knowledge-mcp-server 1.0.0

package/dist/formatter.js

@@ -0,0 +1,273 @@
+// Word budgets per relevance tier and detail level
+const WORD_BUDGETS = {
+    summary: { ancestor: 40, "graph-expanded": 150, primary: 500 },
+    normal: { ancestor: 80, "graph-expanded": 300, primary: 1500 },
+    full: { ancestor: Infinity, "graph-expanded": Infinity, primary: Infinity },
+};
+function parseSections(content) {
+    const lines = content.split("\n");
+    const sections = [];
+    let currentHeading = "";
+    let currentLines = [];
+    for (const line of lines) {
+        if (/^#{1,6}\s+/.test(line)) {
+            // Flush previous section
+            const body = currentLines.join("\n").trim();
+            if (body || sections.length > 0) {
+                sections.push({
+                    heading: currentHeading,
+                    body,
+                    wordCount: body.split(/\s+/).filter(Boolean).length,
+                });
+            }
+            currentHeading = line;
+            currentLines = [];
+        }
+        else {
+            currentLines.push(line);
+        }
+    }
+    // Flush final section
+    const body = currentLines.join("\n").trim();
+    sections.push({
+        heading: currentHeading,
+        body,
+        wordCount: body.split(/\s+/).filter(Boolean).length,
+    });
+    return sections;
+}
+function truncateContent(content, wordBudget) {
+    if (!Number.isFinite(wordBudget))
+        return content;
+    const sections = parseSections(content);
+    // No headings found — fall back to paragraph-based truncation
+    const hasHeadings = sections.some((s) => s.heading !== "");
+    if (!hasHeadings) {
+        return truncateByParagraphs(content, wordBudget);
+    }
+    const kept = [];
+    let wordCount = 0;
+    for (const section of sections) {
+        const sectionWords = section.wordCount + (section.heading ? section.heading.split(/\s+/).length : 0);
+        if (wordCount + sectionWords > wordBudget && kept.length > 0) {
+            break;
+        }
+        kept.push(section);
+        wordCount += sectionWords;
+    }
+    // Build output from kept sections
+    const parts = [];
+    for (const section of kept) {
+        if (section.heading)
+            parts.push(section.heading);
+        if (section.body)
+            parts.push(section.body);
+    }
+    // Summarize omitted sections
+    const omitted = sections.slice(kept.length);
+    if (omitted.length > 0) {
+        const omittedSummary = omitted
+            .filter((s) => s.heading)
+            .map((s) => `${s.heading.replace(/^#+\s+/, "")} (${s.wordCount} words)`)
+            .join(", ");
+        if (omittedSummary) {
+            parts.push(`\n[Sections omitted: ${omittedSummary}]`);
+        }
+        else {
+            const remaining = omitted.reduce((sum, s) => sum + s.wordCount, 0);
+            if (remaining > 0)
+                parts.push(`\n[... ${remaining} more words]`);
+        }
+    }
+    return parts.join("\n");
+}
+function truncateByParagraphs(content, wordBudget) {
+    const paragraphs = content.split(/\n\n/);
+    const kept = [];
+    let wordCount = 0;
+    for (const paragraph of paragraphs) {
+        const words = paragraph.split(/\s+/).filter(Boolean);
+        if (wordCount + words.length > wordBudget && kept.length > 0) {
+            const totalWords = content.split(/\s+/).filter(Boolean).length;
+            const remaining = totalWords - wordCount;
+            if (remaining > 0) {
+                kept.push(`[... ${remaining} more words]`);
+            }
+            break;
+        }
+        kept.push(paragraph);
+        wordCount += words.length;
+    }
+    return kept.join("\n\n");
+}
+function escapeXml(text) {
+    return text
+        .replace(/&/g, "&")
+        .replace(/</g, "&lt;")
+        .replace(/>/g, "&gt;")
+        .replace(/"/g, "&quot;");
+}
+function formatSingleDoc(entry, detailLevel) {
+    const { doc, relevance, similarity, matchedOn, scoringMethod, expandedFrom } = entry;
+    const attrs = [`id="${escapeXml(doc.id)}"`, `type="${doc.type}"`, `relevance="${relevance}"`];
+    if (doc.status !== "active") {
+        attrs.push(`status="${doc.status}"`);
+    }
+    if (doc.supersededBy) {
+        attrs.push(`superseded_by="${escapeXml(doc.supersededBy)}"`);
+    }
+    if (similarity !== undefined) {
+        attrs.push(`similarity="${similarity.toFixed(2)}"`);
+    }
+    if (matchedOn) {
+        attrs.push(`matched_on="${escapeXml(matchedOn)}"`);
+    }
+    if (scoringMethod) {
+        attrs.push(`scoring_method="${escapeXml(scoringMethod)}"`);
+    }
+    if (expandedFrom) {
+        attrs.push(`expanded_from="${escapeXml(expandedFrom)}"`);
+    }
+    attrs.push(`path="${escapeXml(doc.filePath)}"`);
+    const parts = [`  <document ${attrs.join(" ")}>`];
+    parts.push(`    <title>${escapeXml(doc.title)}</title>`);
+    if (doc.tags.length > 0) {
+        parts.push(`    <tags>${escapeXml(doc.tags.join(", "))}</tags>`);
+    }
+    if (doc.related.length > 0) {
+        parts.push(`    <related>${escapeXml(doc.related.join(", "))}</related>`);
+    }
+    if (doc.type === "decision") {
+        const meta = [];
+        if (doc.decisionStatus)
+            meta.push(`status="${escapeXml(doc.decisionStatus)}"`);
+        if (doc.decisionDate)
+            meta.push(`date="${escapeXml(doc.decisionDate)}"`);
+        if (meta.length > 0) {
+            parts.push(`    <decision_meta ${meta.join(" ")}>`);
+            if (doc.alternativesConsidered && doc.alternativesConsidered.length > 0) {
+                parts.push(`      <alternatives>${escapeXml(doc.alternativesConsidered.join(", "))}</alternatives>`);
+            }
+            parts.push(`    </decision_meta>`);
+        }
+    }
+    const budget = WORD_BUDGETS[detailLevel][relevance];
+    const content = truncateContent(doc.contentBody, budget);
+    parts.push(`    <content>\n${content}\n    </content>`);
+    parts.push(`  </document>`);
+    return parts.join("\n");
+}
+function formatFacets(facets) {
+    const parts = [`  <facets>`];
+    for (const [name, count] of [...facets.domains].sort((a, b) => b[1] - a[1])) {
+        parts.push(`    <domain name="${escapeXml(name)}" count="${count}"/>`);
+    }
+    for (const [name, count] of [...facets.types].sort((a, b) => b[1] - a[1])) {
+        parts.push(`    <type name="${escapeXml(name)}" count="${count}"/>`);
+    }
+    for (const [name, count] of [...facets.phases].sort((a, b) => b[1] - a[1])) {
+        parts.push(`    <phase name="${escapeXml(name)}" count="${count}"/>`);
+    }
+    parts.push(`  </facets>`);
+    return parts.join("\n");
+}
+export function formatSearchResults(query, results, detailLevel = "normal", searchMethod, facets) {
+    const methodAttr = searchMethod ? ` search_method="${escapeXml(searchMethod)}"` : "";
+    const parts = [
+        `<knowledge_context query="${escapeXml(query)}" total_docs="${results.length}"${methodAttr}>`,
+    ];
+    // Order: ancestors first, then primaries by similarity, then expanded
+    const ancestors = results.filter((r) => r.relevance === "ancestor");
+    const primaries = results.filter((r) => r.relevance === "primary");
+    const expanded = results.filter((r) => r.relevance === "graph-expanded");
+    for (const entry of [...ancestors, ...primaries, ...expanded]) {
+        parts.push(formatSingleDoc(entry, detailLevel));
+    }
+    if (facets) {
+        parts.push(formatFacets(facets));
+    }
+    parts.push(`</knowledge_context>`);
+    return parts.join("\n");
+}
+export function formatLookupResult(doc, ancestors, related, contentLevel = "full") {
+    const detailLevel = contentLevel === "summary" ? "normal" : "full";
+    const parts = [`<knowledge_context total_docs="${1 + ancestors.length + related.length}">`];
+    for (const a of ancestors) {
+        parts.push(formatSingleDoc({ doc: a, relevance: "ancestor" }, detailLevel));
+    }
+    parts.push(formatSingleDoc({ doc, relevance: "primary" }, detailLevel));
+    for (const r of related) {
+        parts.push(formatSingleDoc({ doc: r, relevance: "graph-expanded" }, detailLevel));
+    }
+    parts.push(`</knowledge_context>`);
+    return parts.join("\n");
+}
+export function formatGraphResult(nodes, edges, totalDocs, rootId) {
+    const parts = [];
+    parts.push(`<knowledge_graph root="${escapeXml(rootId)}" total_docs="${totalDocs}" nodes_shown="${nodes.length}">`);
+    for (const node of nodes) {
+        parts.push(`  <node id="${escapeXml(node.id)}" type="${escapeXml(node.type)}" domain="${escapeXml(node.domain)}" word_count="${node.wordCount}" children_count="${node.childrenCount}">`);
+        parts.push(`    <title>${escapeXml(node.title)}</title>`);
+        parts.push(`  </node>`);
+    }
+    parts.push(`  <edges>`);
+    for (const edge of edges) {
+        parts.push(`    <edge source="${escapeXml(edge.source)}" target="${escapeXml(edge.target)}" type="${escapeXml(edge.type)}"/>`);
+    }
+    parts.push(`  </edges>`);
+    parts.push(`</knowledge_graph>`);
+    return parts.join("\n");
+}
+export function formatWriteResult(result) {
+    const lines = [
+        `Document ${result.status}: "${result.id}"`,
+        `  File: ${result.filePath}`,
+        `  Parent: ${result.parentId ?? "(root)"}`,
+        ``,
+        `BM25 search index updated — document is immediately searchable.`,
+        `Note: Embedding vectors update automatically when VOYAGE_API_KEY is set.`,
+    ];
+    if (result.warnings && result.warnings.length > 0) {
+        lines.push(``);
+        lines.push(`Warnings:`);
+        for (const w of result.warnings) {
+            lines.push(`  - ${w}`);
+        }
+    }
+    return lines.join("\n");
+}
+export function formatDeleteResult(result) {
+    const lines = [`Document deleted: "${result.id}"`, ``, `BM25 search index updated.`];
+    if (result.warnings.length > 0) {
+        lines.push(``);
+        lines.push(`Warnings:`);
+        for (const w of result.warnings) {
+            lines.push(`  - ${w}`);
+        }
+    }
+    return lines.join("\n");
+}
+export function formatListResult(docs, totalDocs) {
+    const parts = [`<knowledge_list total="${docs.length}" of="${totalDocs}">`];
+    for (const doc of docs) {
+        const attrs = [
+            `id="${escapeXml(doc.id)}"`,
+            `type="${doc.type}"`,
+            `domain="${escapeXml(doc.domain)}"`,
+            `words="${doc.wordCount}"`,
+        ];
+        if (doc.status !== "active")
+            attrs.push(`status="${doc.status}"`);
+        if (doc.lastUpdated)
+            attrs.push(`updated="${doc.lastUpdated}"`);
+        parts.push(`  <doc ${attrs.join(" ")}>`);
+        parts.push(`    <title>${escapeXml(doc.title)}</title>`);
+        if (doc.tags.length > 0) {
+            parts.push(`    <tags>${escapeXml(doc.tags.join(", "))}</tags>`);
+        }
+        parts.push(`  </doc>`);
+    }
+    parts.push(`</knowledge_list>`);
+    return parts.join("\n");
+}
+//# sourceMappingURL=formatter.js.map

package/dist/formatter.js.map

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package/dist/generate-embeddings.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Generate embeddings for all knowledge documents using Voyage AI.
+ * Writes to <knowledge-dir>/.embeddings.json
+ *
+ * Skips documents whose content hash hasn't changed since last run.
+ * Reads knowledge.config.yaml for embedding provider settings if present.
+ */
+export declare function generateEmbeddings(knowledgeDir: string): Promise<void>;

package/dist/generate-embeddings.js

@@ -0,0 +1,146 @@
+/**
+ * Generate embeddings for all knowledge documents using Voyage AI.
+ * Writes to <knowledge-dir>/.embeddings.json
+ *
+ * Skips documents whose content hash hasn't changed since last run.
+ * Reads knowledge.config.yaml for embedding provider settings if present.
+ */
+import { readFileSync, writeFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+import { createHash } from "node:crypto";
+import { parse as parseYaml } from "yaml";
+import { collectMarkdownFiles } from "./loader.js";
+function loadEmbeddingConfig(knowledgeDir) {
+    const configPath = join(knowledgeDir, "knowledge.config.yaml");
+    try {
+        const raw = readFileSync(configPath, "utf-8");
+        const parsed = parseYaml(raw);
+        const embeddings = parsed?.embeddings;
+        return {
+            model: embeddings?.model || "voyage-3-lite",
+            apiKeyEnv: embeddings?.api_key_env || "VOYAGE_API_KEY",
+        };
+    }
+    catch {
+        return { model: "voyage-3-lite", apiKeyEnv: "VOYAGE_API_KEY" };
+    }
+}
+function parseFrontmatter(raw) {
+    const match = raw.match(/^---\n([\s\S]*?)\n---\n([\s\S]*)$/);
+    if (!match)
+        return { body: raw };
+    const fm = parseYaml(match[1]);
+    return {
+        id: fm.id,
+        title: fm.title,
+        domain: fm.domain,
+        subdomain: fm.subdomain,
+        tags: fm.tags,
+        body: match[2].trim(),
+    };
+}
+function buildEmbeddingInput(doc) {
+    const parts = [];
+    if (doc.title)
+        parts.push(doc.title);
+    const domainPart = [doc.domain, doc.subdomain].filter(Boolean).join("/");
+    if (domainPart)
+        parts.push(`Domain: ${domainPart}`);
+    if (doc.tags?.length)
+        parts.push(`Tags: ${doc.tags.join(", ")}`);
+    parts.push("");
+    parts.push(doc.body);
+    return parts.join("\n");
+}
+async function embedBatch(texts, model, apiKey) {
+    const response = await fetch("https://api.voyageai.com/v1/embeddings", {
+        method: "POST",
+        headers: {
+            "Content-Type": "application/json",
+            Authorization: `Bearer ${apiKey}`,
+        },
+        body: JSON.stringify({
+            model,
+            input: texts,
+            input_type: "document",
+        }),
+    });
+    if (!response.ok) {
+        const err = await response.text();
+        throw new Error(`Voyage AI API error (${response.status}): ${err}`);
+    }
+    const data = (await response.json());
+    console.log(`  Batch embedded: ${texts.length} docs, ${data.usage.total_tokens} tokens`);
+    return data.data.map((d) => d.embedding);
+}
+export async function generateEmbeddings(knowledgeDir) {
+    if (!existsSync(knowledgeDir)) {
+        console.error(`Error: Knowledge directory not found: ${knowledgeDir}`);
+        process.exit(1);
+    }
+    const embeddingConfig = loadEmbeddingConfig(knowledgeDir);
+    const embeddingsPath = join(knowledgeDir, ".embeddings.json");
+    const hashesPath = join(knowledgeDir, ".embeddings-hashes.json");
+    const apiKey = process.env[embeddingConfig.apiKeyEnv];
+    if (!apiKey) {
+        console.error(`Error: ${embeddingConfig.apiKeyEnv} environment variable is required`);
+        process.exit(1);
+    }
+    console.log(`Knowledge dir: ${knowledgeDir}`);
+    console.log(`Embedding model: ${embeddingConfig.model}`);
+    // Load existing embeddings and hashes
+    let existingEmbeddings = {};
+    let existingHashes = {};
+    if (existsSync(embeddingsPath)) {
+        existingEmbeddings = JSON.parse(readFileSync(embeddingsPath, "utf-8"));
+    }
+    if (existsSync(hashesPath)) {
+        existingHashes = JSON.parse(readFileSync(hashesPath, "utf-8"));
+    }
+    // Collect all docs
+    const files = collectMarkdownFiles(knowledgeDir);
+    const docs = [];
+    for (const filePath of files) {
+        const raw = readFileSync(filePath, "utf-8");
+        const parsed = parseFrontmatter(raw);
+        if (!parsed.id)
+            continue;
+        const text = buildEmbeddingInput(parsed);
+        const hash = createHash("sha256").update(text).digest("hex");
+        docs.push({ id: parsed.id, text, hash });
+    }
+    console.log(`Found ${docs.length} documents`);
+    // Find docs that need (re-)embedding
+    const toEmbed = docs.filter((d) => !existingHashes[d.id] || existingHashes[d.id] !== d.hash);
+    console.log(`${toEmbed.length} documents need embedding (${docs.length - toEmbed.length} cached)`);
+    if (toEmbed.length === 0) {
+        console.log("All embeddings up to date!");
+        return;
+    }
+    // Embed in batches of 20
+    const BATCH_SIZE = 20;
+    const newEmbeddings = { ...existingEmbeddings };
+    const newHashes = { ...existingHashes };
+    for (let i = 0; i < toEmbed.length; i += BATCH_SIZE) {
+        const batch = toEmbed.slice(i, i + BATCH_SIZE);
+        console.log(`Embedding batch ${Math.floor(i / BATCH_SIZE) + 1}/${Math.ceil(toEmbed.length / BATCH_SIZE)}...`);
+        const vectors = await embedBatch(batch.map((d) => d.text), embeddingConfig.model, apiKey);
+        for (let j = 0; j < batch.length; j++) {
+            newEmbeddings[batch[j].id] = vectors[j];
+            newHashes[batch[j].id] = batch[j].hash;
+        }
+    }
+    // Remove embeddings for deleted docs
+    const validIds = new Set(docs.map((d) => d.id));
+    for (const id of Object.keys(newEmbeddings)) {
+        if (!validIds.has(id)) {
+            delete newEmbeddings[id];
+            delete newHashes[id];
+        }
+    }
+    // Write output
+    writeFileSync(embeddingsPath, JSON.stringify(newEmbeddings));
+    writeFileSync(hashesPath, JSON.stringify(newHashes));
+    console.log(`\nDone! Wrote ${Object.keys(newEmbeddings).length} embeddings to ${embeddingsPath}`);
+}
+//# sourceMappingURL=generate-embeddings.js.map

package/dist/generate-embeddings.js.map

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

@@ -0,0 +1,20 @@
+import { type KnowledgeDocument } from "./loader.js";
+import { type EmbeddingsStore } from "./embeddings.js";
+export interface TagTaxonomy {
+    knownTags: Set<string>;
+    aliases: Map<string, string>;
+}
+export interface KnowledgeGraph {
+    documents: Map<string, KnowledgeDocument>;
+    embeddings: EmbeddingsStore;
+    tagIndex: Map<string, Set<string>>;
+    domainIndex: Map<string, Set<string>>;
+    phaseIndex: Map<number, Set<string>>;
+    typeIndex: Map<string, Set<string>>;
+    backlinkIndex: Map<string, Set<string>>;
+    tagTaxonomy: TagTaxonomy | null;
+}
+export declare function loadTagTaxonomy(knowledgeDir: string): TagTaxonomy | null;
+export declare function buildGraph(knowledgeDir: string, validDomains?: string[] | null): KnowledgeGraph;
+export declare function getAncestors(graph: KnowledgeGraph, docId: string): KnowledgeDocument[];
+export declare function getRelated(graph: KnowledgeGraph, docId: string): KnowledgeDocument[];

package/dist/graph.js

@@ -0,0 +1,133 @@
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+import { loadDocuments } from "./loader.js";
+import { loadEmbeddings } from "./embeddings.js";
+import { log } from "./logger.js";
+function buildTagIndex(docs) {
+    const index = new Map();
+    for (const doc of docs.values()) {
+        for (const tag of doc.tags) {
+            const lower = tag.toLowerCase();
+            if (!index.has(lower))
+                index.set(lower, new Set());
+            index.get(lower).add(doc.id);
+        }
+    }
+    return index;
+}
+function buildDomainIndex(docs) {
+    const index = new Map();
+    for (const doc of docs.values()) {
+        const domain = doc.domain.toLowerCase();
+        if (!index.has(domain))
+            index.set(domain, new Set());
+        index.get(domain).add(doc.id);
+    }
+    return index;
+}
+function buildPhaseIndex(docs) {
+    const index = new Map();
+    for (const doc of docs.values()) {
+        for (const phase of doc.phase) {
+            if (!index.has(phase))
+                index.set(phase, new Set());
+            index.get(phase).add(doc.id);
+        }
+    }
+    return index;
+}
+function buildTypeIndex(docs) {
+    const index = new Map();
+    for (const doc of docs.values()) {
+        if (!index.has(doc.type))
+            index.set(doc.type, new Set());
+        index.get(doc.type).add(doc.id);
+    }
+    return index;
+}
+function buildBacklinkIndex(docs) {
+    const index = new Map();
+    for (const doc of docs.values()) {
+        for (const targetId of doc.related) {
+            if (!index.has(targetId))
+                index.set(targetId, new Set());
+            index.get(targetId).add(doc.id);
+        }
+    }
+    return index;
+}
+export function loadTagTaxonomy(knowledgeDir) {
+    const tagsPath = join(knowledgeDir, ".tags.json");
+    try {
+        const raw = readFileSync(tagsPath, "utf-8");
+        const parsed = JSON.parse(raw);
+        const knownTags = new Set();
+        if (parsed.categories) {
+            for (const tags of Object.values(parsed.categories)) {
+                for (const tag of tags) {
+                    knownTags.add(tag);
+                }
+            }
+        }
+        const aliases = new Map();
+        if (parsed.aliases) {
+            for (const [alias, canonical] of Object.entries(parsed.aliases)) {
+                aliases.set(alias.toLowerCase(), canonical);
+            }
+        }
+        log.info("tag-taxonomy-loaded", { tagCount: knownTags.size, aliasCount: aliases.size });
+        return { knownTags, aliases };
+    }
+    catch {
+        log.debug("tag-taxonomy-skipped", { reason: "No .tags.json found or failed to parse" });
+        return null;
+    }
+}
+export function buildGraph(knowledgeDir, validDomains) {
+    const documents = loadDocuments(knowledgeDir, validDomains);
+    const embeddings = loadEmbeddings(knowledgeDir);
+    const tagIndex = buildTagIndex(documents);
+    const domainIndex = buildDomainIndex(documents);
+    const phaseIndex = buildPhaseIndex(documents);
+    const typeIndex = buildTypeIndex(documents);
+    const backlinkIndex = buildBacklinkIndex(documents);
+    const tagTaxonomy = loadTagTaxonomy(knowledgeDir);
+    return {
+        documents,
+        embeddings,
+        tagIndex,
+        domainIndex,
+        phaseIndex,
+        typeIndex,
+        backlinkIndex,
+        tagTaxonomy,
+    };
+}
+export function getAncestors(graph, docId) {
+    const ancestors = [];
+    let currentId = graph.documents.get(docId)?.parentId ?? null;
+    while (currentId) {
+        const parent = graph.documents.get(currentId);
+        if (!parent)
+            break;
+        ancestors.unshift(parent);
+        currentId = parent.parentId;
+    }
+    return ancestors;
+}
+export function getRelated(graph, docId) {
+    const doc = graph.documents.get(docId);
+    if (!doc)
+        return [];
+    // Merge forward links + backlinks, deduplicate
+    const relatedIds = new Set(doc.related);
+    const backlinks = graph.backlinkIndex.get(docId);
+    if (backlinks) {
+        for (const id of backlinks)
+            relatedIds.add(id);
+    }
+    return [...relatedIds]
+        .map((id) => graph.documents.get(id))
+        .filter((d) => d !== undefined);
+}
+//# sourceMappingURL=graph.js.map

package/dist/graph.js.map

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

@@ -0,0 +1,14 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { type TfIdfIndex } from "./search.js";
+import type { KnowledgeGraph } from "./graph.js";
+import { type KnowledgeConfig } from "./config.js";
+export interface KnowledgeServerResult {
+    server: McpServer;
+    graph: KnowledgeGraph;
+    tfidfIndex: TfIdfIndex;
+    config: KnowledgeConfig | null;
+}
+export declare function createKnowledgeServer(knowledgeDir: string): KnowledgeServerResult;
+export type { KnowledgeGraph } from "./graph.js";
+export type { KnowledgeDocument } from "./loader.js";
+export type { KnowledgeConfig } from "./config.js";