ralph-hero-knowledge-index 0.1.0

package/.claude-plugin/plugin.json

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+{
+  "name": "ralph-knowledge",
+  "version": "0.1.0",
+  "description": "Knowledge graph for ralph-hero: semantic search, relationship traversal, and document indexing across thoughts/ documents. Optional companion to ralph-hero.",
+  "author": {
+    "name": "Chad Dubiel",
+    "url": "https://github.com/cdubiel08"
+  },
+  "homepage": "https://github.com/cdubiel08/ralph-hero",
+  "repository": "https://github.com/cdubiel08/ralph-hero",
+  "license": "MIT",
+  "keywords": [
+    "knowledge-graph",
+    "semantic-search",
+    "obsidian",
+    "ralph-hero",
+    "document-indexing",
+    "fts5",
+    "embeddings"
+  ]
+}

package/.mcp.json

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+{
+  "mcpServers": {
+    "ralph-knowledge": {
+      "command": "npx",
+      "args": ["-y", "ralph-hero-knowledge-index@0.1.0"],
+      "cwd": "${CLAUDE_PLUGIN_ROOT}",
+      "env": {
+        "RALPH_KNOWLEDGE_DB": "${RALPH_KNOWLEDGE_DB:-knowledge.db}"
+      }
+    }
+  }
+}

package/dist/db.d.ts

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+import type { Database as DatabaseType } from "better-sqlite3";
+export interface DocumentRow {
+    id: string;
+    path: string;
+    title: string;
+    date: string | null;
+    type: string | null;
+    status: string | null;
+    githubIssue: number | null;
+    content: string;
+}
+export interface RelationshipRow {
+    sourceId: string;
+    targetId: string;
+    type: string;
+}
+export declare class KnowledgeDB {
+    readonly db: DatabaseType;
+    constructor(dbPath: string);
+    private createSchema;
+    upsertDocument(doc: DocumentRow): void;
+    getDocument(id: string): DocumentRow | undefined;
+    setTags(docId: string, tags: string[]): void;
+    getTags(docId: string): string[];
+    addRelationship(sourceId: string, targetId: string, type: string): void;
+    getRelationshipsFrom(sourceId: string): RelationshipRow[];
+    getRelationshipsTo(targetId: string): RelationshipRow[];
+    clearAll(): void;
+    close(): void;
+}

package/dist/db.js

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+import Database from "better-sqlite3";
+export class KnowledgeDB {
+    db;
+    constructor(dbPath) {
+        this.db = new Database(dbPath);
+        this.db.pragma("journal_mode = WAL");
+        this.createSchema();
+    }
+    createSchema() {
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS documents (
+        id TEXT PRIMARY KEY,
+        path TEXT NOT NULL,
+        title TEXT,
+        date TEXT,
+        type TEXT,
+        status TEXT,
+        github_issue INTEGER,
+        content TEXT
+      );
+      CREATE TABLE IF NOT EXISTS tags (
+        doc_id TEXT REFERENCES documents(id) ON DELETE CASCADE,
+        tag TEXT,
+        PRIMARY KEY (doc_id, tag)
+      );
+      CREATE TABLE IF NOT EXISTS relationships (
+        source_id TEXT REFERENCES documents(id) ON DELETE CASCADE,
+        target_id TEXT,
+        type TEXT CHECK(type IN ('builds_on', 'tensions', 'superseded_by')),
+        PRIMARY KEY (source_id, target_id, type)
+      );
+      CREATE INDEX IF NOT EXISTS idx_rel_target ON relationships(target_id, type);
+      CREATE INDEX IF NOT EXISTS idx_tags_tag ON tags(tag);
+    `);
+    }
+    upsertDocument(doc) {
+        this.db.prepare(`
+      INSERT INTO documents (id, path, title, date, type, status, github_issue, content)
+      VALUES (@id, @path, @title, @date, @type, @status, @githubIssue, @content)
+      ON CONFLICT(id) DO UPDATE SET
+        path = @path, title = @title, date = @date, type = @type,
+        status = @status, github_issue = @githubIssue, content = @content
+    `).run(doc);
+    }
+    getDocument(id) {
+        return this.db.prepare(`SELECT id, path, title, date, type, status, github_issue AS githubIssue, content FROM documents WHERE id = ?`).get(id);
+    }
+    setTags(docId, tags) {
+        this.db.prepare("DELETE FROM tags WHERE doc_id = ?").run(docId);
+        const insert = this.db.prepare("INSERT INTO tags (doc_id, tag) VALUES (?, ?)");
+        for (const tag of tags)
+            insert.run(docId, tag);
+    }
+    getTags(docId) {
+        return this.db.prepare("SELECT tag FROM tags WHERE doc_id = ? ORDER BY tag").all(docId).map(r => r.tag);
+    }
+    addRelationship(sourceId, targetId, type) {
+        this.db.prepare("INSERT OR IGNORE INTO relationships (source_id, target_id, type) VALUES (?, ?, ?)").run(sourceId, targetId, type);
+    }
+    getRelationshipsFrom(sourceId) {
+        return this.db.prepare("SELECT source_id AS sourceId, target_id AS targetId, type FROM relationships WHERE source_id = ?").all(sourceId);
+    }
+    getRelationshipsTo(targetId) {
+        return this.db.prepare("SELECT source_id AS sourceId, target_id AS targetId, type FROM relationships WHERE target_id = ?").all(targetId);
+    }
+    clearAll() {
+        this.db.exec("DELETE FROM relationships; DELETE FROM tags; DELETE FROM documents;");
+    }
+    close() {
+        this.db.close();
+    }
+}
+//# sourceMappingURL=db.js.map

package/dist/db.js.map

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package/dist/embedder.d.ts

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+import { type FeatureExtractionPipeline } from "@huggingface/transformers";
+export declare function getEmbedder(): Promise<FeatureExtractionPipeline>;
+export declare function embed(text: string): Promise<Float32Array>;
+export declare function prepareTextForEmbedding(title: string, content: string): string;

package/dist/embedder.js

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+import { pipeline, } from "@huggingface/transformers";
+const MODEL_ID = "Xenova/all-MiniLM-L6-v2";
+const MAX_CHARS = 500;
+let embedderInstance = null;
+export async function getEmbedder() {
+    if (!embedderInstance) {
+        // @ts-expect-error pipeline() overload union is too complex for TS
+        embedderInstance = (await pipeline("feature-extraction", MODEL_ID));
+    }
+    return embedderInstance;
+}
+export async function embed(text) {
+    const embedder = await getEmbedder();
+    const truncated = text.slice(0, MAX_CHARS);
+    const output = await embedder(truncated, {
+        pooling: "mean",
+        normalize: true,
+    });
+    return new Float32Array(output.data);
+}
+export function prepareTextForEmbedding(title, content) {
+    return `${title}\n${content}`.slice(0, MAX_CHARS);
+}
+//# sourceMappingURL=embedder.js.map

package/dist/embedder.js.map

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package/dist/hybrid-search.d.ts

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+import type { KnowledgeDB } from "./db.js";
+import type { FtsSearch, SearchOptions, SearchResult } from "./search.js";
+import type { VectorSearch } from "./vector-search.js";
+export type EmbedFn = (text: string) => Promise<Float32Array>;
+export declare class HybridSearch {
+    private readonly db;
+    private readonly fts;
+    private readonly vec;
+    private readonly embedFn;
+    private static readonly RRF_K;
+    constructor(db: KnowledgeDB, fts: FtsSearch, vec: VectorSearch, embedFn: EmbedFn);
+    search(query: string, options?: SearchOptions): Promise<SearchResult[]>;
+}

package/dist/hybrid-search.js

@@ -0,0 +1,85 @@
+export class HybridSearch {
+    db;
+    fts;
+    vec;
+    embedFn;
+    static RRF_K = 60;
+    constructor(db, fts, vec, embedFn) {
+        this.db = db;
+        this.fts = fts;
+        this.vec = vec;
+        this.embedFn = embedFn;
+    }
+    async search(query, options = {}) {
+        const { type, tags, includeSuperseded = false, limit = 20 } = options;
+        // Run FTS and vector search
+        const ftsResults = this.fts.search(query, {
+            includeSuperseded: true,
+            limit: limit * 2,
+        });
+        const queryEmbedding = await this.embedFn(query);
+        const vecResults = this.vec.search(queryEmbedding, limit * 2);
+        // Build RRF score map
+        const scores = new Map();
+        for (let i = 0; i < ftsResults.length; i++) {
+            const id = ftsResults[i].id;
+            const rrfScore = 1 / (HybridSearch.RRF_K + i + 1);
+            scores.set(id, (scores.get(id) ?? 0) + rrfScore);
+        }
+        for (let i = 0; i < vecResults.length; i++) {
+            const id = vecResults[i].id;
+            const rrfScore = 1 / (HybridSearch.RRF_K + i + 1);
+            scores.set(id, (scores.get(id) ?? 0) + rrfScore);
+        }
+        // Build a lookup of FTS results by id for quick access
+        const ftsById = new Map();
+        for (const r of ftsResults) {
+            ftsById.set(r.id, r);
+        }
+        // Assemble combined results
+        const combined = [];
+        for (const [id, rrfScore] of scores) {
+            const ftsHit = ftsById.get(id);
+            if (ftsHit) {
+                combined.push({ ...ftsHit, score: rrfScore });
+            }
+            else {
+                // Vector-only result: fetch document metadata from db
+                const doc = this.db.getDocument(id);
+                if (!doc)
+                    continue;
+                combined.push({
+                    id: doc.id,
+                    path: doc.path,
+                    title: doc.title,
+                    type: doc.type,
+                    status: doc.status,
+                    date: doc.date,
+                    score: rrfScore,
+                    snippet: "",
+                });
+            }
+        }
+        // Sort by RRF score descending
+        combined.sort((a, b) => b.score - a.score);
+        // Post-filter: superseded
+        let filtered = combined;
+        if (!includeSuperseded) {
+            filtered = filtered.filter((r) => r.status !== "superseded");
+        }
+        // Post-filter: type
+        if (type) {
+            filtered = filtered.filter((r) => r.type === type);
+        }
+        // Post-filter: tags
+        if (tags && tags.length > 0) {
+            const tagSet = new Set(tags);
+            filtered = filtered.filter((r) => {
+                const docTags = this.db.getTags(r.id);
+                return docTags.some((t) => tagSet.has(t));
+            });
+        }
+        return filtered.slice(0, limit);
+    }
+}
+//# sourceMappingURL=hybrid-search.js.map

package/dist/hybrid-search.js.map

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package/dist/index.d.ts

@@ -0,0 +1,14 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { KnowledgeDB } from "./db.js";
+import { FtsSearch } from "./search.js";
+import { VectorSearch } from "./vector-search.js";
+import { HybridSearch } from "./hybrid-search.js";
+import { Traverser } from "./traverse.js";
+export declare function createServer(dbPath: string): {
+    server: McpServer;
+    db: KnowledgeDB;
+    fts: FtsSearch;
+    vec: VectorSearch;
+    hybrid: HybridSearch;
+    traverser: Traverser;
+};

package/dist/index.js

@@ -0,0 +1,64 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { z } from "zod";
+import { KnowledgeDB } from "./db.js";
+import { FtsSearch } from "./search.js";
+import { VectorSearch } from "./vector-search.js";
+import { HybridSearch } from "./hybrid-search.js";
+import { Traverser } from "./traverse.js";
+import { embed } from "./embedder.js";
+export function createServer(dbPath) {
+    const server = new McpServer({ name: "ralph-hero-knowledge", version: "0.1.0" });
+    const db = new KnowledgeDB(dbPath);
+    const fts = new FtsSearch(db);
+    const vec = new VectorSearch(db);
+    const hybrid = new HybridSearch(db, fts, vec, embed);
+    const traverser = new Traverser(db);
+    server.tool("knowledge_search", "Search the knowledge base by keyword, semantic similarity, and tags. Returns ranked documents.", {
+        query: z.string().describe("Search query (keywords or natural language)"),
+        tags: z.array(z.string()).optional().describe("Filter by tags"),
+        type: z.string().optional().describe("Filter by document type (research, plan, review, idea, report)"),
+        limit: z.number().optional().describe("Max results (default: 10)"),
+        includeSuperseded: z.boolean().optional().describe("Include superseded documents (default: false)"),
+    }, async (args) => {
+        try {
+            const results = await hybrid.search(args.query, {
+                tags: args.tags,
+                type: args.type,
+                limit: args.limit ?? 10,
+                includeSuperseded: args.includeSuperseded,
+            });
+            const enriched = results.map(r => ({ ...r, tags: db.getTags(r.id) }));
+            return { content: [{ type: "text", text: JSON.stringify(enriched, null, 2) }] };
+        }
+        catch (e) {
+            return { content: [{ type: "text", text: `Error: ${e.message}` }], isError: true };
+        }
+    });
+    server.tool("knowledge_traverse", "Walk typed relationship edges (builds_on, tensions, superseded_by) from a document.", {
+        from: z.string().describe("Document ID (filename without extension)"),
+        type: z.enum(["builds_on", "tensions", "superseded_by"]).optional().describe("Filter by relationship type"),
+        depth: z.number().optional().describe("Max traversal depth (default: 3)"),
+        direction: z.enum(["outgoing", "incoming"]).optional().describe("Edge direction (default: outgoing)"),
+    }, async (args) => {
+        try {
+            const opts = { type: args.type, depth: args.depth ?? 3 };
+            const results = args.direction === "incoming"
+                ? traverser.traverseIncoming(args.from, opts)
+                : traverser.traverse(args.from, opts);
+            return { content: [{ type: "text", text: JSON.stringify(results, null, 2) }] };
+        }
+        catch (e) {
+            return { content: [{ type: "text", text: `Error: ${e.message}` }], isError: true };
+        }
+    });
+    return { server, db, fts, vec, hybrid, traverser };
+}
+const isMain = process.argv[1]?.endsWith("index.js");
+if (isMain) {
+    const dbPath = process.env.RALPH_KNOWLEDGE_DB ?? "knowledge.db";
+    const { server } = createServer(dbPath);
+    const transport = new StdioServerTransport();
+    server.connect(transport).catch(console.error);
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/parser.d.ts

@@ -0,0 +1,18 @@
+export interface Relationship {
+    sourceId: string;
+    targetId: string;
+    type: "builds_on" | "tensions" | "superseded_by";
+}
+export interface ParsedDocument {
+    id: string;
+    path: string;
+    title: string;
+    date: string | null;
+    type: string | null;
+    status: string | null;
+    githubIssue: number | null;
+    tags: string[];
+    relationships: Relationship[];
+    content: string;
+}
+export declare function parseDocument(id: string, path: string, raw: string): ParsedDocument;

package/dist/parser.js

@@ -0,0 +1,39 @@
+import { parse as parseYaml } from "yaml";
+const FRONTMATTER_RE = /^---\n([\s\S]*?)\n---/;
+const TITLE_RE = /^# (.+)$/m;
+const WIKILINK_REL_RE = /^- (builds_on|tensions):: \[\[(.+?)\]\]/gm;
+const SUPERSEDED_BY_RE = /\[\[(.+?)\]\]/;
+export function parseDocument(id, path, raw) {
+    const fmMatch = raw.match(FRONTMATTER_RE);
+    const frontmatter = fmMatch ? parseYaml(fmMatch[1]) ?? {} : {};
+    const body = fmMatch ? raw.slice(fmMatch[0].length).trim() : raw.trim();
+    const titleMatch = body.match(TITLE_RE);
+    const title = titleMatch ? titleMatch[1].trim() : id;
+    const relationships = [];
+    let match;
+    const relRe = new RegExp(WIKILINK_REL_RE.source, "gm");
+    while ((match = relRe.exec(body)) !== null) {
+        relationships.push({
+            sourceId: id,
+            targetId: match[2],
+            type: match[1],
+        });
+    }
+    const supersededBy = frontmatter.superseded_by;
+    if (typeof supersededBy === "string") {
+        const wlMatch = supersededBy.match(SUPERSEDED_BY_RE);
+        if (wlMatch) {
+            relationships.push({ sourceId: id, targetId: wlMatch[1], type: "superseded_by" });
+        }
+    }
+    const tags = Array.isArray(frontmatter.tags) ? frontmatter.tags.map(String) : [];
+    return {
+        id, path, title,
+        date: frontmatter.date ? String(frontmatter.date) : null,
+        type: frontmatter.type ?? null,
+        status: frontmatter.status ?? null,
+        githubIssue: typeof frontmatter.github_issue === "number" ? frontmatter.github_issue : null,
+        tags, relationships, content: body,
+    };
+}
+//# sourceMappingURL=parser.js.map

package/dist/parser.js.map

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

@@ -0,0 +1 @@
+export {};

package/dist/reindex.js

@@ -0,0 +1,77 @@
+import { readFileSync, readdirSync } from "node:fs";
+import { join, relative, basename } from "node:path";
+import { KnowledgeDB } from "./db.js";
+import { FtsSearch } from "./search.js";
+import { VectorSearch } from "./vector-search.js";
+import { embed, prepareTextForEmbedding } from "./embedder.js";
+import { parseDocument } from "./parser.js";
+function findMarkdownFiles(dir) {
+    const results = [];
+    function walk(d) {
+        for (const entry of readdirSync(d, { withFileTypes: true })) {
+            const fullPath = join(d, entry.name);
+            if (entry.isDirectory() && !entry.name.startsWith(".")) {
+                walk(fullPath);
+            }
+            else if (entry.isFile() && entry.name.endsWith(".md")) {
+                results.push(fullPath);
+            }
+        }
+    }
+    walk(dir);
+    return results;
+}
+async function reindex(thoughtsDir, dbPath) {
+    console.log(`Indexing ${thoughtsDir} -> ${dbPath}`);
+    const db = new KnowledgeDB(dbPath);
+    const fts = new FtsSearch(db);
+    const vec = new VectorSearch(db);
+    vec.createIndex();
+    db.clearAll();
+    vec.dropIndex();
+    vec.createIndex();
+    const files = findMarkdownFiles(thoughtsDir);
+    console.log(`Found ${files.length} markdown files`);
+    let indexed = 0;
+    for (const filePath of files) {
+        const raw = readFileSync(filePath, "utf-8");
+        const relPath = relative(join(thoughtsDir, ".."), filePath);
+        const id = basename(filePath, ".md");
+        const parsed = parseDocument(id, relPath, raw);
+        db.upsertDocument({
+            id: parsed.id,
+            path: parsed.path,
+            title: parsed.title,
+            date: parsed.date,
+            type: parsed.type,
+            status: parsed.status,
+            githubIssue: parsed.githubIssue,
+            content: parsed.content,
+        });
+        if (parsed.tags.length > 0) {
+            db.setTags(parsed.id, parsed.tags);
+        }
+        for (const rel of parsed.relationships) {
+            db.addRelationship(rel.sourceId, rel.targetId, rel.type);
+        }
+        const text = prepareTextForEmbedding(parsed.title, parsed.content);
+        try {
+            const embedding = await embed(text);
+            vec.upsertEmbedding(parsed.id, embedding);
+        }
+        catch (e) {
+            console.warn(`Failed to embed ${id}: ${e.message}`);
+        }
+        indexed++;
+        if (indexed % 50 === 0) {
+            console.log(`  ${indexed}/${files.length} indexed`);
+        }
+    }
+    fts.rebuildIndex();
+    console.log(`Done. ${indexed} documents indexed.`);
+    db.close();
+}
+const thoughtsDir = process.argv[2] ?? "../../thoughts";
+const dbPath = process.argv[3] ?? "knowledge.db";
+reindex(thoughtsDir, dbPath).catch(console.error);
+//# sourceMappingURL=reindex.js.map

package/dist/reindex.js.map

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

@@ -0,0 +1,23 @@
+import type { KnowledgeDB } from "./db.js";
+export interface SearchOptions {
+    type?: string;
+    tags?: string[];
+    includeSuperseded?: boolean;
+    limit?: number;
+}
+export interface SearchResult {
+    id: string;
+    path: string;
+    title: string;
+    type: string | null;
+    status: string | null;
+    date: string | null;
+    score: number;
+    snippet: string;
+}
+export declare class FtsSearch {
+    private readonly db;
+    constructor(db: KnowledgeDB);
+    rebuildIndex(): void;
+    search(query: string, options?: SearchOptions): SearchResult[];
+}

package/dist/search.js

@@ -0,0 +1,63 @@
+export class FtsSearch {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    rebuildIndex() {
+        this.db.db.exec(`DROP TABLE IF EXISTS documents_fts`);
+        this.db.db.exec(`
+      CREATE VIRTUAL TABLE documents_fts USING fts5(
+        title,
+        path,
+        content,
+        content='documents',
+        content_rowid='rowid'
+      )
+    `);
+        this.db.db.exec(`
+      INSERT INTO documents_fts(rowid, title, path, content)
+      SELECT rowid, title, path, content FROM documents
+    `);
+    }
+    search(query, options = {}) {
+        const { type, tags, includeSuperseded = false, limit = 20 } = options;
+        const conditions = ["documents_fts MATCH @query"];
+        const params = { query, limit };
+        if (!includeSuperseded) {
+            conditions.push("d.status IS NOT 'superseded'");
+        }
+        if (type) {
+            conditions.push("d.type = @type");
+            params.type = type;
+        }
+        let joinClause = "";
+        if (tags && tags.length > 0) {
+            joinClause = "JOIN tags t ON t.doc_id = d.id";
+            const tagPlaceholders = tags.map((_, i) => `@tag${i}`);
+            conditions.push(`t.tag IN (${tagPlaceholders.join(", ")})`);
+            tags.forEach((tag, i) => {
+                params[`tag${i}`] = tag;
+            });
+        }
+        const whereClause = conditions.join(" AND ");
+        const sql = `
+      SELECT
+        d.id,
+        d.path,
+        d.title,
+        d.type,
+        d.status,
+        d.date,
+        rank AS score,
+        snippet(documents_fts, 2, '<b>', '</b>', '...', 32) AS snippet
+      FROM documents_fts
+      JOIN documents d ON d.rowid = documents_fts.rowid
+      ${joinClause}
+      WHERE ${whereClause}
+      ORDER BY rank ASC
+      LIMIT @limit
+    `;
+        return this.db.db.prepare(sql).all(params);
+    }
+}
+//# sourceMappingURL=search.js.map

package/dist/search.js.map

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package/dist/traverse.d.ts

@@ -0,0 +1,22 @@
+import type { KnowledgeDB } from "./db.js";
+export interface TraverseOptions {
+    type?: string;
+    depth?: number;
+}
+export interface TraverseResult {
+    sourceId: string;
+    targetId: string;
+    type: string;
+    depth: number;
+    doc: {
+        title: string;
+        status: string | null;
+        date: string | null;
+    } | null;
+}
+export declare class Traverser {
+    private readonly db;
+    constructor(db: KnowledgeDB);
+    traverse(fromId: string, options?: TraverseOptions): TraverseResult[];
+    traverseIncoming(toId: string, options?: TraverseOptions): TraverseResult[];
+}