cf-doctor 1.0.0

package/dist/persistence/episodes.js

@@ -0,0 +1,160 @@
+/**
+ * Episode Recall with TF-IDF Similarity
+ *
+ * Searches past agent episodes by text similarity to provide
+ * relevant context to newly spawned agents.
+ */
+import { readFileSync, writeFileSync, mkdirSync, existsSync, renameSync } from 'fs';
+import { join } from 'path';
+const MEMORY_DIR = '.claude-flow/memory';
+const EPISODES_FILE = join(MEMORY_DIR, 'episodes.json');
+const MAX_EPISODES = 1000; // keep last 1000 episodes
+// --- TF-IDF Implementation ---
+function tokenize(text) {
+    return text
+        .toLowerCase()
+        .replace(/[^a-z0-9\s]/g, ' ')
+        .split(/\s+/)
+        .filter((t) => t.length > 2); // skip tiny words
+}
+function termFrequency(tokens) {
+    const tf = new Map();
+    for (const token of tokens) {
+        tf.set(token, (tf.get(token) || 0) + 1);
+    }
+    // Normalize by document length
+    if (tokens.length > 0) {
+        for (const [term, count] of tf) {
+            tf.set(term, count / tokens.length);
+        }
+    }
+    return tf;
+}
+function computeIDF(documents) {
+    const docCount = documents.length;
+    const docFreq = new Map();
+    for (const doc of documents) {
+        const seen = new Set(doc);
+        for (const term of seen) {
+            docFreq.set(term, (docFreq.get(term) || 0) + 1);
+        }
+    }
+    const idf = new Map();
+    for (const [term, freq] of docFreq) {
+        idf.set(term, Math.log((docCount + 1) / (freq + 1)) + 1); // smoothed IDF
+    }
+    return idf;
+}
+function tfidfVector(tokens, idf) {
+    const tf = termFrequency(tokens);
+    const tfidf = new Map();
+    for (const [term, tfVal] of tf) {
+        tfidf.set(term, tfVal * (idf.get(term) || 1));
+    }
+    return tfidf;
+}
+function cosineSimilarity(a, b) {
+    let dotProduct = 0;
+    let normA = 0;
+    let normB = 0;
+    for (const [term, val] of a) {
+        normA += val * val;
+        if (b.has(term)) {
+            dotProduct += val * b.get(term);
+        }
+    }
+    for (const [, val] of b) {
+        normB += val * val;
+    }
+    if (normA === 0 || normB === 0)
+        return 0;
+    return dotProduct / (Math.sqrt(normA) * Math.sqrt(normB));
+}
+// --- Episode Store ---
+export function loadEpisodes() {
+    try {
+        if (existsSync(EPISODES_FILE)) {
+            const raw = readFileSync(EPISODES_FILE, 'utf-8');
+            const store = JSON.parse(raw);
+            if (store.version === 1)
+                return store.episodes;
+        }
+    }
+    catch (err) {
+        console.warn('[episodes] Failed to load episodes:', err.message);
+    }
+    return [];
+}
+export function saveEpisode(episode) {
+    if (!existsSync(MEMORY_DIR)) {
+        mkdirSync(MEMORY_DIR, { recursive: true });
+    }
+    const episodes = loadEpisodes();
+    episodes.push(episode);
+    // Trim to MAX_EPISODES (keep most recent)
+    const trimmed = episodes.length > MAX_EPISODES
+        ? episodes.slice(episodes.length - MAX_EPISODES)
+        : episodes;
+    const store = {
+        version: 1,
+        episodes: trimmed,
+        idf: {},
+        lastRecomputed: Date.now(),
+    };
+    try {
+        const tmpFile = EPISODES_FILE + '.tmp';
+        writeFileSync(tmpFile, JSON.stringify(store, null, 2), 'utf-8');
+        renameSync(tmpFile, EPISODES_FILE);
+    }
+    catch (err) {
+        console.warn('[episodes] Failed to save episode:', err.message);
+    }
+}
+/**
+ * Recall episodes relevant to the given context using TF-IDF similarity.
+ *
+ * @param context - Text describing what the agent needs to do
+ * @param topK - Number of episodes to return (default: 5)
+ * @param minSimilarity - Minimum similarity threshold (default: 0.1)
+ * @returns Array of relevant episodes sorted by similarity (descending)
+ */
+export function recallRelevantEpisodes(context, topK = 5, minSimilarity = 0.1) {
+    const episodes = loadEpisodes();
+    if (episodes.length === 0)
+        return [];
+    // Tokenize all episode descriptions (input + outcome)
+    const episodeTokens = episodes.map((ep) => tokenize(`${ep.input} ${ep.outcome}`));
+    const queryTokens = tokenize(context);
+    // Compute IDF across all documents
+    const allDocs = [...episodeTokens, queryTokens];
+    const idf = computeIDF(allDocs);
+    // Compute TF-IDF vectors
+    const queryVector = tfidfVector(queryTokens, idf);
+    // Score each episode
+    const scored = episodes.map((ep, i) => ({
+        ...ep,
+        similarity: cosineSimilarity(queryVector, tfidfVector(episodeTokens[i], idf)),
+    }));
+    // Filter and sort
+    return scored
+        .filter((ep) => ep.similarity >= minSimilarity)
+        .sort((a, b) => b.similarity - a.similarity)
+        .slice(0, topK);
+}
+/**
+ * Format episodes as context string for injection into agent prompts.
+ */
+export function formatEpisodesAsContext(episodes) {
+    if (episodes.length === 0)
+        return '';
+    const lines = ['## Relevant Past Episodes', ''];
+    for (const ep of episodes) {
+        lines.push(`### Episode (${new Date(ep.timestamp).toISOString().split('T')[0]}, relevance: ${(ep.similarity * 100).toFixed(0)}%)`);
+        lines.push(`**Task:** ${ep.input.slice(0, 200)}`);
+        lines.push(`**Outcome:** ${ep.outcome.slice(0, 200)}`);
+        lines.push(`**Reward:** ${ep.reward}`);
+        lines.push('');
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=episodes.js.map

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package/dist/persistence/index.d.ts

@@ -0,0 +1,4 @@
+export { loadQTable, saveQTable, updateQValue, qKey, getBestAction, epsilonGreedyAction, ensureLearningDir, } from './q-table.js';
+export { PersistentSonaEngine, loadSonaPatterns, saveSonaPatterns, registerSonaExitHandler, } from './sona.js';
+export { saveEpisode, loadEpisodes, recallRelevantEpisodes, formatEpisodesAsContext, type Episode, type EpisodeStore, } from './episodes.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/persistence/index.d.ts.map

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package/dist/persistence/index.js

@@ -0,0 +1,4 @@
+export { loadQTable, saveQTable, updateQValue, qKey, getBestAction, epsilonGreedyAction, ensureLearningDir, } from './q-table.js';
+export { PersistentSonaEngine, loadSonaPatterns, saveSonaPatterns, registerSonaExitHandler, } from './sona.js';
+export { saveEpisode, loadEpisodes, recallRelevantEpisodes, formatEpisodesAsContext, } from './episodes.js';
+//# sourceMappingURL=index.js.map

package/dist/persistence/index.js.map

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package/dist/persistence/q-table.d.ts

@@ -0,0 +1,42 @@
+/**
+ * Q-Table Persistence Layer
+ *
+ * Wraps the Q-learning router's in-memory Q-table with file-based persistence.
+ * Pattern: save on update, load on init (same as saveStore/loadStore in tool files).
+ */
+interface QEntry {
+    state: string;
+    action: string;
+    value: number;
+    visits: number;
+    lastUpdated: number;
+}
+export declare function ensureLearningDir(): void;
+export declare function loadQTable(): Map<string, QEntry>;
+export declare function saveQTable(table: Map<string, QEntry>, totalUpdates: number): void;
+/**
+ * Q-Table key format: "state::action"
+ * Where state = serialized agent context, action = chosen routing decision
+ */
+export declare function qKey(state: string, action: string): string;
+/**
+ * Update Q-value using standard Q-learning formula:
+ * Q(s,a) = Q(s,a) + alpha * (reward + gamma * max_a' Q(s',a') - Q(s,a))
+ */
+export declare function updateQValue(table: Map<string, QEntry>, state: string, action: string, reward: number, nextStateBestValue?: number, learningRate?: number, discountFactor?: number): QEntry;
+/**
+ * Get the best action for a given state (greedy policy).
+ * Returns null if the state has never been visited.
+ */
+export declare function getBestAction(table: Map<string, QEntry>, state: string): {
+    action: string;
+    value: number;
+} | null;
+/**
+ * Epsilon-greedy action selection.
+ * With probability epsilon, return a random action from the candidates.
+ * Otherwise, return the best known action for this state.
+ */
+export declare function epsilonGreedyAction(table: Map<string, QEntry>, state: string, candidateActions: string[], epsilon?: number): string;
+export {};
+//# sourceMappingURL=q-table.d.ts.map

package/dist/persistence/q-table.d.ts.map

@@ -0,0 +1 @@
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package/dist/persistence/q-table.js

@@ -0,0 +1,138 @@
+/**
+ * Q-Table Persistence Layer
+ *
+ * Wraps the Q-learning router's in-memory Q-table with file-based persistence.
+ * Pattern: save on update, load on init (same as saveStore/loadStore in tool files).
+ */
+import { readFileSync, writeFileSync, mkdirSync, existsSync, renameSync } from 'fs';
+import { join } from 'path';
+const LEARNING_DIR = '.claude-flow/learning';
+const Q_TABLE_FILE = join(LEARNING_DIR, 'q-table.json');
+export function ensureLearningDir() {
+    if (!existsSync(LEARNING_DIR)) {
+        mkdirSync(LEARNING_DIR, { recursive: true });
+    }
+}
+export function loadQTable() {
+    const map = new Map();
+    try {
+        if (existsSync(Q_TABLE_FILE)) {
+            const raw = readFileSync(Q_TABLE_FILE, 'utf-8');
+            const store = JSON.parse(raw);
+            if (store.version === 1 && store.entries) {
+                for (const [key, entry] of Object.entries(store.entries)) {
+                    map.set(key, entry);
+                }
+            }
+        }
+    }
+    catch (err) {
+        // Corrupted file -- start fresh but don't crash
+        console.warn('[q-table] Failed to load Q-table, starting fresh:', err.message);
+    }
+    return map;
+}
+export function saveQTable(table, totalUpdates) {
+    ensureLearningDir();
+    // Preserve original createdAt if the file already exists
+    let createdAt = Date.now();
+    try {
+        if (existsSync(Q_TABLE_FILE)) {
+            const raw = readFileSync(Q_TABLE_FILE, 'utf-8');
+            const existing = JSON.parse(raw);
+            if (existing.metadata?.createdAt) {
+                createdAt = existing.metadata.createdAt;
+            }
+        }
+    }
+    catch {
+        // If we can't read the existing file, use current timestamp
+    }
+    const store = {
+        version: 1,
+        entries: Object.fromEntries(table),
+        metadata: {
+            totalUpdates,
+            createdAt,
+            lastSavedAt: Date.now(),
+        },
+    };
+    try {
+        // Atomic write: write to temp file then rename
+        const tmpFile = Q_TABLE_FILE + '.tmp';
+        writeFileSync(tmpFile, JSON.stringify(store, null, 2), 'utf-8');
+        renameSync(tmpFile, Q_TABLE_FILE);
+    }
+    catch (err) {
+        console.warn('[q-table] Failed to save Q-table:', err.message);
+    }
+}
+/**
+ * Q-Table key format: "state::action"
+ * Where state = serialized agent context, action = chosen routing decision
+ */
+export function qKey(state, action) {
+    return `${state}::${action}`;
+}
+/**
+ * Update Q-value using standard Q-learning formula:
+ * Q(s,a) = Q(s,a) + alpha * (reward + gamma * max_a' Q(s',a') - Q(s,a))
+ */
+export function updateQValue(table, state, action, reward, nextStateBestValue = 0, learningRate = 0.1, discountFactor = 0.95) {
+    const key = qKey(state, action);
+    const existing = table.get(key) || {
+        state,
+        action,
+        value: 0,
+        visits: 0,
+        lastUpdated: 0,
+    };
+    const newValue = existing.value +
+        learningRate * (reward + discountFactor * nextStateBestValue - existing.value);
+    const updated = {
+        state,
+        action,
+        value: newValue,
+        visits: existing.visits + 1,
+        lastUpdated: Date.now(),
+    };
+    table.set(key, updated);
+    return updated;
+}
+/**
+ * Get the best action for a given state (greedy policy).
+ * Returns null if the state has never been visited.
+ */
+export function getBestAction(table, state) {
+    let best = null;
+    for (const [key, entry] of table) {
+        if (key.startsWith(`${state}::`)) {
+            if (best === null || entry.value > best.value) {
+                best = { action: entry.action, value: entry.value };
+            }
+        }
+    }
+    return best;
+}
+/**
+ * Epsilon-greedy action selection.
+ * With probability epsilon, return a random action from the candidates.
+ * Otherwise, return the best known action for this state.
+ */
+export function epsilonGreedyAction(table, state, candidateActions, epsilon = 0.1) {
+    if (candidateActions.length === 0) {
+        throw new Error('No candidate actions provided');
+    }
+    if (Math.random() < epsilon) {
+        // Explore: pick a random action
+        return candidateActions[Math.floor(Math.random() * candidateActions.length)];
+    }
+    // Exploit: pick the best known action
+    const best = getBestAction(table, state);
+    if (best && candidateActions.includes(best.action)) {
+        return best.action;
+    }
+    // Fallback: no knowledge for this state, pick randomly
+    return candidateActions[Math.floor(Math.random() * candidateActions.length)];
+}
+//# sourceMappingURL=q-table.js.map

package/dist/persistence/q-table.js.map

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package/dist/persistence/sona.d.ts

@@ -0,0 +1,45 @@
+/**
+ * SONA Pattern Persistence Layer
+ *
+ * Persists learned patterns to disk so they survive process restarts.
+ * Works with both the real @ruvector/sona engine and the mock fallback.
+ */
+interface SonaPattern {
+    key: string;
+    pattern: unknown;
+    confidence: number;
+    learnCount: number;
+    createdAt: number;
+    lastAccessedAt: number;
+}
+export declare function loadSonaPatterns(): Map<string, SonaPattern>;
+export declare function saveSonaPatterns(patterns: Map<string, SonaPattern>): void;
+/**
+ * PersistentSonaEngine - wraps the mock with disk persistence
+ *
+ * Use this as a drop-in replacement for MockSonaEngine in sona-integration.ts
+ */
+export declare class PersistentSonaEngine {
+    private patterns;
+    private saveDebounceTimer;
+    constructor();
+    store(key: string, pattern: unknown): Promise<void>;
+    recall(key: string): Promise<unknown>;
+    learn(_input: unknown, feedback: number): Promise<void>;
+    private scheduleSave;
+    /** Force save immediately (call on process exit) */
+    flush(): void;
+    getPatternCount(): number;
+    /**
+     * Get patterns sorted by confidence (descending).
+     * Useful for debugging and introspection.
+     */
+    getTopPatterns(limit?: number): SonaPattern[];
+}
+/**
+ * Register a process exit handler to flush patterns.
+ * Call this once during application bootstrap.
+ */
+export declare function registerSonaExitHandler(engine: PersistentSonaEngine): void;
+export {};
+//# sourceMappingURL=sona.d.ts.map

package/dist/persistence/sona.d.ts.map

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package/dist/persistence/sona.js

@@ -0,0 +1,142 @@
+/**
+ * SONA Pattern Persistence Layer
+ *
+ * Persists learned patterns to disk so they survive process restarts.
+ * Works with both the real @ruvector/sona engine and the mock fallback.
+ */
+import { readFileSync, writeFileSync, mkdirSync, existsSync, renameSync } from 'fs';
+import { join } from 'path';
+const LEARNING_DIR = '.claude-flow/learning';
+const SONA_FILE = join(LEARNING_DIR, 'sona-patterns.json');
+export function loadSonaPatterns() {
+    const map = new Map();
+    try {
+        if (existsSync(SONA_FILE)) {
+            const raw = readFileSync(SONA_FILE, 'utf-8');
+            const store = JSON.parse(raw);
+            if (store.version === 1 && store.patterns) {
+                for (const [key, pattern] of Object.entries(store.patterns)) {
+                    map.set(key, pattern);
+                }
+            }
+        }
+    }
+    catch (err) {
+        console.warn('[sona] Failed to load patterns, starting fresh:', err.message);
+    }
+    return map;
+}
+export function saveSonaPatterns(patterns) {
+    if (!existsSync(LEARNING_DIR)) {
+        mkdirSync(LEARNING_DIR, { recursive: true });
+    }
+    let totalLearnings = 0;
+    for (const p of patterns.values()) {
+        totalLearnings += p.learnCount;
+    }
+    const store = {
+        version: 1,
+        patterns: Object.fromEntries(patterns),
+        metadata: {
+            totalPatterns: patterns.size,
+            totalLearnings,
+            lastSavedAt: Date.now(),
+        },
+    };
+    try {
+        const tmpFile = SONA_FILE + '.tmp';
+        writeFileSync(tmpFile, JSON.stringify(store, null, 2), 'utf-8');
+        renameSync(tmpFile, SONA_FILE);
+    }
+    catch (err) {
+        console.warn('[sona] Failed to save patterns:', err.message);
+    }
+}
+/**
+ * PersistentSonaEngine - wraps the mock with disk persistence
+ *
+ * Use this as a drop-in replacement for MockSonaEngine in sona-integration.ts
+ */
+export class PersistentSonaEngine {
+    patterns;
+    saveDebounceTimer = null;
+    constructor() {
+        this.patterns = loadSonaPatterns();
+    }
+    async store(key, pattern) {
+        const existing = this.patterns.get(key);
+        this.patterns.set(key, {
+            key,
+            pattern,
+            confidence: existing?.confidence ?? 0.5,
+            learnCount: existing?.learnCount ?? 0,
+            createdAt: existing?.createdAt ?? Date.now(),
+            lastAccessedAt: Date.now(),
+        });
+        this.scheduleSave();
+    }
+    async recall(key) {
+        const entry = this.patterns.get(key);
+        if (entry) {
+            entry.lastAccessedAt = Date.now();
+            return entry.pattern;
+        }
+        return null;
+    }
+    async learn(_input, feedback) {
+        // Update confidence of most recently accessed patterns based on feedback
+        const recentThreshold = Date.now() - 60_000; // last 60 seconds
+        for (const pattern of this.patterns.values()) {
+            if (pattern.lastAccessedAt > recentThreshold) {
+                // Bayesian-style confidence update
+                const alpha = pattern.confidence * pattern.learnCount + (feedback > 0 ? 1 : 0);
+                const beta = (1 - pattern.confidence) * pattern.learnCount + (feedback <= 0 ? 1 : 0);
+                pattern.learnCount += 1;
+                pattern.confidence = alpha / (alpha + beta);
+            }
+        }
+        this.scheduleSave();
+    }
+    scheduleSave() {
+        if (this.saveDebounceTimer)
+            clearTimeout(this.saveDebounceTimer);
+        this.saveDebounceTimer = setTimeout(() => {
+            saveSonaPatterns(this.patterns);
+        }, 1000); // debounce: save at most once per second
+    }
+    /** Force save immediately (call on process exit) */
+    flush() {
+        if (this.saveDebounceTimer)
+            clearTimeout(this.saveDebounceTimer);
+        saveSonaPatterns(this.patterns);
+    }
+    getPatternCount() {
+        return this.patterns.size;
+    }
+    /**
+     * Get patterns sorted by confidence (descending).
+     * Useful for debugging and introspection.
+     */
+    getTopPatterns(limit = 10) {
+        return Array.from(this.patterns.values())
+            .sort((a, b) => b.confidence - a.confidence)
+            .slice(0, limit);
+    }
+}
+/**
+ * Register a process exit handler to flush patterns.
+ * Call this once during application bootstrap.
+ */
+export function registerSonaExitHandler(engine) {
+    const flush = () => engine.flush();
+    process.on('exit', flush);
+    process.on('SIGINT', () => {
+        flush();
+        process.exit(0);
+    });
+    process.on('SIGTERM', () => {
+        flush();
+        process.exit(0);
+    });
+}
+//# sourceMappingURL=sona.js.map

package/dist/persistence/sona.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,63 @@
+{
+  "name": "cf-doctor",
+  "version": "1.0.0",
+  "description": "Setup validator, auto-fixer, and learning persistence for claude-flow + ruvector integration on Linux/Ubuntu",
+  "type": "module",
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "bin": {
+    "cf-doctor": "./bin/cf-doctor.js"
+  },
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts"
+    },
+    "./persistence": {
+      "import": "./dist/persistence/index.js",
+      "types": "./dist/persistence/index.d.ts"
+    },
+    "./mcp": {
+      "import": "./dist/mcp-server.js",
+      "types": "./dist/mcp-server.d.ts"
+    }
+  },
+  "scripts": {
+    "build": "tsc",
+    "test": "bash tests/run-all-tests.sh",
+    "doctor": "bash scripts/cf-doctor.sh",
+    "doctor:fix": "bash scripts/cf-doctor.sh --fix",
+    "doctor:json": "bash scripts/cf-doctor.sh --json",
+    "prepublishOnly": "npm run build"
+  },
+  "keywords": [
+    "claude-flow",
+    "ruvector",
+    "claude-code",
+    "mcp",
+    "doctor",
+    "integration",
+    "linux",
+    "ubuntu"
+  ],
+  "author": "FoxFlow",
+  "license": "MIT",
+  "engines": {
+    "node": ">=20.0.0"
+  },
+  "files": [
+    "dist/",
+    "bin/",
+    "scripts/",
+    "patches/",
+    "tests/"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/foxflow/cf-doctor"
+  },
+  "devDependencies": {
+    "@types/node": "^22.0.0",
+    "typescript": "^5.5.0"
+  }
+}