knowledge-mcp-server 1.0.0

package/dist/index.js

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+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { z } from "zod";
+import { buildGraph, getAncestors, getRelated } from "./graph.js";
+import { knowledgeSearch } from "./search.js";
+import { buildTfIdfIndex } from "./embeddings.js";
+import { formatLookupResult, formatGraphResult, formatWriteResult, formatDeleteResult, formatListResult, } from "./formatter.js";
+import { writeDocument, deleteDocument } from "./writer.js";
+import { validateGraph, formatValidationReport } from "./validator.js";
+import { computeStats, formatStats } from "./analytics.js";
+import { log } from "./logger.js";
+import { loadConfig, getEffectiveDomains, getEffectivePhaseIds } from "./config.js";
+import { buildClassifierConfig } from "./query-classifier.js";
+// --- Fuzzy ID matching for knowledge_lookup ---
+function fuzzyMatchId(g, query) {
+    const lower = query.toLowerCase();
+    const queryTokens = lower.split(/[\s\-/]+/).filter(Boolean);
+    const candidates = [];
+    for (const doc of g.documents.values()) {
+        let score = 0;
+        const idLower = doc.id.toLowerCase();
+        const titleLower = doc.title.toLowerCase();
+        // Substring match on ID
+        if (idLower.includes(lower))
+            score += 3;
+        else if (lower.includes(idLower))
+            score += 2;
+        // Substring match on title
+        if (titleLower.includes(lower))
+            score += 2;
+        // Token overlap
+        const idTokens = idLower.split(/[-/]+/);
+        const titleTokens = titleLower.split(/\s+/);
+        for (const qt of queryTokens) {
+            if (idTokens.some((t) => t.includes(qt) || qt.includes(t)))
+                score += 1;
+            if (titleTokens.some((t) => t.includes(qt) || qt.includes(t)))
+                score += 1;
+        }
+        if (score > 0)
+            candidates.push({ id: doc.id, title: doc.title, score });
+    }
+    candidates.sort((a, b) => b.score - a.score);
+    return candidates.slice(0, 5);
+}
+export function createKnowledgeServer(knowledgeDir) {
+    const start = Date.now();
+    const config = loadConfig(knowledgeDir);
+    const validDomains = getEffectiveDomains(config, knowledgeDir);
+    const validPhaseIds = getEffectivePhaseIds(config);
+    const graph = buildGraph(knowledgeDir, validDomains);
+    let tfidfIndex = buildTfIdfIndex(graph.documents);
+    const classifierConfig = buildClassifierConfig(config);
+    const elapsed = Date.now() - start;
+    log.info("startup", {
+        docs: graph.documents.size,
+        embeddings: graph.embeddings.vectors.size,
+        embeddingsAvailable: graph.embeddings.available,
+        ms: elapsed,
+    });
+    // --- Write serialization queue (prevents concurrent index corruption) ---
+    let writeQueue = Promise.resolve();
+    function enqueueWrite(fn) {
+        const result = writeQueue.then(fn);
+        writeQueue = result.catch(() => { });
+        return result;
+    }
+    const server = new McpServer({
+        name: "knowledge",
+        version: "1.0.0",
+    });
+    // Tool 1: knowledge_search
+    server.tool("knowledge_search", `Semantic search over the ${config?.name || "project"} knowledge graph. Returns relevant documents with ancestor context and cross-references, formatted as XML.`, {
+        query: z.string().describe("Natural language query"),
+        domains: z
+            .array(z.string())
+            .optional()
+            .describe(validDomains
+            ? `Pre-filter to specific domains: ${validDomains.join(", ")}`
+            : "Pre-filter to specific domains (auto-discovered from directory structure)"),
+        phases: z
+            .array(z.number())
+            .optional()
+            .describe(validPhaseIds
+            ? `Pre-filter to specific phases: ${validPhaseIds.join(", ")}`
+            : "Pre-filter to specific phases (positive integers)"),
+        tags: z.array(z.string()).optional().describe("Require specific tags"),
+        type: z
+            .enum(["summary", "detail", "decision", "reference"])
+            .optional()
+            .describe("Filter by document type"),
+        max_results: z
+            .number()
+            .optional()
+            .default(10)
+            .describe("Maximum number of documents to return (default 10)"),
+        detail_level: z
+            .enum(["summary", "normal", "full"])
+            .optional()
+            .default("normal")
+            .describe('Content detail level: "summary" (~40-500 words per doc), "normal" (~80-1500 words, default), "full" (no truncation)'),
+        include_drafts: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe("Include draft documents in results (default false)"),
+    }, async ({ query, domains, phases, tags, type, max_results, detail_level, include_drafts }) => {
+        const result = await knowledgeSearch(graph, tfidfIndex, {
+            query,
+            domains,
+            phases,
+            tags,
+            type,
+            maxResults: max_results,
+            detailLevel: detail_level,
+            includeDrafts: include_drafts,
+        }, classifierConfig);
+        return { content: [{ type: "text", text: result }] };
+    });
+    // Tool 2: knowledge_lookup
+    server.tool("knowledge_lookup", "Retrieve one or more documents by ID. Accepts a single `id` string or an `ids` array (max 10). Returns documents with optional ancestor summaries and related documents.", {
+        id: z
+            .string()
+            .optional()
+            .describe('Single document ID, e.g., "business/pricing-tiers" or "technology/audio-detection/pitch-detection"'),
+        ids: z
+            .array(z.string())
+            .optional()
+            .describe("Array of document IDs for batch retrieval (max 10)"),
+        include_ancestors: z
+            .boolean()
+            .optional()
+            .default(true)
+            .describe("Include parent summary documents (default true)"),
+        include_related: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe("Include related documents (default false)"),
+        content: z
+            .enum(["full", "summary"])
+            .optional()
+            .default("full")
+            .describe('Content level: "full" (complete content, default) or "summary" (truncated)'),
+    }, async ({ id, ids, include_ancestors, include_related, content }) => {
+        // Resolve list of IDs (single or batch)
+        const lookupIds = ids ? ids.slice(0, 10) : id ? [id] : [];
+        if (lookupIds.length === 0) {
+            return {
+                content: [
+                    { type: "text", text: "Error: provide either `id` or `ids` parameter." },
+                ],
+                isError: true,
+            };
+        }
+        // Single document lookup (original behavior with fuzzy matching)
+        if (lookupIds.length === 1) {
+            const docId = lookupIds[0];
+            const doc = graph.documents.get(docId);
+            if (!doc) {
+                const suggestions = fuzzyMatchId(graph, docId);
+                const hint = suggestions.length > 0
+                    ? `\n\nDid you mean:\n${suggestions.map((s) => `  - ${s.id} ("${s.title}")`).join("\n")}`
+                    : "\n\nUse knowledge_graph to browse available documents.";
+                return {
+                    content: [
+                        {
+                            type: "text",
+                            text: `Document not found: "${docId}".${hint}`,
+                        },
+                    ],
+                };
+            }
+            const ancestors = include_ancestors ? getAncestors(graph, docId) : [];
+            const related = include_related ? getRelated(graph, docId) : [];
+            const result = formatLookupResult(doc, ancestors, related, content);
+            return { content: [{ type: "text", text: result }] };
+        }
+        // Batch lookup: collect all docs, deduplicate ancestors/related
+        const seen = new Set();
+        const allAncestors = [];
+        const allPrimary = [];
+        const allRelated = [];
+        const notFound = [];
+        for (const docId of lookupIds) {
+            const doc = graph.documents.get(docId);
+            if (!doc) {
+                notFound.push(docId);
+                continue;
+            }
+            if (!seen.has(doc.id)) {
+                seen.add(doc.id);
+                allPrimary.push(doc);
+            }
+            if (include_ancestors) {
+                for (const a of getAncestors(graph, docId)) {
+                    if (!seen.has(a.id)) {
+                        seen.add(a.id);
+                        allAncestors.push(a);
+                    }
+                }
+            }
+            if (include_related) {
+                for (const r of getRelated(graph, docId)) {
+                    if (!seen.has(r.id)) {
+                        seen.add(r.id);
+                        allRelated.push(r);
+                    }
+                }
+            }
+        }
+        // Format as combined lookup (first primary doc is the "main", rest are related-style)
+        const parts = [];
+        if (notFound.length > 0) {
+            parts.push(`Documents not found: ${notFound.join(", ")}`);
+        }
+        // Use first primary as the main doc, rest as additional
+        if (allPrimary.length > 0) {
+            const result = formatLookupResult(allPrimary[0], allAncestors, [...allPrimary.slice(1), ...allRelated], content);
+            parts.push(result);
+        }
+        return { content: [{ type: "text", text: parts.join("\n\n") }] };
+    });
+    // Tool 3: knowledge_graph
+    server.tool("knowledge_graph", "Returns the graph structure for a subtree. Useful for understanding document relationships and navigating the knowledge base.", {
+        root_id: z.string().optional().default("root").describe('Starting node ID (default "root")'),
+        depth: z
+            .number()
+            .optional()
+            .default(2)
+            .describe("Levels deep to traverse (default 2, max 4)"),
+        include_related: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe("Include related edges (default false)"),
+        max_nodes: z
+            .number()
+            .optional()
+            .default(50)
+            .describe("Maximum number of nodes to return (default 50)"),
+    }, async ({ root_id, depth, include_related, max_nodes }) => {
+        const rootDoc = graph.documents.get(root_id);
+        if (!rootDoc) {
+            return {
+                content: [
+                    {
+                        type: "text",
+                        text: `Document not found: "${root_id}". Available root domains: ${[...graph.domainIndex.keys()].join(", ")}`,
+                    },
+                ],
+            };
+        }
+        // Cap depth at 4
+        const effectiveDepth = Math.min(depth, 4);
+        const nodes = [];
+        const edges = [];
+        const visited = new Set();
+        function walk(id, currentDepth) {
+            if (visited.has(id) || currentDepth > effectiveDepth || nodes.length >= max_nodes)
+                return;
+            visited.add(id);
+            const doc = graph.documents.get(id);
+            if (!doc)
+                return;
+            nodes.push({
+                id: doc.id,
+                title: doc.title,
+                type: doc.type,
+                domain: doc.domain,
+                wordCount: doc.wordCount,
+                childrenCount: doc.childrenIds.length,
+            });
+            // Child edges
+            for (const childId of doc.childrenIds) {
+                if (nodes.length >= max_nodes)
+                    break;
+                edges.push({ source: id, target: childId, type: "child" });
+                walk(childId, currentDepth + 1);
+            }
+            // Related edges (non-recursive)
+            if (include_related) {
+                for (const relatedId of doc.related) {
+                    if (graph.documents.has(relatedId)) {
+                        edges.push({
+                            source: id,
+                            target: relatedId,
+                            type: "related",
+                        });
+                        // Add related node if not visited (but don't recurse into it)
+                        if (!visited.has(relatedId) && nodes.length < max_nodes) {
+                            const relDoc = graph.documents.get(relatedId);
+                            nodes.push({
+                                id: relDoc.id,
+                                title: relDoc.title,
+                                type: relDoc.type,
+                                domain: relDoc.domain,
+                                wordCount: relDoc.wordCount,
+                                childrenCount: relDoc.childrenIds.length,
+                            });
+                            visited.add(relatedId);
+                        }
+                    }
+                }
+            }
+        }
+        walk(root_id, 0);
+        const result = formatGraphResult(nodes, edges, graph.documents.size, root_id);
+        return { content: [{ type: "text", text: result }] };
+    });
+    // Tool 4: knowledge_list
+    server.tool("knowledge_list", "List documents in the knowledge graph with metadata only (no content). Supports filtering by domain, type, phase, tags, and title search.", {
+        domain: z.string().optional().describe("Filter by domain"),
+        type: z
+            .enum(["summary", "detail", "decision", "reference"])
+            .optional()
+            .describe("Filter by document type"),
+        phase: z.number().optional().describe("Filter by phase (1, 2, or 3)"),
+        tags: z.array(z.string()).optional().describe("Require specific tags"),
+        title_search: z.string().optional().describe("Substring search on document titles"),
+        include_drafts: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe("Include draft documents (default false)"),
+    }, async ({ domain, type, phase, tags, title_search, include_drafts }) => {
+        const results = [];
+        for (const doc of graph.documents.values()) {
+            // Apply filters
+            if (!include_drafts && doc.status === "draft")
+                continue;
+            if (domain && doc.domain.toLowerCase() !== domain.toLowerCase())
+                continue;
+            if (type && doc.type !== type)
+                continue;
+            if (phase && !doc.phase.includes(phase))
+                continue;
+            if (tags && tags.length > 0) {
+                const docTagsLower = new Set(doc.tags.map((t) => t.toLowerCase()));
+                if (!tags.every((t) => docTagsLower.has(t.toLowerCase())))
+                    continue;
+            }
+            if (title_search && !doc.title.toLowerCase().includes(title_search.toLowerCase()))
+                continue;
+            results.push({
+                id: doc.id,
+                title: doc.title,
+                type: doc.type,
+                domain: doc.domain,
+                tags: doc.tags,
+                wordCount: doc.wordCount,
+                status: doc.status,
+                lastUpdated: doc.lastUpdated,
+            });
+        }
+        // Sort by domain, then ID
+        results.sort((a, b) => a.domain.localeCompare(b.domain) || a.id.localeCompare(b.id));
+        const result = formatListResult(results, graph.documents.size);
+        return { content: [{ type: "text", text: result }] };
+    });
+    // Tool 5: knowledge_write
+    server.tool("knowledge_write", "Create or update a document in the knowledge graph. Validates inputs, writes to disk, and updates in-memory indices so the document is immediately searchable.", {
+        id: z
+            .string()
+            .describe('Document ID, e.g., "technology/audio-detection/pitch-detection". Lowercase, hyphens, slashes only.'),
+        title: z.string().describe("Human-readable document title"),
+        type: z
+            .enum(["summary", "detail", "decision", "reference"])
+            .describe("Document type: summary (domain/subdomain overview), detail (deep analysis), decision (choice with alternatives), reference (external tools/datasets)"),
+        domain: z
+            .string()
+            .describe(validDomains
+            ? `Top-level domain: ${validDomains.join(", ")}`
+            : "Top-level domain (any valid domain directory)"),
+        subdomain: z.string().optional().describe("Optional subdomain within the domain"),
+        tags: z.array(z.string()).describe("Searchable tags"),
+        phase: z
+            .array(z.number())
+            .describe(validPhaseIds
+            ? `Applicable phases: ${validPhaseIds.join(", ")}`
+            : "Applicable phases (positive integers)"),
+        related: z
+            .array(z.string())
+            .optional()
+            .describe("IDs of related documents for cross-referencing"),
+        children: z
+            .array(z.string())
+            .optional()
+            .describe("Child document IDs (only for summary type)"),
+        content: z.string().describe("Markdown body content (no frontmatter)"),
+        status: z
+            .enum(["active", "draft", "deprecated"])
+            .optional()
+            .describe('Document status: "active" (default), "draft" (excluded from search), "deprecated" (ranked lower)'),
+        superseded_by: z
+            .string()
+            .optional()
+            .describe("ID of document that supersedes this one (for deprecated docs)"),
+        decision_status: z
+            .enum(["proposed", "accepted", "deprecated", "superseded", "finalized"])
+            .optional()
+            .describe("Decision status (only for decision type)"),
+        alternatives_considered: z
+            .array(z.string())
+            .optional()
+            .describe("List of alternatives that were considered (only for decision type)"),
+        decision_date: z
+            .string()
+            .optional()
+            .describe("Date when decision was made, ISO format (only for decision type)"),
+    }, async ({ id, title, type, domain, subdomain, tags, phase, related, children, content, status, superseded_by, decision_status, alternatives_considered, decision_date, }) => enqueueWrite(async () => {
+        try {
+            const result = writeDocument(graph, tfidfIndex, knowledgeDir, {
+                id,
+                title,
+                type,
+                domain,
+                subdomain,
+                tags,
+                phase,
+                related,
+                children,
+                content,
+                status,
+                superseded_by,
+                decision_status,
+                alternatives_considered,
+                decision_date,
+            }, validDomains, validPhaseIds);
+            tfidfIndex = result.tfidfIndex;
+            log.info("write", { id, status: result.status });
+            return {
+                content: [{ type: "text", text: formatWriteResult(result) }],
+            };
+        }
+        catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            log.error("write_error", { id, error: message });
+            return {
+                content: [{ type: "text", text: `Error: ${message}` }],
+                isError: true,
+            };
+        }
+    }));
+    // Tool 6: knowledge_delete
+    server.tool("knowledge_delete", "Delete a document from the knowledge graph. Removes from disk and all in-memory indices. Warns about orphaned children and broken cross-references.", {
+        id: z.string().describe("Document ID to delete"),
+    }, async ({ id }) => enqueueWrite(async () => {
+        try {
+            const result = deleteDocument(graph, tfidfIndex, knowledgeDir, id);
+            tfidfIndex = result.tfidfIndex;
+            log.info("delete", { id });
+            return {
+                content: [{ type: "text", text: formatDeleteResult(result) }],
+            };
+        }
+        catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            log.error("delete_error", { id, error: message });
+            return {
+                content: [{ type: "text", text: `Error: ${message}` }],
+                isError: true,
+            };
+        }
+    }));
+    // Tool 7: knowledge_validate
+    server.tool("knowledge_validate", "Run graph integrity checks. Reports orphaned documents, broken references, circular parents, missing tags, empty summaries, stale documents, and embedding coverage.", {}, async () => {
+        const report = validateGraph(graph);
+        return {
+            content: [{ type: "text", text: formatValidationReport(report) }],
+        };
+    });
+    // Tool 8: knowledge_stats
+    server.tool("knowledge_stats", "Returns read-only metrics about the knowledge graph: document counts by type/domain/phase, tag distribution, cross-link density, most-connected documents, and embedding coverage.", {}, async () => {
+        const stats = computeStats(graph);
+        return {
+            content: [{ type: "text", text: formatStats(stats) }],
+        };
+    });
+    return { server, graph, tfidfIndex, config };
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/init.d.ts

@@ -0,0 +1 @@
+export declare function initKnowledgeDir(knowledgeDir: string): void;

package/dist/init.js

@@ -0,0 +1,65 @@
+import { mkdirSync, writeFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+const CONFIG_TEMPLATE = `# Knowledge graph configuration
+# See: https://github.com/rossng/knowledge-mcp-server#configuration
+
+# name: "my-project"
+
+# Uncomment and customize domains to enforce strict validation:
+# domains:
+#   - technology
+#   - architecture
+#   - business
+
+# Uncomment to define project phases:
+# phases:
+#   - id: 1
+#     name: "Phase 1"
+#   - id: 2
+#     name: "Phase 2"
+
+# Uncomment to add query hints for domain classification:
+# query_hints:
+#   technology: ["api", "database", "framework"]
+
+# Uncomment to define synonym expansion:
+# synonyms:
+#   ml: ["machine learning"]
+#   ai: ["artificial intelligence"]
+
+# Embedding configuration (optional, enables semantic search):
+# embeddings:
+#   provider: "voyage"
+#   model: "voyage-3-lite"
+#   api_key_env: "VOYAGE_API_KEY"
+`;
+const ROOT_SUMMARY_TEMPLATE = `---
+id: root
+title: Knowledge Root
+type: summary
+domain: root
+tags: []
+phase: []
+---
+
+Root node of the knowledge graph. Add domain directories and documents below this.
+`;
+export function initKnowledgeDir(knowledgeDir) {
+    const configPath = join(knowledgeDir, "knowledge.config.yaml");
+    if (existsSync(configPath)) {
+        console.log(`Already initialized: ${configPath} exists.`);
+        return;
+    }
+    mkdirSync(knowledgeDir, { recursive: true });
+    writeFileSync(configPath, CONFIG_TEMPLATE);
+    writeFileSync(join(knowledgeDir, "_summary.md"), ROOT_SUMMARY_TEMPLATE);
+    console.log(`Initialized knowledge directory at ${knowledgeDir}`);
+    console.log("  Created: knowledge.config.yaml");
+    console.log("  Created: _summary.md (root node)");
+    console.log("");
+    console.log("Next steps:");
+    console.log("  1. Edit knowledge.config.yaml to configure domains and phases");
+    console.log("  2. Create domain directories (e.g., mkdir knowledge/technology)");
+    console.log("  3. Add documents with YAML frontmatter (see README for format)");
+}
+//# sourceMappingURL=init.js.map

package/dist/init.js.map

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+{"version":3,"file":"init.js","sourceRoot":"","sources":["../src/init.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AAC/D,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEjC,MAAM,eAAe,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgCvB,CAAC;AAEF,MAAM,qBAAqB,GAAG;;;;;;;;;;CAU7B,CAAC;AAEF,MAAM,UAAU,gBAAgB,CAAC,YAAoB;IACnD,MAAM,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,uBAAuB,CAAC,CAAC;IAE/D,IAAI,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC3B,OAAO,CAAC,GAAG,CAAC,wBAAwB,UAAU,UAAU,CAAC,CAAC;QAC1D,OAAO;IACT,CAAC;IAED,SAAS,CAAC,YAAY,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAC7C,aAAa,CAAC,UAAU,EAAE,eAAe,CAAC,CAAC;IAC3C,aAAa,CAAC,IAAI,CAAC,YAAY,EAAE,aAAa,CAAC,EAAE,qBAAqB,CAAC,CAAC;IAExE,OAAO,CAAC,GAAG,CAAC,sCAAsC,YAAY,EAAE,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,kCAAkC,CAAC,CAAC;IAChD,OAAO,CAAC,GAAG,CAAC,oCAAoC,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAChB,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;IAC3B,OAAO,CAAC,GAAG,CAAC,iEAAiE,CAAC,CAAC;IAC/E,OAAO,CAAC,GAAG,CAAC,mEAAmE,CAAC,CAAC;IACjF,OAAO,CAAC,GAAG,CAAC,kEAAkE,CAAC,CAAC;AAClF,CAAC"}

package/dist/loader.d.ts

@@ -0,0 +1,26 @@
+export type DocumentStatus = "active" | "draft" | "deprecated";
+export interface KnowledgeDocument {
+    id: string;
+    title: string;
+    type: "summary" | "detail" | "decision" | "reference";
+    domain: string;
+    subdomain?: string;
+    tags: string[];
+    phase: number[];
+    related: string[];
+    parentId: string | null;
+    childrenIds: string[];
+    contentBody: string;
+    filePath: string;
+    wordCount: number;
+    status: DocumentStatus;
+    supersededBy?: string;
+    lastUpdated?: string;
+    decisionStatus?: "proposed" | "accepted" | "deprecated" | "superseded" | "finalized";
+    alternativesConsidered?: string[];
+    decisionDate?: string;
+}
+export declare const VALID_TYPES: readonly ["summary", "detail", "decision", "reference"];
+export declare function deriveParentId(id: string): string | null;
+export declare function collectMarkdownFiles(dir: string): string[];
+export declare function loadDocuments(knowledgeDir: string, validDomains?: string[] | null): Map<string, KnowledgeDocument>;