nlm-memory 0.12.0 → 0.13.1

package/dist/llm/ollama-code-embedder.d.ts

@@ -0,0 +1,28 @@
+/**
+ * OllamaCodeEmbedder — CodeEmbedder backed by a local Ollama endpoint.
+ *
+ * Default model: hf.co/awhiteside/CodeRankEmbed-Q8_0-GGUF (146 MB Q8).
+ * Override via NLM_CODE_EMBED_MODEL env var.
+ *
+ * CodeRankEmbed prefix convention:
+ *   query    → "Represent this query for searching relevant code: <text>"
+ *   document → raw text (no prefix)
+ *
+ * Falls back to nomic-embed-text conventions when the configured model
+ * starts with "nomic" (for the graceful-degradation path).
+ *
+ * Vectors are L2-normalised before return so vec0 cosine retrieval is correct.
+ */
+import type { CodeEmbedder, EmbedCodeResult } from "../ports/code-embedder.js";
+export interface OllamaCodeEmbedderOptions {
+    readonly baseUrl?: string;
+    readonly model?: string;
+}
+export declare class OllamaCodeEmbedder implements CodeEmbedder {
+    private readonly baseUrl;
+    private readonly model;
+    private readonly isNomic;
+    constructor(opts?: OllamaCodeEmbedderOptions);
+    embed(text: string, role: "query" | "document"): Promise<EmbedCodeResult>;
+    private buildPrompt;
+}

package/dist/llm/ollama-code-embedder.js

@@ -0,0 +1,73 @@
+/**
+ * OllamaCodeEmbedder — CodeEmbedder backed by a local Ollama endpoint.
+ *
+ * Default model: hf.co/awhiteside/CodeRankEmbed-Q8_0-GGUF (146 MB Q8).
+ * Override via NLM_CODE_EMBED_MODEL env var.
+ *
+ * CodeRankEmbed prefix convention:
+ *   query    → "Represent this query for searching relevant code: <text>"
+ *   document → raw text (no prefix)
+ *
+ * Falls back to nomic-embed-text conventions when the configured model
+ * starts with "nomic" (for the graceful-degradation path).
+ *
+ * Vectors are L2-normalised before return so vec0 cosine retrieval is correct.
+ */
+import { LLMUnreachableError } from "../ports/llm-client.js";
+const DEFAULT_CODE_EMBED_MODEL = "hf.co/awhiteside/CodeRankEmbed-Q8_0-GGUF";
+const CODE_RANK_QUERY_PREFIX = "Represent this query for searching relevant code: ";
+function l2Normalize(v) {
+    let sumSq = 0;
+    for (let i = 0; i < v.length; i++) {
+        const x = v[i] ?? 0;
+        sumSq += x * x;
+    }
+    if (sumSq === 0)
+        return v;
+    const norm = Math.sqrt(sumSq);
+    const out = new Float32Array(v.length);
+    for (let i = 0; i < v.length; i++)
+        out[i] = (v[i] ?? 0) / norm;
+    return out;
+}
+export class OllamaCodeEmbedder {
+    baseUrl;
+    model;
+    isNomic;
+    constructor(opts = {}) {
+        this.baseUrl = opts.baseUrl ?? (process.env["OLLAMA_HOST"] ?? "http://localhost:11434");
+        this.model = opts.model ?? (process.env["NLM_CODE_EMBED_MODEL"] ?? DEFAULT_CODE_EMBED_MODEL);
+        this.isNomic = this.model.startsWith("nomic");
+    }
+    async embed(text, role) {
+        const prompt = this.buildPrompt(text, role);
+        let res;
+        try {
+            res = await fetch(`${this.baseUrl}/api/embeddings`, {
+                method: "POST",
+                headers: { "Content-Type": "application/json" },
+                body: JSON.stringify({ model: this.model, prompt }),
+            });
+        }
+        catch (e) {
+            throw new LLMUnreachableError("ollama-code-embedder", String(e));
+        }
+        if (!res.ok) {
+            throw new LLMUnreachableError("ollama-code-embedder", `HTTP ${res.status}`);
+        }
+        const data = (await res.json());
+        if (!data.embedding || data.embedding.length === 0) {
+            throw new LLMUnreachableError("ollama-code-embedder", "empty embedding");
+        }
+        const raw = new Float32Array(data.embedding);
+        const vector = l2Normalize(raw);
+        return { vector, dim: vector.length };
+    }
+    buildPrompt(text, role) {
+        if (this.isNomic) {
+            return role === "query" ? `search_query: ${text}` : `search_document: ${text}`;
+        }
+        return role === "query" ? `${CODE_RANK_QUERY_PREFIX}${text}` : text;
+    }
+}
+//# sourceMappingURL=ollama-code-embedder.js.map

package/dist/llm/ollama-code-embedder.js.map

@@ -0,0 +1 @@
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package/dist/mcp/server.d.ts

@@ -21,6 +21,11 @@ export interface McpDeps {
     /** Optional — when absent, fact tools are not registered. */
     readonly factRecall?: FactRecallService;
     readonly factStore?: FactStore;
+    /** Optional — when present, recall_code tool is registered. */
+    readonly exemplarStore?: import("../ports/code-exemplar-store.js").CodeExemplarStore;
+    /** Optional code embedder for recall_code semantic search. */
+    readonly codeEmbedder?: import("../ports/code-embedder.js").CodeEmbedder;
+    readonly installScope?: string;
 }
 export interface ToolResult {
     content: {
@@ -67,5 +72,10 @@ export interface MarkSupersededInput {
     readonly reason?: string | undefined;
 }
 export declare function markSupersededHandler(deps: McpDeps, input: MarkSupersededInput): Promise<ToolResult>;
+export interface SupersedeFactInput {
+    readonly fact_id: string;
+    readonly reason?: string | undefined;
+}
+export declare function supersedeFactHandler(deps: McpDeps, input: SupersedeFactInput): Promise<ToolResult>;
 export declare function citeSessionHandler(input: CiteSessionInput): Promise<ToolResult>;
 export declare function createMcpServer(deps: McpDeps): McpServer;

package/dist/mcp/server.js

@@ -15,7 +15,8 @@ import { z } from "zod";
 import { logQuery } from "../core/recall/query-log.js";
 import { logFactQuery } from "../core/recall-facts/fact-query-log.js";
 import { appendCitation } from "../core/recall/citation-log.js";
-import { appendSupersedence, readSupersedenceLog } from "../core/storage/supersedence-log.js";
+import { appendFactSupersedence, appendSupersedence, readSupersedenceLog } from "../core/storage/supersedence-log.js";
+import { recallCode } from "../core/exemplars/recall-code.js";
 const CHARACTER_LIMIT = 25_000;
 const DEFAULT_LIMIT = 10;
 const SERVER_NAME = "nlm-memory-mcp-server";
@@ -364,6 +365,51 @@ export async function markSupersededHandler(deps, input) {
         return err(e);
     }
 }
+const SUPERSEDE_FACT_DESCRIPTION = `Retroactively mark a specific NLM fact as superseded when the operator states
+that a previously-stored decision or attribute no longer holds.
+
+Use this when the user says things like "that's wrong now," "we changed the
+framework to X," "that decision is stale," or corrects a specific fact that
+recall_facts returned. Pass the fact id returned by recall_facts.
+
+Unlike mark_superseded (session-level), this targets a single (subject,
+predicate, value) row. The fact remains in the store for history but is
+excluded from future recall_facts results (superseded_by is set to null,
+meaning retired without a known successor — the replacement will be ingested
+from the current conversation when it closes).
+
+Deterministic: no LLM in the loop, immediate state change.
+
+Args:
+  - fact_id: the id field returned by recall_facts for the stale fact.
+  - reason:  optional human-readable rationale. Logged for provenance.
+
+Idempotent: calling it twice on the same id is a no-op. Errors if fact_id
+is unknown.`;
+export async function supersedeFactHandler(deps, input) {
+    if (!input.fact_id || input.fact_id.length < 4) {
+        return err(new Error("fact_id is required"));
+    }
+    if (!deps.factStore) {
+        return err(new Error("fact store not available"));
+    }
+    try {
+        await deps.factStore.retire(input.fact_id);
+        void appendFactSupersedence({
+            factId: input.fact_id,
+            source: "mcp",
+            ...(input.reason !== undefined ? { reason: input.reason } : {}),
+        });
+        return ok({
+            marked: true,
+            fact_id: input.fact_id,
+            ...(input.reason !== undefined ? { reason: input.reason } : {}),
+        });
+    }
+    catch (e) {
+        return err(e);
+    }
+}
 export async function citeSessionHandler(input) {
     if (!input.id || input.id.length < MIN_CITE_ID_LEN) {
         return err(new Error(`id must be at least ${MIN_CITE_ID_LEN} characters`));
@@ -505,6 +551,26 @@ export function createMcpServer(deps) {
                 openWorldHint: true,
             },
         }, async (args) => getFactHistoryHandler(deps, args));
+        server.registerTool("supersede_fact", {
+            title: "Supersede a Stale NLM Fact",
+            description: SUPERSEDE_FACT_DESCRIPTION,
+            inputSchema: {
+                fact_id: z
+                    .string()
+                    .min(4)
+                    .describe("Fact ID returned by recall_facts for the stale fact."),
+                reason: z
+                    .string()
+                    .optional()
+                    .describe("Why this fact is being retired. Optional but encouraged for audit trail."),
+            },
+            annotations: {
+                readOnlyHint: false,
+                destructiveHint: false,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
+        }, async (args) => supersedeFactHandler(deps, args));
     }
     server.registerTool("cite_session", {
         title: "Cite NLM Session",
@@ -551,6 +617,71 @@ export function createMcpServer(deps) {
             openWorldHint: false,
         },
     }, async (args) => markSupersededHandler(deps, args));
+    if (deps.exemplarStore &&
+        deps.installScope &&
+        process.env["NLM_CODE_EXEMPLARS_ENABLED"] === "1") {
+        const exemplarStore = deps.exemplarStore;
+        const codeEmbedder = deps.codeEmbedder ?? null;
+        const installScope = deps.installScope;
+        server.registerTool("recall_code", {
+            title: "Recall Code Exemplars",
+            description: RECALL_CODE_DESCRIPTION,
+            inputSchema: {
+                query: z
+                    .string()
+                    .min(1)
+                    .describe("Natural-language description of the task you are about to implement."),
+                repo: z
+                    .string()
+                    .optional()
+                    .describe("Narrow to one repository path."),
+                lang: z
+                    .string()
+                    .optional()
+                    .describe("Filter by language (ts, py, go, etc.)."),
+                k: z
+                    .number()
+                    .int()
+                    .min(1)
+                    .max(20)
+                    .optional()
+                    .describe("Max results to return (default 5)."),
+                include_negatives: z
+                    .boolean()
+                    .optional()
+                    .describe("Include fail/exhausted exemplars as labeled cautionary examples (default true)."),
+            },
+            annotations: {
+                readOnlyHint: true,
+                destructiveHint: false,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
+        }, async (args) => {
+            const result = await recallCode({
+                query: args.query,
+                installScope,
+                ...(args.repo ? { repo: args.repo } : {}),
+                ...(args.lang ? { lang: args.lang } : {}),
+                k: args.k ?? 5,
+                includeNegatives: args.include_negatives ?? true,
+            }, exemplarStore, codeEmbedder, null);
+            return { content: [{ type: "text", text: format(result) }] };
+        });
+    }
     return server;
 }
+const RECALL_CODE_DESCRIPTION = `\
+Retrieve code exemplars — concrete chunks of code from past sessions with \
+deterministic outcome labels (pass/fail/fix/exhausted). Use when you are \
+about to implement something and want to see what code passed or failed the \
+gate for a similar task in this repository.
+
+Returns two lists:
+- **positives**: code that passed or was fixed to a passing state
+- **negatives**: code that failed or was exhausted (labeled "avoid")
+
+Outcome labels come from git-survival and test exit codes, not LLM judgment. \
+Model-agnostic: exemplars from any agent or model vendor are included. \
+Scoped to your install by default; narrow by repo or lang as needed.`;
 //# sourceMappingURL=server.js.map

package/dist/mcp/server.js.map

@@ -1 +1 @@
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package/dist/ports/code-embedder.d.ts

@@ -0,0 +1,27 @@
+/**
+ * CodeEmbedder — minimal port for the code-specific embedding lane.
+ *
+ * Separate from LLMClient because code embedding uses different models
+ * (CodeRankEmbed vs nomic-embed-text) and different prefix conventions.
+ * Keeping the port focused prevents cross-contamination between the prose
+ * and code vector spaces.
+ *
+ * Graceful degradation: when no CodeEmbedder is wired (e.g. Ollama doesn't
+ * have the model), callers fall back to the prose embedder or skip the vec
+ * insert. The feature flag NLM_CODE_EXEMPLARS_ENABLED controls whether the
+ * lane is active at all.
+ */
+export interface EmbedCodeResult {
+    readonly vector: Float32Array;
+    /** Actual dimension of the returned vector. */
+    readonly dim: number;
+}
+export interface CodeEmbedder {
+    /**
+     * Embed text for the code lane.
+     *
+     * `role: "query"` — apply the model's query prefix (if any).
+     * `role: "document"` — embed the chunk as-is (or with a document prefix).
+     */
+    embed(text: string, role: "query" | "document"): Promise<EmbedCodeResult>;
+}

package/dist/ports/code-embedder.js

@@ -0,0 +1,15 @@
+/**
+ * CodeEmbedder — minimal port for the code-specific embedding lane.
+ *
+ * Separate from LLMClient because code embedding uses different models
+ * (CodeRankEmbed vs nomic-embed-text) and different prefix conventions.
+ * Keeping the port focused prevents cross-contamination between the prose
+ * and code vector spaces.
+ *
+ * Graceful degradation: when no CodeEmbedder is wired (e.g. Ollama doesn't
+ * have the model), callers fall back to the prose embedder or skip the vec
+ * insert. The feature flag NLM_CODE_EXEMPLARS_ENABLED controls whether the
+ * lane is active at all.
+ */
+export {};
+//# sourceMappingURL=code-embedder.js.map

package/dist/ports/code-embedder.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"code-embedder.js","sourceRoot":"","sources":["../../src/ports/code-embedder.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG"}

package/dist/ports/code-exemplar-store.d.ts

@@ -0,0 +1,45 @@
+/**
+ * CodeExemplarStore — the only way core/ reads or writes the code-exemplar
+ * corpus.
+ *
+ * Sibling to SignalStore: append-only, idempotent on a deterministic id
+ * (same code_hash in the same scope is a no-op), no supersedence. The
+ * vec lane is optional — inserts succeed without an embedding; search
+ * requires one.
+ */
+import type { CodeExemplar, CodeExemplarHit, CodeExemplarInput } from "../shared/types.js";
+export interface CodeExemplarSearchFilter {
+    readonly installScope: string;
+    readonly repo?: string;
+    readonly lang?: string;
+    readonly model?: string;
+    readonly includeNegatives?: boolean;
+    /** Number of results to return. Default 5. */
+    readonly k?: number;
+}
+export interface CodeExemplarStore {
+    /** Insert one exemplar. Duplicate code_hash in the same install_scope is a no-op. */
+    insert(input: CodeExemplarInput): Promise<{
+        id: string;
+        skipped: boolean;
+    }>;
+    /** Insert many in one transaction. Duplicates are skipped. */
+    insertMany(inputs: ReadonlyArray<CodeExemplarInput>): Promise<number>;
+    /** Insert or update the embedding for an exemplar_id. */
+    upsertEmbedding(exemplarId: string, vector: Float32Array): Promise<void>;
+    /** Vector search + rerank. Returns up to k results nearest the query vector. */
+    searchByVector(queryVector: Float32Array, filter: CodeExemplarSearchFilter): Promise<ReadonlyArray<CodeExemplarHit>>;
+    /** Fetch exemplar by id. */
+    getById(id: string): Promise<CodeExemplar | null>;
+    /**
+     * Per-bucket cap enforcement: delete oldest rows beyond maxPerBucket,
+     * bucketed by (install_scope, repo, lang, outcome_class).
+     * outcome_class = 'positive' for pass/fix, 'negative' for fail/exhausted.
+     * Returns total rows deleted.
+     */
+    applyBucketCap(installScope: string, maxPerBucket: number): Promise<number>;
+    /** Delete exemplars with survived=0 (reverted code). Returns rows deleted. */
+    pruneReverted(installScope: string): Promise<number>;
+    /** Delete exemplars with ts < olderThanTs (optional clock-based escape hatch). */
+    pruneOlderThan(olderThanTs: string): Promise<number>;
+}

package/dist/ports/code-exemplar-store.js

@@ -0,0 +1,11 @@
+/**
+ * CodeExemplarStore — the only way core/ reads or writes the code-exemplar
+ * corpus.
+ *
+ * Sibling to SignalStore: append-only, idempotent on a deterministic id
+ * (same code_hash in the same scope is a no-op), no supersedence. The
+ * vec lane is optional — inserts succeed without an embedding; search
+ * requires one.
+ */
+export {};
+//# sourceMappingURL=code-exemplar-store.js.map

package/dist/ports/code-exemplar-store.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"code-exemplar-store.js","sourceRoot":"","sources":["../../src/ports/code-exemplar-store.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG"}

package/dist/ports/fact-store.js.map

@@ -1 +1 @@
-{"version":3,"file":"fact-store.js","sourceRoot":"","sources":["../../src/ports/fact-store.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AA0IH,uDAAuD;AACvD,MAAM,UAAU,gBAAgB,CAAC,OAAe,EAAE,SAAiB,EAAE,KAAa;IAChF,OAAO,GAAG,OAAO,IAAI,SAAS,IAAI,KAAK,EAAE,CAAC;AAC5C,CAAC"}
+{"version":3,"file":"fact-store.js","sourceRoot":"","sources":["../../src/ports/fact-store.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AA4JH,uDAAuD;AACvD,MAAM,UAAU,gBAAgB,CAAC,OAAe,EAAE,SAAiB,EAAE,KAAa;IAChF,OAAO,GAAG,OAAO,IAAI,SAAS,IAAI,KAAK,EAAE,CAAC;AAC5C,CAAC"}

package/dist/ports/storage.d.ts

@@ -10,9 +10,12 @@
  *
  * See docs/plans/2026-05-30-factstore-storage-port.md.
  */
+import type { CodeExemplarStore } from "./code-exemplar-store.js";
 import type { FactStore } from "./fact-store.js";
 import type { SessionStore } from "./session-store.js";
 import type { SignalStore } from "./signal-store.js";
+import type { SourceRegistryPort } from "../core/sources/source-registry.js";
+import type { ProviderRegistryPort } from "../core/providers/provider-registry.js";
 export interface StorageContext {
     readonly facts: FactStore;
     readonly sessions: SessionStore;
@@ -21,6 +24,11 @@ export interface Storage {
     readonly facts: FactStore;
     readonly sessions: SessionStore;
     readonly signals: SignalStore;
+    readonly exemplars: CodeExemplarStore;
+    /** Transcript-source registry (claude-code/hermes/webhook/…). */
+    readonly sources: SourceRegistryPort;
+    /** LLM-provider registry (ollama/deepseek/openai/…). */
+    readonly providers: ProviderRegistryPort;
     /**
      * Run `fn` inside an adapter-defined transaction. The handles on the
      * provided StorageContext are bound to that transaction; reads and writes

package/dist/shared/types.d.ts

@@ -241,3 +241,38 @@ export interface Signal {
     readonly ts: string;
     readonly createdAt: string;
 }
+export type CodeExemplarOutcome = "pass" | "fail" | "fix" | "exhausted";
+/** Producer-side payload for a single code chunk. */
+export interface CodeExemplarInput {
+    readonly installScope: string;
+    readonly signalId: string | null;
+    readonly sessionId: string | null;
+    readonly repo: string;
+    readonly model: string;
+    readonly lang: string | null;
+    readonly taskContext: string;
+    readonly code: string;
+    readonly codeHash: string;
+    readonly outcome: CodeExemplarOutcome;
+    readonly gitSha: string | null;
+    readonly survived: 0 | 1 | null;
+    readonly ts: string;
+}
+/** Stored exemplar. */
+export interface CodeExemplar extends CodeExemplarInput {
+    readonly id: string;
+    readonly createdAt: string;
+}
+/** One result row from recall_code. */
+export interface CodeExemplarHit {
+    readonly id: string;
+    readonly code: string;
+    readonly taskContext: string;
+    readonly outcome: CodeExemplarOutcome;
+    readonly repo: string;
+    readonly model: string;
+    readonly lang: string | null;
+    readonly survived: 0 | 1 | null;
+    readonly gitSha: string | null;
+    readonly distance: number;
+}