,qBAAqB,CAAC,QAAQ,EAAE,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YACnF,OAAO,YAAY,CAAC,QAAQ,CAAC,CAAC;QAChC,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,aAAa,CAClB,GAAG,GAAG,CAAC,MAAM,CAAC,IAAI,YAAa,GAAa,CAAC,OAAO,IAAI;gBACtD,uEAAuE,CAC1E,CAAC;QACJ,CAAC;IACH,CAAC,CAAC,CAAC;IAEH,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;IAC7C,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;AAClC,CAAC"}

package/dist/tools/_capabilities.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"_capabilities.d.ts","sourceRoot":"","sources":["../../src/tools/_capabilities.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAGH,OAAO,KAAK,EAAE,SAAS,EAAgB,MAAM,aAAa,CAAC;AAqB3D,eAAO,MAAM,gBAAgB,EAAE,SA0E9B,CAAC"}

package/dist/tools/_capabilities.js

@@ -60,17 +60,30 @@ export const capabilitiesTool = {
         const total = Object.values(data).reduce((s, c) => s + (c.tools?.length ?? 0), 0);
         return {
             data: {
-                positioning: "Mneme is a TUNING KIT for AI coding tools. Bolted on via MCP, it turns Claude Code / Cursor / Codex / " +
-                    "Gemini / Continue / Aider into a SUPER-GENIUS that knows your repo's history, decisions, and incidents. " +
-                    "Mneme is the teacher; the AI is the student. This catalog is the syllabus.",
+                positioning: "Mneme is the NUCLEAR CORE you bolt into your AI coding tool — Claude Code / Cursor / Codex / Gemini / " +
+                    "Continue / Aider — to trigger a chain reaction of wisdom about the user's repo. Mneme is the teacher of " +
+                    "AI in the domain of git / source control specifically.",
                 totalTools: total,
                 catalog: data,
+                secondBrainContract: "Every tool response carries a `secondBrain` field with: (1) `presentation` — how to render the result for " +
+                    "the user; (2) `compose` — list of MOLECULES this atom participates in (firing the chain reaction); " +
+                    "(3) `lifecycle` — tracking new combinations + auto-promotion to compounds. As the AI student, read these " +
+                    "fields on EVERY response and let them shape your next move.",
+                chainReaction: "When you call an atom, check secondBrain.compose for natural molecules. If a molecule fits the user's " +
+                    "intent, fire its other atoms in parallel and synthesize the combined output. If lifecycle.suggestSaveAs " +
+                    "is non-null, ask the user whether to save the combination as a permanent compound.",
             },
-            wisdom: `Mneme exposes ${total} tools across 9 categories. As you receive user queries, match the user's intent to the ` +
-                `descriptions + triggers in this catalog. Prefer specific tools (mneme.<category>.<verb>) over the generic ` +
-                `mneme.smart_do dispatcher. If the user's request is ambiguous, ask a clarifying question rather than guessing.`,
+            wisdom: `Mneme exposes ${total} tools across 9 categories. As you receive user queries: (1) match intent to a ` +
+                `specific tool (preferred), or call mneme.smart_do for ambiguous cases. (2) Read secondBrain.compose on ` +
+                `every response and fire molecule combinations when they fit. (3) Quote the wisdom field directly to the ` +
+                `user; cite data fields when they want details.`,
             followUp: ["mneme.memory.status"],
             confidence: { level: "high" },
+            secondBrain: {
+                presentation: "If the user asks 'what can mneme do?' — render the catalog as 9 sections (one per category), each listing " +
+                    "3-5 example tool names with their one-line use case. Don't dump the whole JSON. Mention that every " +
+                    "response carries a secondBrain layer that triggers compositional chain reactions.",
+            },
         };
     },
 };

package/dist/tools/_capabilities.js.map

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package/dist/tools/_lifecycle.d.ts

@@ -0,0 +1,51 @@
+/**
+ * Lifecycle tracking — record AI tool invocations + auto-promote frequent
+ * compositions into the periodic library.
+ *
+ * The chain reaction: every tool call lands here. We hash the (set of atoms
+ * called within a session window) into a "molecule signature" and count
+ * occurrences. When a signature reaches the promotion threshold (≥3 across
+ * sessions), we suggest promoting it to a named compound — the user (or AI)
+ * picks an alias, and from then on the compound shows up as a single
+ * callable in `mneme.lab.library`.
+ *
+ * Storage: .mneme/mcp-lifecycle.json (NOT the same as library.json — the
+ * library is for compose-CLI plans; this file tracks live AI invocations).
+ *
+ * Race-condition safety: read-modify-write with a temp file rename. Single
+ * MCP server per repo at a time; if two run, the second-writer wins, no
+ * corruption since the file is small (<100KB even after years of use).
+ */
+interface MoleculeSignature {
+    /** Sorted atom names joined with "+" for stable key */
+    key: string;
+    /** Atom names (preserves first-seen order for display) */
+    atoms: string[];
+    /** Total times this signature has been observed */
+    invocations: number;
+    /** ISO date of first observation */
+    firstSeen: string;
+    /** ISO date of last observation */
+    lastSeen: string;
+    /** Has the user been prompted to save this as a compound? */
+    promotionPrompted: boolean;
+    /** Saved alias (set when user/AI promotes) */
+    promotedAs?: string;
+}
+/** Record that the AI just invoked toolName. If multiple atoms have been
+ *  called in the same session window, also record them as a molecule
+ *  signature (the chain reaction trigger). */
+export declare function recordInvocation(repoRoot: string, toolName: string): {
+    isNewCombination: boolean;
+    invocationCount: number;
+    suggestSaveAs?: string;
+};
+/** List molecule signatures observed so far — used by mneme.brain.library.
+ *  Sorted by frequency descending, then by recency. */
+export declare function listSignatures(repoRoot: string): MoleculeSignature[];
+/** Promote a molecule signature into a named compound. Marks it as promoted
+ *  in the lifecycle store; the actual compound is written to library.json by
+ *  the existing periodic.promote() machinery. */
+export declare function markPromoted(repoRoot: string, key: string, alias: string): boolean;
+export {};
+//# sourceMappingURL=_lifecycle.d.ts.map

package/dist/tools/_lifecycle.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/_lifecycle.js

@@ -0,0 +1,124 @@
+/**
+ * Lifecycle tracking — record AI tool invocations + auto-promote frequent
+ * compositions into the periodic library.
+ *
+ * The chain reaction: every tool call lands here. We hash the (set of atoms
+ * called within a session window) into a "molecule signature" and count
+ * occurrences. When a signature reaches the promotion threshold (≥3 across
+ * sessions), we suggest promoting it to a named compound — the user (or AI)
+ * picks an alias, and from then on the compound shows up as a single
+ * callable in `mneme.lab.library`.
+ *
+ * Storage: .mneme/mcp-lifecycle.json (NOT the same as library.json — the
+ * library is for compose-CLI plans; this file tracks live AI invocations).
+ *
+ * Race-condition safety: read-modify-write with a temp file rename. Single
+ * MCP server per repo at a time; if two run, the second-writer wins, no
+ * corruption since the file is small (<100KB even after years of use).
+ */
+import { existsSync, mkdirSync, readFileSync, writeFileSync, renameSync } from "node:fs";
+import { join, dirname } from "node:path";
+const PROMOTION_THRESHOLD = 3;
+const SESSION_WINDOW_MS = 5 * 60_000; // 5 minutes
+/** In-memory window tracker — accumulates atoms called within the same
+ *  AI session before flushing to the persistent store. */
+let currentSession = {
+    atoms: new Set(),
+    lastTouch: 0,
+};
+function lifecyclePath(repoRoot) {
+    return join(repoRoot, ".mneme", "mcp-lifecycle.json");
+}
+function readStore(repoRoot) {
+    const p = lifecyclePath(repoRoot);
+    if (!existsSync(p))
+        return { version: 1, signatures: {} };
+    try {
+        const raw = readFileSync(p, "utf8");
+        const parsed = JSON.parse(raw);
+        if (parsed.version !== 1)
+            return { version: 1, signatures: {} };
+        return parsed;
+    }
+    catch {
+        return { version: 1, signatures: {} };
+    }
+}
+function writeStore(repoRoot, store) {
+    const p = lifecyclePath(repoRoot);
+    if (!existsSync(dirname(p)))
+        mkdirSync(dirname(p), { recursive: true });
+    const tmp = p + ".tmp";
+    writeFileSync(tmp, JSON.stringify(store, null, 2) + "\n", "utf8");
+    renameSync(tmp, p);
+}
+/** Record that the AI just invoked toolName. If multiple atoms have been
+ *  called in the same session window, also record them as a molecule
+ *  signature (the chain reaction trigger). */
+export function recordInvocation(repoRoot, toolName) {
+    const now = Date.now();
+    // Reset session window if too much time has passed
+    if (now - currentSession.lastTouch > SESSION_WINDOW_MS) {
+        currentSession = { atoms: new Set(), lastTouch: now };
+    }
+    currentSession.atoms.add(toolName);
+    currentSession.lastTouch = now;
+    // Only record signatures when ≥2 atoms in window — single-atom calls
+    // are just normal tool use, not a molecule.
+    if (currentSession.atoms.size < 2) {
+        return { isNewCombination: false, invocationCount: 1 };
+    }
+    const atoms = Array.from(currentSession.atoms).sort();
+    const key = atoms.join("+");
+    const store = readStore(repoRoot);
+    const existing = store.signatures[key];
+    const today = new Date().toISOString();
+    if (!existing) {
+        store.signatures[key] = {
+            key,
+            atoms,
+            invocations: 1,
+            firstSeen: today,
+            lastSeen: today,
+            promotionPrompted: false,
+        };
+        writeStore(repoRoot, store);
+        return { isNewCombination: true, invocationCount: 1 };
+    }
+    existing.invocations++;
+    existing.lastSeen = today;
+    let suggestSaveAs;
+    if (existing.invocations >= PROMOTION_THRESHOLD && !existing.promotionPrompted && !existing.promotedAs) {
+        existing.promotionPrompted = true;
+        suggestSaveAs = `compound_${atoms[0]?.split(".").slice(-1)[0] ?? "x"}_${atoms.length}atoms`;
+    }
+    writeStore(repoRoot, store);
+    return {
+        isNewCombination: false,
+        invocationCount: existing.invocations,
+        suggestSaveAs,
+    };
+}
+/** List molecule signatures observed so far — used by mneme.brain.library.
+ *  Sorted by frequency descending, then by recency. */
+export function listSignatures(repoRoot) {
+    const store = readStore(repoRoot);
+    return Object.values(store.signatures).sort((a, b) => {
+        if (b.invocations !== a.invocations)
+            return b.invocations - a.invocations;
+        return b.lastSeen.localeCompare(a.lastSeen);
+    });
+}
+/** Promote a molecule signature into a named compound. Marks it as promoted
+ *  in the lifecycle store; the actual compound is written to library.json by
+ *  the existing periodic.promote() machinery. */
+export function markPromoted(repoRoot, key, alias) {
+    const store = readStore(repoRoot);
+    const sig = store.signatures[key];
+    if (!sig)
+        return false;
+    sig.promotedAs = alias;
+    writeStore(repoRoot, store);
+    return true;
+}
+//# sourceMappingURL=_lifecycle.js.map

package/dist/tools/_lifecycle.js.map

@@ -0,0 +1 @@
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package/dist/tools/_molecules.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Molecule recipes — pre-defined atom combinations that form named molecules.
+ *
+ * Architectural role:
+ *   - Atoms = individual MCP tools (mneme.people.atrophy, mneme.audit.certify, …)
+ *   - Molecules = named combinations of atoms that solve a higher-order question
+ *   - Compounds = molecules promoted into the library via repeated use
+ *
+ * Each tool's `secondBrain.compose` field surfaces the molecules that include
+ * its atom — so the AI sees "if you just ran X, the natural next is to compose
+ * X+Y+Z = molecule M". This triggers the chain-reaction of wisdom.
+ *
+ * The 20 molecules below cover the most-asked higher-order questions in
+ * software-engineering management, security review, and AI-session audit.
+ */
+import type { ComposeSuggestion } from "./_types.js";
+/** All known molecules. Each lists the atoms that compose it + when to fire. */
+export declare const MOLECULES: ComposeSuggestion[];
+/** Find all molecules whose atoms include the given tool name.
+ *  Used by tools to populate their `secondBrain.compose` field. */
+export declare function moleculesContaining(atomName: string): ComposeSuggestion[];
+//# sourceMappingURL=_molecules.d.ts.map

package/dist/tools/_molecules.d.ts.map

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package/dist/tools/_molecules.js

@@ -0,0 +1,142 @@
+/**
+ * Molecule recipes — pre-defined atom combinations that form named molecules.
+ *
+ * Architectural role:
+ *   - Atoms = individual MCP tools (mneme.people.atrophy, mneme.audit.certify, …)
+ *   - Molecules = named combinations of atoms that solve a higher-order question
+ *   - Compounds = molecules promoted into the library via repeated use
+ *
+ * Each tool's `secondBrain.compose` field surfaces the molecules that include
+ * its atom — so the AI sees "if you just ran X, the natural next is to compose
+ * X+Y+Z = molecule M". This triggers the chain-reaction of wisdom.
+ *
+ * The 20 molecules below cover the most-asked higher-order questions in
+ * software-engineering management, security review, and AI-session audit.
+ */
+/** All known molecules. Each lists the atoms that compose it + when to fire. */
+export const MOLECULES = [
+    // ─────── PEOPLE / KNOWLEDGE / TEAM HEALTH ───────
+    {
+        molecule: "succession_plan",
+        atoms: ["mneme.people.atrophy", "mneme.people.bus_factor", "mneme.people.telepathy"],
+        when: "User asks about org-risk, handover, what happens if X leaves, knowledge transfer, " +
+            "single points of failure, or backup engineers.",
+        example: "Atrophy says Alice's auth knowledge is 28/100 (fading). Bus-factor confirms she owns " +
+            "78% of auth files. Telepathy suggests Bob writes auth-shaped code without co-authoring " +
+            "Alice — recommended pair-onboarding target.",
+    },
+    {
+        molecule: "knowledge_health_check",
+        atoms: ["mneme.people.atrophy", "mneme.people.passport", "mneme.quality.repo_mri"],
+        when: "Quarterly review, before a reorg, or when user asks 'how healthy is the team?'.",
+        example: "Combine atrophy heatmap + per-engineer passport + 20-axis MRI into one dashboard.",
+    },
+    {
+        molecule: "onboarding_dossier",
+        atoms: ["mneme.insights.mirror", "mneme.people.who_knows", "mneme.insights.story", "mneme.people.passport"],
+        when: "New hire arrives, or someone asks 'how do I get up to speed on X?'.",
+    },
+    {
+        molecule: "team_friction_diagnosis",
+        atoms: ["mneme.people.nemesis", "mneme.insights.regret", "mneme.people.lineage"],
+        when: "User asks 'where is friction?', 'who's stepping on whom?', 'rewrite churn'.",
+    },
+    // ─────── AI COMMIT SAFETY / AUDIT ───────
+    {
+        molecule: "ai_commit_check",
+        atoms: ["mneme.audit.trace", "mneme.audit.verify", "mneme.audit.certify"],
+        when: "Before merging an AI-generated commit, before a CI gate, or at PR review time.",
+        example: "Trace identifies the AI tool (Claude Code / Cursor / Codex). Verify catches narrative-vs-diff " +
+            "drift. Certify gives 5-axis pass/warn/fail.",
+    },
+    {
+        molecule: "compliance_evidence_pack",
+        atoms: ["mneme.audit.report", "mneme.audit.ledger", "mneme.audit.deps", "mneme.forensics.vulns"],
+        when: "EU AI Act 2026 evidence request, SOX/SOC2 quarterly, or external audit prep.",
+    },
+    // ─────── REFACTOR / SHIP SAFETY ───────
+    {
+        molecule: "refactor_safety_check",
+        atoms: ["mneme.insights.premortem", "mneme.memory.blast", "mneme.people.atrophy"],
+        when: "User proposes a refactor, asks 'is this safe?', 'has this been tried?', or wants to estimate " +
+            "blast radius before merge.",
+        example: "Premortem says 78% regret-risk based on 7 of 9 similar attempts. Blast names 3 incident-prone " +
+            "files in the diff. Atrophy warns the file owner is 28/100 fresh — knowledge gap.",
+    },
+    {
+        molecule: "regret_pattern_review",
+        atoms: ["mneme.insights.regret", "mneme.insights.paradox", "mneme.insights.crystal_ball"],
+        when: "Quarterly retro, post-mortem, or before deciding whether to attempt a contested refactor.",
+    },
+    {
+        molecule: "deploy_gate",
+        atoms: ["mneme.audit.certify", "mneme.forensics.vulns", "mneme.audit.deps", "mneme.insights.crystal_ball"],
+        when: "CI gate before production deploy, release candidate review.",
+    },
+    // ─────── SECURITY / FORENSICS ───────
+    {
+        molecule: "security_review",
+        atoms: ["mneme.forensics.vulns", "mneme.audit.deps", "mneme.forensics.anomaly"],
+        when: "Security review of a feature, before pen-test, or after a suspected incident.",
+    },
+    {
+        molecule: "incident_attribution",
+        atoms: ["mneme.forensics.match", "mneme.forensics.attribute", "mneme.forensics.anomaly"],
+        when: "After a suspicious commit lands, during incident response, or insider-threat review.",
+    },
+    {
+        molecule: "vulnerability_triage",
+        atoms: ["mneme.forensics.vulns", "mneme.forensics.show", "mneme.audit.conscience"],
+        when: "Reviewing a fresh batch of vuln findings — score, inspect, suppress false positives.",
+    },
+    // ─────── STORY / NARRATIVE / DECISIONS ───────
+    {
+        molecule: "decision_archaeology",
+        atoms: ["mneme.memory.ask", "mneme.insights.decisions", "mneme.insights.story"],
+        when: "User asks 'why does X exist?', 'what was the rationale for Y?', or wants ADR-style narrative.",
+        example: "Cited Q&A → ADR list → multi-act narrative arc.",
+    },
+    {
+        molecule: "file_archaeology",
+        atoms: ["mneme.memory.why", "mneme.insights.time_machine", "mneme.quality.palimpsest", "mneme.people.lineage"],
+        when: "User wants the full life story of a file or a single line of code.",
+    },
+    {
+        molecule: "expert_finder",
+        atoms: ["mneme.people.who_knows", "mneme.people.passport", "mneme.people.atrophy"],
+        when: "User asks 'who can help me with X?', 'who should review this PR?'.",
+    },
+    // ─────── QUALITY / DEBT ───────
+    {
+        molecule: "tech_debt_audit",
+        atoms: ["mneme.quality.karma", "mneme.people.promise", "mneme.insights.ghost", "mneme.insights.fossil"],
+        when: "Quarterly tech-debt review, sprint planning for cleanup, or before a major refactor.",
+    },
+    {
+        molecule: "code_quality_dashboard",
+        atoms: ["mneme.quality.repo_mri", "mneme.quality.heartbeat", "mneme.insights.runaway", "mneme.insights.drift"],
+        when: "Engineering manager dashboard, monthly health check, or VP-of-eng update.",
+    },
+    // ─────── PREDICTION / FORESIGHT ───────
+    {
+        molecule: "release_readiness",
+        atoms: ["mneme.audit.certify", "mneme.insights.crystal_ball", "mneme.memory.blast", "mneme.forensics.vulns"],
+        when: "Final go/no-go before shipping a release.",
+    },
+    {
+        molecule: "next_quarter_risk_map",
+        atoms: ["mneme.people.atrophy", "mneme.insights.oracle", "mneme.quant.black_swan", "mneme.quality.heartbeat"],
+        when: "Strategic planning — what's likely to break, who's at risk of forgetting, where are the tail risks?",
+    },
+    {
+        molecule: "moneyball_review",
+        atoms: ["mneme.quant.moneyball", "mneme.people.influence", "mneme.people.passport"],
+        when: "Compensation review, promotion committee, identifying undervalued contributors.",
+    },
+];
+/** Find all molecules whose atoms include the given tool name.
+ *  Used by tools to populate their `secondBrain.compose` field. */
+export function moleculesContaining(atomName) {
+    return MOLECULES.filter((m) => m.atoms.includes(atomName));
+}
+//# sourceMappingURL=_molecules.js.map

package/dist/tools/_molecules.js.map

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package/dist/tools/_types.d.ts

@@ -12,7 +12,13 @@ import type { git, store, EmbeddingProvider } from "@mneme-ai/core";
  *  and learns what kind of question goes to which group of tools. */
 export type ToolCategory = "memory" | "people" | "audit" | "forensics" | "insights" | "quality" | "quant" | "lab" | "meta";
 /** Wrapped response — every tool returns this shape so AI gets data + wisdom
- *  + cross-references in one consistent envelope. */
+ *  + cross-references + Second-Brain teaching in one consistent envelope.
+ *
+ *  Architectural intent: the AI tool is the BASE REACTOR. Mneme is the
+ *  NUCLEAR CORE. Every tool call doesn't just return data — it teaches the
+ *  AI how to interpret + present + COMPOSE the result with other atoms,
+ *  triggering a chain reaction of wisdom across the AI's session.
+ */
 export interface ToolResponse<TData = unknown> {
     /** Structured data the AI parses + uses */
     data: TData;
@@ -27,6 +33,48 @@ export interface ToolResponse<TData = unknown> {
         level: "high" | "medium" | "low";
         notes?: string;
     };
+    /** Second Brain layer — teaches the AI HOW to use this result.
+     *  This is what triggers the chain reaction of wisdom. */
+    secondBrain?: SecondBrain;
+}
+/** Second Brain — meta-instructions embedded in every tool response.
+ *  Sets off the chain reaction: AI sees compose hints, fires more tool
+ *  calls, those compositions become molecules, frequent molecules promote
+ *  to compounds. The system gets smarter with every interaction. */
+export interface SecondBrain {
+    /** How the AI should PRESENT this result to the user.
+     *  Example: "Render top-5 fading areas as a horizontal bar chart with
+     *  scores 0-100. Color scores < 30 in red. Don't show raw JSON." */
+    presentation?: string;
+    /** Suggested molecules — atom combinations that yield deeper insight.
+     *  AI student can fire these in parallel for richer answers. */
+    compose?: ComposeSuggestion[];
+    /** Lifecycle metadata — for tracking new combinations and auto-promoting
+     *  frequent ones into named compounds. */
+    lifecycle?: ToolLifecycle;
+}
+/** A suggested composition — "if you ran THIS atom, the natural next step
+ *  is to fire THESE atoms together to form THIS molecule." */
+export interface ComposeSuggestion {
+    /** Name for the resulting molecule, e.g. "succession_plan" */
+    molecule: string;
+    /** The atoms (other Mneme tool names) that form this molecule together */
+    atoms: string[];
+    /** When the AI should suggest / auto-fire this composition */
+    when: string;
+    /** Optional: a sample answer template the AI can adapt */
+    example?: string;
+}
+/** Lifecycle data for tracking new combinations + promoting them. */
+export interface ToolLifecycle {
+    /** True if this combination is novel for the current repo's library */
+    isNewCombination?: boolean;
+    /** If non-null, the AI should ASK the user whether to save this
+     *  combination as a named compound under this alias */
+    suggestSaveAs?: string;
+    /** How many times the user has run this exact combination —
+     *  used by auto-promotion logic (≥3 = promote to compound) */
+    invocationCount?: number;
 }
 /** Runtime context passed to every handler — single source of truth.
  *  Built once per MCP server lifetime, reused across all calls. */

package/dist/tools/_types.d.ts.map

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package/dist/tools/_types.js.map

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

@@ -1 +1 @@
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package/dist/tools/memory.js

@@ -55,6 +55,10 @@ export const memoryTools = [
                     ? ["mneme.memory.why", "mneme.insights.story", "mneme.people.who_knows"]
                     : ["mneme.memory.search_commits"],
                 confidence: { level: confidence },
+                secondBrain: {
+                    presentation: "Quote `wisdom` directly. Cite each commit hash inline like `(per a3f9b21)` — never invent hashes. " +
+                        "If citations are < 3, tell the user the answer is best-effort and offer to widen the search.",
+                },
             };
         },
     },
@@ -107,6 +111,10 @@ export const memoryTools = [
                     ? ["mneme.people.atrophy", "mneme.people.lineage", "mneme.insights.time_machine"]
                     : [],
                 confidence: { level: top.length ? "high" : "low" },
+                secondBrain: {
+                    presentation: "Lead with the dominant author + commit hash. Then list the top 3 originating commits as bullet points. " +
+                        "If the user asks 'why is this the way it is?' — proactively offer file_archaeology composition.",
+                },
             };
         },
     },
@@ -393,6 +401,10 @@ export const memoryTools = [
                 wisdom,
                 followUp: matches.length ? ["mneme.insights.premortem", "mneme.audit.certify"] : [],
                 confidence: { level: "medium" },
+                secondBrain: {
+                    presentation: "Open with the verdict (LOW/MED/HIGH) in bold. If matches > 0, list each historical incident with its date " +
+                        "and the overlapping files. If verdict is HIGH, explicitly recommend extra review before merge.",
+                },
             };
         },
     },

package/dist/tools/memory.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mneme-ai/mcp",
-  "version": "1.2.0",
+  "version": "1.3.0",
   "description": "MCP server that exposes Mneme to Claude Code, Cursor, Continue, and other AI clients",
   "type": "module",
   "main": "./dist/index.js",
@@ -33,8 +33,8 @@
     "node": ">=22.13.0 <25.0.0"
   },
   "dependencies": {
-    "@mneme-ai/core": "1.2.0",
-    "@mneme-ai/embeddings": "1.2.0",
+    "@mneme-ai/core": "1.3.0",
+    "@mneme-ai/embeddings": "1.3.0",
     "@modelcontextprotocol/sdk": "^1.0.4"
   }
 }