@goondocks/myco 0.1.0

package/dist/src/intelligence/ollama.js

@@ -0,0 +1,64 @@
+import { CHARS_PER_TOKEN, LLM_REQUEST_TIMEOUT_MS, EMBEDDING_REQUEST_TIMEOUT_MS, DAEMON_CLIENT_TIMEOUT_MS } from '../constants.js';
+export class OllamaBackend {
+    name = 'ollama';
+    baseUrl;
+    model;
+    contextWindow;
+    defaultMaxTokens;
+    constructor(config) {
+        this.baseUrl = config?.base_url ?? 'http://localhost:11434';
+        this.model = config?.model ?? config?.summary_model ?? 'llama3.2';
+        this.contextWindow = config?.context_window ?? 8192;
+        this.defaultMaxTokens = config?.max_tokens ?? 1024;
+    }
+    async summarize(prompt, opts) {
+        const maxTokens = opts?.maxTokens ?? this.defaultMaxTokens;
+        const promptTokens = Math.ceil(prompt.length / CHARS_PER_TOKEN);
+        const numCtx = Math.max(promptTokens + maxTokens, this.contextWindow);
+        const response = await fetch(`${this.baseUrl}/api/generate`, {
+            method: 'POST',
+            headers: { 'Content-Type': 'application/json' },
+            body: JSON.stringify({
+                model: this.model,
+                prompt,
+                stream: false,
+                options: { num_ctx: numCtx },
+            }),
+            signal: AbortSignal.timeout(LLM_REQUEST_TIMEOUT_MS),
+        });
+        if (!response.ok) {
+            throw new Error(`Ollama summarize failed: ${response.status} ${response.statusText}`);
+        }
+        const data = await response.json();
+        return { text: data.response, model: data.model };
+    }
+    async embed(text) {
+        const response = await fetch(`${this.baseUrl}/api/embed`, {
+            method: 'POST',
+            headers: { 'Content-Type': 'application/json' },
+            body: JSON.stringify({
+                model: this.model,
+                input: text,
+            }),
+            signal: AbortSignal.timeout(EMBEDDING_REQUEST_TIMEOUT_MS),
+        });
+        if (!response.ok) {
+            throw new Error(`Ollama embed failed: ${response.status} ${response.statusText}`);
+        }
+        const data = await response.json();
+        const embedding = data.embeddings[0];
+        return { embedding, model: data.model, dimensions: embedding.length };
+    }
+    async isAvailable() {
+        try {
+            const response = await fetch(`${this.baseUrl}/api/tags`, {
+                signal: AbortSignal.timeout(DAEMON_CLIENT_TIMEOUT_MS),
+            });
+            return response.ok;
+        }
+        catch {
+            return false;
+        }
+    }
+}
+//# sourceMappingURL=ollama.js.map

package/dist/src/intelligence/ollama.js.map

@@ -0,0 +1 @@
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package/dist/src/intelligence/response.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Clean LLM response text before parsing.
+ *
+ * Reasoning models (DeepSeek, Qwen, GLM, etc.) embed chain-of-thought
+ * in the response using special tags. These must be stripped before
+ * JSON parsing or value extraction.
+ */
+/**
+ * Strip reasoning/chain-of-thought tokens from LLM response text.
+ * Returns the final answer without the thinking process.
+ */
+export declare function stripReasoningTokens(text: string): string;
+/**
+ * Extract JSON from an LLM response that may contain markdown fences,
+ * reasoning tokens, or other wrapper text.
+ *
+ * Tries in order:
+ * 1. Strip reasoning tokens
+ * 2. Extract from ```json ... ``` code fences
+ * 3. Find bare {...} JSON object
+ * 4. Parse the cleaned text directly
+ */
+export declare function extractJson(text: string): unknown;
+/**
+ * Extract a numeric value from an LLM response that may contain
+ * reasoning tokens or extra text around the number.
+ */
+export declare function extractNumber(text: string): number;
+//# sourceMappingURL=response.d.ts.map

package/dist/src/intelligence/response.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/intelligence/response.js

@@ -0,0 +1,71 @@
+/**
+ * Clean LLM response text before parsing.
+ *
+ * Reasoning models (DeepSeek, Qwen, GLM, etc.) embed chain-of-thought
+ * in the response using special tags. These must be stripped before
+ * JSON parsing or value extraction.
+ */
+// Patterns for reasoning model chain-of-thought tokens.
+// Order matters: most specific patterns first.
+const REASONING_PATTERNS = [
+    // <think>...</think>answer  (DeepSeek, Qwen, GLM, many others)
+    /<think>[\s\S]*?<\/think>\s*/gi,
+    // Implicit opening: reasoning...</think>answer  (GLM-4.7 observed)
+    /^[\s\S]*?<\/think>\s*/i,
+    // <reasoning>...</reasoning>answer
+    /<reasoning>[\s\S]*?<\/reasoning>\s*/gi,
+    // <|thinking|>...<|/thinking|>answer
+    /<\|thinking\|>[\s\S]*?<\|\/thinking\|>\s*/gi,
+];
+/**
+ * Strip reasoning/chain-of-thought tokens from LLM response text.
+ * Returns the final answer without the thinking process.
+ */
+export function stripReasoningTokens(text) {
+    if (!text)
+        return text;
+    for (const pattern of REASONING_PATTERNS) {
+        const stripped = text.replace(pattern, '').trim();
+        if (stripped && stripped !== text.trim()) {
+            return stripped;
+        }
+    }
+    return text;
+}
+/**
+ * Extract JSON from an LLM response that may contain markdown fences,
+ * reasoning tokens, or other wrapper text.
+ *
+ * Tries in order:
+ * 1. Strip reasoning tokens
+ * 2. Extract from ```json ... ``` code fences
+ * 3. Find bare {...} JSON object
+ * 4. Parse the cleaned text directly
+ */
+export function extractJson(text) {
+    const cleaned = stripReasoningTokens(text);
+    // Try code fence extraction
+    const fenceMatch = cleaned.match(/```(?:json)?\s*\n?([\s\S]*?)\n?```/);
+    if (fenceMatch) {
+        return JSON.parse(fenceMatch[1].trim());
+    }
+    // Try bare JSON object
+    const objectMatch = cleaned.match(/\{[\s\S]*\}/);
+    if (objectMatch) {
+        return JSON.parse(objectMatch[0]);
+    }
+    // Try direct parse
+    return JSON.parse(cleaned);
+}
+/**
+ * Extract a numeric value from an LLM response that may contain
+ * reasoning tokens or extra text around the number.
+ */
+export function extractNumber(text) {
+    const cleaned = stripReasoningTokens(text).trim();
+    const match = cleaned.match(/(\d+\.?\d*)/);
+    if (match)
+        return parseFloat(match[1]);
+    return parseFloat(cleaned);
+}
+//# sourceMappingURL=response.js.map

package/dist/src/intelligence/response.js.map

@@ -0,0 +1 @@
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package/dist/src/intelligence/service.d.ts

@@ -0,0 +1,18 @@
+interface ServiceStatus {
+    running: boolean;
+    pid: number | null;
+    uptime: number | null;
+}
+export declare function getServicePidPath(vaultDir: string): string;
+export declare function isServiceRunning(vaultDir: string): boolean;
+export declare function writeServicePid(vaultDir: string): void;
+export declare function removeServicePid(vaultDir: string): void;
+export declare function getServiceStatus(vaultDir: string): ServiceStatus;
+export interface IdleShutdownHandle {
+    timer: NodeJS.Timeout;
+    refresh(): void;
+    stop(): void;
+}
+export declare function setupIdleShutdown(vaultDir: string, timeoutMs?: number): IdleShutdownHandle;
+export {};
+//# sourceMappingURL=service.d.ts.map

package/dist/src/intelligence/service.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/intelligence/service.js

@@ -0,0 +1,66 @@
+import fs from 'node:fs';
+import path from 'node:path';
+const IDLE_TIMEOUT_MS = 5 * 60 * 1000; // 5 minutes
+export function getServicePidPath(vaultDir) {
+    return path.join(vaultDir, 'service.pid');
+}
+export function isServiceRunning(vaultDir) {
+    const pidPath = getServicePidPath(vaultDir);
+    if (!fs.existsSync(pidPath))
+        return false;
+    const pid = parseInt(fs.readFileSync(pidPath, 'utf-8').trim(), 10);
+    if (isNaN(pid))
+        return false;
+    try {
+        // Signal 0 checks if process exists without killing it
+        process.kill(pid, 0);
+        return true;
+    }
+    catch {
+        // Process doesn't exist — clean up stale PID file
+        fs.unlinkSync(pidPath);
+        return false;
+    }
+}
+export function writeServicePid(vaultDir) {
+    const pidPath = getServicePidPath(vaultDir);
+    fs.writeFileSync(pidPath, String(process.pid));
+}
+export function removeServicePid(vaultDir) {
+    const pidPath = getServicePidPath(vaultDir);
+    if (fs.existsSync(pidPath)) {
+        fs.unlinkSync(pidPath);
+    }
+}
+export function getServiceStatus(vaultDir) {
+    const pidPath = getServicePidPath(vaultDir);
+    if (!fs.existsSync(pidPath)) {
+        return { running: false, pid: null, uptime: null };
+    }
+    const pid = parseInt(fs.readFileSync(pidPath, 'utf-8').trim(), 10);
+    const running = isServiceRunning(vaultDir);
+    return {
+        running,
+        pid: running ? pid : null,
+        uptime: running ? Date.now() - fs.statSync(pidPath).mtimeMs : null,
+    };
+}
+export function setupIdleShutdown(vaultDir, timeoutMs = IDLE_TIMEOUT_MS) {
+    let lastActivity = Date.now();
+    const timer = setInterval(() => {
+        if (Date.now() - lastActivity > timeoutMs) {
+            removeServicePid(vaultDir);
+            process.exit(0);
+        }
+    }, 30_000); // Check every 30s
+    return {
+        timer,
+        refresh() {
+            lastActivity = Date.now();
+        },
+        stop() {
+            clearInterval(timer);
+        },
+    };
+}
+//# sourceMappingURL=service.js.map

package/dist/src/intelligence/service.js.map

@@ -0,0 +1 @@
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package/dist/src/logs/format.d.ts

@@ -0,0 +1,6 @@
+import type { LogEntry } from '../daemon/logger.js';
+export declare function formatLogLine(entry: LogEntry): string;
+export declare function formatLocalTime(iso: string): string;
+export declare function parseIntFlag(args: string[], long: string, short?: string): number | undefined;
+export declare function parseStringFlag(args: string[], long: string, short?: string): string | undefined;
+//# sourceMappingURL=format.d.ts.map

package/dist/src/logs/format.d.ts.map

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

@@ -0,0 +1,46 @@
+/** Max display length for extra field values in pretty-printed output. */
+const LOG_VALUE_MAX_DISPLAY = 80;
+/** Core fields that are handled positionally, not as extras. */
+const CORE_FIELDS = ['timestamp', 'level', 'component', 'message'];
+export function formatLogLine(entry) {
+    const time = formatLocalTime(entry.timestamp);
+    const lvl = entry.level.toUpperCase().padEnd(5);
+    const comp = `[${entry.component}]`.padEnd(14);
+    const extras = [];
+    for (const [key, value] of Object.entries(entry)) {
+        if (CORE_FIELDS.includes(key))
+            continue;
+        const str = String(value);
+        const display = str.length > LOG_VALUE_MAX_DISPLAY
+            ? str.slice(0, LOG_VALUE_MAX_DISPLAY) + '...'
+            : str;
+        extras.push(`${key}=${display}`);
+    }
+    const extraStr = extras.length > 0 ? '  ' + extras.join(' ') : '';
+    return `${time} ${lvl} ${comp} ${entry.message}${extraStr}`;
+}
+export function formatLocalTime(iso) {
+    const d = new Date(iso);
+    const hh = String(d.getHours()).padStart(2, '0');
+    const mm = String(d.getMinutes()).padStart(2, '0');
+    const ss = String(d.getSeconds()).padStart(2, '0');
+    return `${hh}:${mm}:${ss}`;
+}
+export function parseIntFlag(args, long, short) {
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === long || (short && args[i] === short)) {
+            const val = parseInt(args[i + 1], 10);
+            return isNaN(val) ? undefined : val;
+        }
+    }
+    return undefined;
+}
+export function parseStringFlag(args, long, short) {
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === long || (short && args[i] === short)) {
+            return args[i + 1];
+        }
+    }
+    return undefined;
+}
+//# sourceMappingURL=format.js.map

package/dist/src/logs/format.js.map

@@ -0,0 +1 @@
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package/dist/src/logs/reader.d.ts

@@ -0,0 +1,28 @@
+import type { LogEntry } from '../daemon/logger.js';
+import { LEVEL_ORDER } from '../daemon/logger.js';
+import type { LogLevel } from '../daemon/logger.js';
+export { LEVEL_ORDER };
+export type { LogEntry, LogLevel };
+export interface LogQuery {
+    limit?: number;
+    level?: LogLevel;
+    component?: string;
+    since?: string;
+    until?: string;
+}
+export interface LogQueryResult {
+    entries: LogEntry[];
+    total: number;
+    truncated: boolean;
+}
+/** Default number of entries returned when no limit is specified. */
+export declare const DEFAULT_LOG_TAIL = 50;
+/**
+ * Query parsed log entries from all JSONL log files on disk.
+ * Reads both daemon logs and MCP activity logs.
+ * Returns the last N matching entries (tail behavior).
+ */
+export declare function queryLogs(logDir: string, query?: LogQuery): LogQueryResult;
+/** Test whether a single entry matches the query filters. */
+export declare function matchesFilter(entry: LogEntry, query: LogQuery): boolean;
+//# sourceMappingURL=reader.d.ts.map

package/dist/src/logs/reader.d.ts.map

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

@@ -0,0 +1,106 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { LEVEL_ORDER } from '../daemon/logger.js';
+export { LEVEL_ORDER };
+/** Default number of entries returned when no limit is specified. */
+export const DEFAULT_LOG_TAIL = 50;
+/** Hard ceiling on entries returned to prevent memory issues. */
+const MAX_LOG_QUERY_LIMIT = 10_000;
+/** Matches daemon.log, rotated daemon.N.log, and mcp.jsonl. */
+const DAEMON_LOG_PATTERN = /^daemon(?:\.(\d+))?\.log$/;
+const MCP_LOG_FILE = 'mcp.jsonl';
+/**
+ * Query parsed log entries from all JSONL log files on disk.
+ * Reads both daemon logs and MCP activity logs.
+ * Returns the last N matching entries (tail behavior).
+ */
+export function queryLogs(logDir, query = {}) {
+    const limit = Math.min(query.limit ?? DEFAULT_LOG_TAIL, MAX_LOG_QUERY_LIMIT);
+    const logFiles = discoverLogFiles(logDir);
+    if (logFiles.length === 0) {
+        return { entries: [], total: 0, truncated: false };
+    }
+    const allEntries = readAndParse(logFiles);
+    // Sort all entries by timestamp so daemon + MCP logs interleave correctly
+    allEntries.sort((a, b) => (a.timestamp ?? '').localeCompare(b.timestamp ?? ''));
+    const filtered = applyFilters(allEntries, query);
+    const total = filtered.length;
+    const truncated = total > limit;
+    const entries = truncated ? filtered.slice(total - limit) : filtered;
+    return { entries, total, truncated };
+}
+/** Discover and sort log files: MCP first, then rotated daemon logs oldest-first, current daemon last. */
+function discoverLogFiles(logDir) {
+    let files;
+    try {
+        files = fs.readdirSync(logDir);
+    }
+    catch {
+        return [];
+    }
+    const matched = [];
+    for (const file of files) {
+        if (file === MCP_LOG_FILE) {
+            matched.push({ path: path.join(logDir, file), order: -1 });
+            continue;
+        }
+        const m = DAEMON_LOG_PATTERN.exec(file);
+        if (!m)
+            continue;
+        const rotationNum = m[1] ? parseInt(m[1], 10) : 0;
+        matched.push({ path: path.join(logDir, file), order: rotationNum });
+    }
+    matched.sort((a, b) => {
+        if (a.order === 0)
+            return 1;
+        if (b.order === 0)
+            return -1;
+        return b.order - a.order;
+    });
+    return matched.map((m) => m.path);
+}
+/** Read all log files and parse each line as JSON. Malformed lines are skipped. */
+function readAndParse(filePaths) {
+    const entries = [];
+    for (const filePath of filePaths) {
+        let content;
+        try {
+            content = fs.readFileSync(filePath, 'utf-8');
+        }
+        catch {
+            continue;
+        }
+        for (const line of content.split('\n')) {
+            if (!line.trim())
+                continue;
+            try {
+                entries.push(JSON.parse(line));
+            }
+            catch {
+                // Malformed line — skip
+            }
+        }
+    }
+    return entries;
+}
+/** Test whether a single entry matches the query filters. */
+export function matchesFilter(entry, query) {
+    if (query.level) {
+        const entryOrder = LEVEL_ORDER[entry.level] ?? 0;
+        const minOrder = LEVEL_ORDER[query.level];
+        if (entryOrder < minOrder)
+            return false;
+    }
+    if (query.component && entry.component !== query.component)
+        return false;
+    if (query.since && entry.timestamp < query.since)
+        return false;
+    if (query.until && entry.timestamp > query.until)
+        return false;
+    return true;
+}
+/** Apply level, component, and time range filters. */
+function applyFilters(entries, query) {
+    return entries.filter((entry) => matchesFilter(entry, query));
+}
+//# sourceMappingURL=reader.js.map

package/dist/src/logs/reader.js.map

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

@@ -0,0 +1,16 @@
+import type { EmbeddingProvider } from '../intelligence/llm.js';
+import { VectorIndex } from '../index/vectors.js';
+interface ServerConfig {
+    vaultDir: string;
+    teamUser?: string;
+    embeddingProvider?: EmbeddingProvider;
+    vectorIndex?: VectorIndex;
+}
+export interface MycoServer {
+    name: string;
+    getRegisteredTools(): string[];
+    start(): Promise<void>;
+}
+export declare function createMycoServer(config: ServerConfig): MycoServer;
+export {};
+//# sourceMappingURL=server.d.ts.map

package/dist/src/mcp/server.d.ts.map

@@ -0,0 +1 @@
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