@goondocks/myco 0.1.0

package/dist/src/mcp/server.js

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+import { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { createRequire } from 'node:module';
+function getPackageVersion() {
+    try {
+        const require = createRequire(import.meta.url);
+        return require('../../../package.json').version;
+    }
+    catch {
+        return '0.0.0';
+    }
+}
+import { ListToolsRequestSchema, CallToolRequestSchema, } from '@modelcontextprotocol/sdk/types.js';
+import { MycoIndex } from '../index/sqlite.js';
+import { initFts } from '../index/fts.js';
+import { handleMycoSearch } from './tools/search.js';
+import { handleMycoRecall } from './tools/recall.js';
+import { handleMycoRemember } from './tools/remember.js';
+import { handleMycoPlans } from './tools/plans.js';
+import { handleMycoSessions } from './tools/sessions.js';
+import { handleMycoTeam } from './tools/team.js';
+import { handleMycoGraph, handleMycoOrphans } from './tools/graph.js';
+import { handleMycoLogs } from './tools/logs.js';
+import { handleMycoSupersede } from './tools/supersede.js';
+import { handleMycoConsolidate } from './tools/consolidate.js';
+import { resolveVaultDir } from '../vault/resolve.js';
+import { loadConfig } from '../config/loader.js';
+import { createEmbeddingProvider } from '../intelligence/llm.js';
+import { VectorIndex } from '../index/vectors.js';
+import { generateEmbedding } from '../intelligence/embeddings.js';
+import { PlanFrontmatterSchema } from '../vault/types.js';
+import { EMBEDDING_INPUT_LIMIT } from '../constants.js';
+import { fileURLToPath } from 'node:url';
+import path from 'node:path';
+import fs from 'node:fs';
+// Common observation types shown as hints in the tool schema; the vault accepts any string
+const OBSERVATION_TYPES = ['gotcha', 'bug_fix', 'decision', 'discovery', 'trade_off', 'cross-cutting'];
+const PLAN_STATUSES = [...PlanFrontmatterSchema.shape.status._def.innerType.options, 'all'];
+const TOOL_DEFINITIONS = [
+    {
+        name: 'myco_search',
+        description: 'Combined semantic + full-text search across the vault',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                query: { type: 'string', description: 'Search query' },
+                type: { type: 'string', enum: ['session', 'plan', 'memory', 'all'] },
+                limit: { type: 'number', default: 10 },
+            },
+            required: ['query'],
+        },
+    },
+    {
+        name: 'myco_recall',
+        description: 'Automatic context retrieval based on current work',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                branch: { type: 'string' },
+                files: { type: 'array', items: { type: 'string' } },
+            },
+        },
+    },
+    {
+        name: 'myco_remember',
+        description: 'Store an observation as a memory note',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                content: { type: 'string' },
+                type: { type: 'string', enum: OBSERVATION_TYPES },
+                tags: { type: 'array', items: { type: 'string' } },
+                related_plan: { type: 'string' },
+            },
+            required: ['content', 'type'],
+        },
+    },
+    {
+        name: 'myco_plans',
+        description: 'List active plans with progress',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                status: { type: 'string', enum: PLAN_STATUSES },
+                id: { type: 'string' },
+            },
+        },
+    },
+    {
+        name: 'myco_sessions',
+        description: 'Query session history with filters',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                plan: { type: 'string' },
+                branch: { type: 'string' },
+                user: { type: 'string' },
+                since: { type: 'string' },
+                limit: { type: 'number' },
+            },
+        },
+    },
+    {
+        name: 'myco_team',
+        description: 'Teammate activity on same files or plan',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                files: { type: 'array', items: { type: 'string' } },
+                plan: { type: 'string' },
+                since: { type: 'string' },
+            },
+        },
+    },
+    {
+        name: 'myco_graph',
+        description: 'Traverse vault connections via wikilinks — find related notes by following links',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                note_id: { type: 'string', description: 'Note ID to start from (e.g. "session-abc123")' },
+                direction: { type: 'string', enum: ['incoming', 'outgoing', 'both'], description: 'Link direction (default: both)' },
+                depth: { type: 'number', description: 'Traversal depth 1-3 (default: 1)' },
+            },
+            required: ['note_id'],
+        },
+    },
+    {
+        name: 'myco_orphans',
+        description: 'Find vault notes with no incoming or outgoing wikilinks',
+        inputSchema: {
+            type: 'object',
+            properties: {},
+        },
+    },
+    {
+        name: 'myco_logs',
+        description: 'View daemon and MCP activity logs with filtering — useful for debugging and auditing',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                limit: { type: 'number', description: 'Max entries to return (default 50)' },
+                level: { type: 'string', enum: ['debug', 'info', 'warn', 'error'], description: 'Minimum log level' },
+                component: { type: 'string', description: 'Filter by component (daemon, processor, hooks, lifecycle, embeddings, mcp, lineage, watcher)' },
+                since: { type: 'string', description: 'ISO timestamp — entries after this time' },
+                until: { type: 'string', description: 'ISO timestamp — entries before this time' },
+            },
+        },
+    },
+    {
+        name: 'myco_supersede',
+        description: 'Mark a memory as superseded by a newer one — use when an older observation is outdated, incorrect, or replaced by better understanding',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                old_memory_id: { type: 'string', description: 'ID of the memory to supersede' },
+                new_memory_id: { type: 'string', description: 'ID of the memory that replaces it' },
+                reason: { type: 'string', description: 'Why this memory is being superseded' },
+            },
+            required: ['old_memory_id', 'new_memory_id'],
+        },
+    },
+    {
+        name: 'myco_consolidate',
+        description: 'Merge multiple related memories into a single wisdom note — use when several observations describe aspects of the same insight or pattern',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                source_memory_ids: { type: 'array', items: { type: 'string' }, description: 'IDs of memories to consolidate' },
+                consolidated_content: { type: 'string', description: 'The merged, comprehensive content for the wisdom note' },
+                observation_type: { type: 'string', enum: OBSERVATION_TYPES, description: 'Type for the consolidated note' },
+                tags: { type: 'array', items: { type: 'string' }, description: 'Tags for the wisdom note' },
+            },
+            required: ['source_memory_ids', 'consolidated_content', 'observation_type'],
+        },
+    },
+];
+export function createMycoServer(config) {
+    const server = new Server({ name: 'myco', version: getPackageVersion() }, { capabilities: { tools: {} } });
+    const dbPath = path.join(config.vaultDir, 'index.db');
+    let index = null;
+    function getIndex() {
+        if (!index) {
+            index = new MycoIndex(dbPath);
+            initFts(index);
+        }
+        return index;
+    }
+    /** Embed a note and upsert into vector index (fire-and-forget). */
+    function embedNote(noteId, text, metadata) {
+        if (!config.embeddingProvider || !config.vectorIndex || !text)
+            return;
+        generateEmbedding(config.embeddingProvider, text.slice(0, EMBEDDING_INPUT_LIMIT))
+            .then((emb) => config.vectorIndex.upsert(noteId, emb.embedding, metadata))
+            .catch(() => { });
+    }
+    server.setRequestHandler(ListToolsRequestSchema, async () => ({
+        tools: TOOL_DEFINITIONS,
+    }));
+    /** Log MCP tool activity to vault logs for auditability. */
+    function logActivity(tool, detail) {
+        const logDir = path.join(config.vaultDir, 'logs');
+        try {
+            fs.mkdirSync(logDir, { recursive: true });
+            const entry = JSON.stringify({ timestamp: new Date().toISOString(), component: 'mcp', level: 'info', tool, ...detail }) + '\n';
+            fs.appendFileSync(path.join(logDir, 'mcp.jsonl'), entry);
+        }
+        catch { /* logging failure is non-fatal */ }
+    }
+    server.setRequestHandler(CallToolRequestSchema, async (request) => {
+        const { name, arguments: args = {} } = request.params;
+        const idx = getIndex();
+        const input = args;
+        switch (name) {
+            case 'myco_search':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoSearch(idx, input, config.vectorIndex, config.embeddingProvider)) }] };
+            case 'myco_recall':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoRecall(idx, input)) }] };
+            case 'myco_remember': {
+                const result = await handleMycoRemember(config.vaultDir, idx, input);
+                embedNote(result.id, String(input.content), { type: 'memory', observation_type: String(input.type ?? ''), importance: 'high' });
+                logActivity('myco_remember', { id: result.id, observation_type: input.type, path: result.note_path });
+                return { content: [{ type: 'text', text: JSON.stringify(result) }] };
+            }
+            case 'myco_plans':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoPlans(idx, input)) }] };
+            case 'myco_sessions':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoSessions(idx, input)) }] };
+            case 'myco_team':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoTeam(idx, input, config.teamUser)) }] };
+            case 'myco_graph':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoGraph(idx, input)) }] };
+            case 'myco_orphans':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoOrphans(idx)) }] };
+            case 'myco_logs':
+                return { content: [{ type: 'text', text: JSON.stringify(await handleMycoLogs(config.vaultDir, input)) }] };
+            case 'myco_supersede': {
+                const result = await handleMycoSupersede(config.vaultDir, idx, input);
+                if (result.status === 'superseded' && config.vectorIndex) {
+                    config.vectorIndex.delete(result.old_memory);
+                }
+                logActivity('myco_supersede', { old: result.old_memory, new: result.new_memory, status: result.status });
+                return { content: [{ type: 'text', text: JSON.stringify(result) }] };
+            }
+            case 'myco_consolidate': {
+                const result = await handleMycoConsolidate(config.vaultDir, idx, input);
+                embedNote(result.wisdom_id, String(input.consolidated_content), { type: 'memory', observation_type: String(input.observation_type ?? ''), importance: 'high' });
+                if (config.vectorIndex && Array.isArray(input.source_memory_ids)) {
+                    for (const id of input.source_memory_ids) {
+                        config.vectorIndex.delete(id);
+                    }
+                }
+                logActivity('myco_consolidate', { wisdom_id: result.wisdom_id, sources: input.source_memory_ids, archived: result.sources_archived });
+                return { content: [{ type: 'text', text: JSON.stringify(result) }] };
+            }
+            default:
+                throw new Error(`Unknown tool: ${name}`);
+        }
+    });
+    return {
+        name: 'myco',
+        getRegisteredTools() {
+            return TOOL_DEFINITIONS.map((t) => t.name);
+        },
+        async start() {
+            const transport = new StdioServerTransport();
+            await server.connect(transport);
+        },
+    };
+}
+// Entry point — invoked by .mcp.json: node dist/src/mcp/server.js
+const __filename = fileURLToPath(import.meta.url);
+if (process.argv[1] === __filename) {
+    main().catch((err) => {
+        process.stderr.write(`[myco-mcp] Fatal: ${err.message}\n`);
+        process.exit(1);
+    });
+}
+async function main() {
+    const vaultDir = resolveVaultDir();
+    const config = fs.existsSync(path.join(vaultDir, 'myco.yaml'))
+        ? loadConfig(vaultDir)
+        : undefined;
+    // Initialize embedding provider + vector index (same as daemon does)
+    let embeddingProvider;
+    let vectorIndex;
+    if (config) {
+        try {
+            embeddingProvider = createEmbeddingProvider(config.intelligence.embedding);
+            const testEmbed = await embeddingProvider.embed('test');
+            vectorIndex = new VectorIndex(path.join(vaultDir, 'vectors.db'), testEmbed.dimensions);
+        }
+        catch {
+            // Embedding unavailable — MCP tools fall back to FTS only
+        }
+    }
+    const server = createMycoServer({
+        vaultDir,
+        teamUser: config?.team?.user,
+        embeddingProvider,
+        vectorIndex,
+    });
+    await server.start();
+}
+//# sourceMappingURL=server.js.map

package/dist/src/mcp/server.js.map

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package/dist/src/mcp/tools/consolidate.d.ts

@@ -0,0 +1,15 @@
+import type { MycoIndex } from '../../index/sqlite.js';
+interface ConsolidateInput {
+    source_memory_ids: string[];
+    consolidated_content: string;
+    observation_type: string;
+    tags?: string[];
+}
+interface ConsolidateResult {
+    wisdom_id: string;
+    wisdom_path: string;
+    sources_archived: number;
+}
+export declare function handleMycoConsolidate(vaultDir: string, index: MycoIndex, input: ConsolidateInput): Promise<ConsolidateResult>;
+export {};
+//# sourceMappingURL=consolidate.d.ts.map

package/dist/src/mcp/tools/consolidate.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/mcp/tools/consolidate.js

@@ -0,0 +1,49 @@
+import { VaultWriter } from '../../vault/writer.js';
+import { indexNote } from '../../index/rebuild.js';
+import { randomBytes } from 'node:crypto';
+import fs from 'node:fs';
+import path from 'node:path';
+export async function handleMycoConsolidate(vaultDir, index, input) {
+    const writer = new VaultWriter(vaultDir);
+    const wisdomId = `${input.observation_type}-wisdom-${randomBytes(4).toString('hex')}`;
+    // Build the wisdom note content with source links for Obsidian graph
+    const sourceLinks = input.source_memory_ids.map((id) => `- [[${id}]]`).join('\n');
+    const fullContent = `${input.consolidated_content}\n\n## Sources\n\nConsolidated from:\n${sourceLinks}`;
+    // Create the consolidated wisdom note
+    const wisdomPath = writer.writeMemory({
+        id: wisdomId,
+        observation_type: input.observation_type,
+        tags: [...(input.tags ?? []), 'wisdom', 'consolidated'],
+        content: fullContent,
+    });
+    // Add consolidated_from to the new note's frontmatter
+    writer.updateNoteFrontmatter(wisdomPath, {
+        consolidated_from: input.source_memory_ids,
+    }, true);
+    // Mark each source memory as superseded by the wisdom note
+    let archived = 0;
+    for (const sourceId of input.source_memory_ids) {
+        const notes = index.queryByIds([sourceId]);
+        if (notes.length > 0) {
+            const notePath = notes[0].path;
+            // Update frontmatter
+            writer.updateNoteFrontmatter(notePath, {
+                status: 'superseded',
+                superseded_by: wisdomId,
+            }, true);
+            // Append supersession notice with wikilink to body
+            const fullPath = path.join(vaultDir, notePath);
+            const content = fs.readFileSync(fullPath, 'utf-8');
+            if (!content.includes('Superseded by::')) {
+                const notice = `\n\n> [!warning] Consolidated\n> This observation has been consolidated into a wisdom note.\n\nSuperseded by:: [[${wisdomId}]]`;
+                fs.writeFileSync(fullPath, content.trimEnd() + notice + '\n', 'utf-8');
+            }
+            indexNote(index, vaultDir, notePath);
+            archived++;
+        }
+    }
+    // Index the new wisdom note
+    indexNote(index, vaultDir, wisdomPath);
+    return { wisdom_id: wisdomId, wisdom_path: wisdomPath, sources_archived: archived };
+}
+//# sourceMappingURL=consolidate.js.map

package/dist/src/mcp/tools/consolidate.js.map

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

@@ -0,0 +1,30 @@
+import type { MycoIndex } from '../../index/sqlite.js';
+interface GraphInput {
+    note_id: string;
+    direction?: 'incoming' | 'outgoing' | 'both';
+    depth?: number;
+}
+interface GraphLink {
+    source: string;
+    target: string;
+    source_type: string;
+    target_type: string;
+    source_title: string;
+    target_title: string;
+}
+interface GraphResult {
+    note_id: string;
+    links: GraphLink[];
+}
+export declare function handleMycoGraph(index: MycoIndex, input: GraphInput): Promise<GraphResult>;
+interface OrphansResult {
+    orphans: Array<{
+        id: string;
+        type: string;
+        title: string;
+        path: string;
+    }>;
+}
+export declare function handleMycoOrphans(index: MycoIndex): Promise<OrphansResult>;
+export {};
+//# sourceMappingURL=graph.d.ts.map

package/dist/src/mcp/tools/graph.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/mcp/tools/graph.js

@@ -0,0 +1,106 @@
+const WIKILINK_RE = /\[\[([^\]|]+)(?:\|[^\]]+)?\]\]/g;
+function extractWikilinks(content) {
+    const links = [];
+    let match;
+    while ((match = WIKILINK_RE.exec(content)) !== null) {
+        links.push(match[1]);
+    }
+    return links;
+}
+function findNoteById(index, noteId) {
+    const results = index.query({ id: noteId, limit: 1 });
+    return results[0] ?? null;
+}
+export async function handleMycoGraph(index, input) {
+    const direction = input.direction ?? 'both';
+    const depth = Math.min(input.depth ?? 1, 3);
+    const visited = new Set();
+    const allLinks = [];
+    function traverse(noteId, currentDepth) {
+        if (currentDepth > depth || visited.has(noteId))
+            return;
+        visited.add(noteId);
+        const note = findNoteById(index, noteId);
+        // Outgoing: wikilinks in this note's content
+        if (direction === 'outgoing' || direction === 'both') {
+            if (note) {
+                const targets = extractWikilinks(note.content);
+                for (const target of targets) {
+                    const targetNote = findNoteById(index, target);
+                    allLinks.push({
+                        source: noteId,
+                        target,
+                        source_type: note.type,
+                        target_type: targetNote?.type ?? 'unknown',
+                        source_title: note.title,
+                        target_title: targetNote?.title ?? target,
+                    });
+                    if (currentDepth < depth)
+                        traverse(target, currentDepth + 1);
+                }
+            }
+        }
+        // Incoming: other notes whose content links to this note
+        if (direction === 'incoming' || direction === 'both') {
+            const allNotes = index.query({ limit: 500 });
+            for (const n of allNotes) {
+                if (n.id === noteId)
+                    continue;
+                const links = extractWikilinks(n.content);
+                if (links.includes(noteId)) {
+                    allLinks.push({
+                        source: n.id,
+                        target: noteId,
+                        source_type: n.type,
+                        target_type: note?.type ?? 'unknown',
+                        source_title: n.title,
+                        target_title: note?.title ?? noteId,
+                    });
+                    if (currentDepth < depth)
+                        traverse(n.id, currentDepth + 1);
+                }
+            }
+        }
+    }
+    traverse(input.note_id, 1);
+    // Deduplicate links
+    const seen = new Set();
+    const unique = allLinks.filter((link) => {
+        const key = `${link.source}->${link.target}`;
+        if (seen.has(key))
+            return false;
+        seen.add(key);
+        return true;
+    });
+    return { note_id: input.note_id, links: unique };
+}
+export async function handleMycoOrphans(index) {
+    const allNotes = index.query({ limit: 1000 });
+    // Build maps of all links
+    const hasOutgoing = new Set();
+    const isLinkedTo = new Set();
+    for (const note of allNotes) {
+        const links = extractWikilinks(note.content);
+        if (links.length > 0)
+            hasOutgoing.add(note.id);
+        for (const target of links) {
+            isLinkedTo.add(target);
+        }
+        // Also check frontmatter session/plan refs
+        const fm = note.frontmatter;
+        if (fm.session && typeof fm.session === 'string') {
+            isLinkedTo.add(fm.session);
+        }
+        if (fm.plan && typeof fm.plan === 'string') {
+            isLinkedTo.add(fm.plan);
+        }
+    }
+    const orphans = allNotes.filter((note) => !hasOutgoing.has(note.id) && !isLinkedTo.has(note.id)).map((note) => ({
+        id: note.id,
+        type: note.type,
+        title: note.title,
+        path: note.path,
+    }));
+    return { orphans };
+}
+//# sourceMappingURL=graph.js.map

package/dist/src/mcp/tools/graph.js.map

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package/dist/src/mcp/tools/logs.d.ts

@@ -0,0 +1,3 @@
+import type { LogQuery, LogQueryResult } from '../../logs/reader.js';
+export declare function handleMycoLogs(vaultDir: string, input: LogQuery): Promise<LogQueryResult>;
+//# sourceMappingURL=logs.d.ts.map

package/dist/src/mcp/tools/logs.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/mcp/tools/logs.js

@@ -0,0 +1,7 @@
+import { queryLogs } from '../../logs/reader.js';
+import path from 'node:path';
+export async function handleMycoLogs(vaultDir, input) {
+    const logDir = path.join(vaultDir, 'logs');
+    return queryLogs(logDir, input);
+}
+//# sourceMappingURL=logs.js.map

package/dist/src/mcp/tools/logs.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"logs.js","sourceRoot":"","sources":["../../../../src/mcp/tools/logs.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AAEjD,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,QAAgB,EAChB,KAAe;IAEf,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAC3C,OAAO,SAAS,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;AAClC,CAAC"}

package/dist/src/mcp/tools/plans.d.ts

@@ -0,0 +1,23 @@
+import type { MycoIndex } from '../../index/sqlite.js';
+interface PlansInput {
+    status?: 'active' | 'in_progress' | 'completed' | 'abandoned' | 'all';
+    id?: string;
+}
+interface PlanSummary {
+    id: string;
+    title: string;
+    status: string;
+    progress: string;
+    tags: string[];
+}
+interface PlanDetail extends PlanSummary {
+    content: string;
+    sessions: Array<{
+        id: string;
+        title: string;
+        started: string;
+    }>;
+}
+export declare function handleMycoPlans(index: MycoIndex, input: PlansInput): Promise<PlanSummary[] | PlanDetail>;
+export {};
+//# sourceMappingURL=plans.d.ts.map

package/dist/src/mcp/tools/plans.d.ts.map

@@ -0,0 +1 @@
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