@hongmaple0820/med-scale-research-os 0.43.0

package/dist/cortex/InstinctStore.js

@@ -0,0 +1,266 @@
+// SCALE Cortex — Instinct Store
+// 对齐 ECC: hierarchical filesystem-based storage under .scale/instincts/
+// Future: SQLite-backed in Cortex v2
+import { existsSync, mkdirSync, readdirSync, readFileSync, writeFileSync, unlinkSync } from 'node:fs';
+import { join } from 'node:path';
+import { createHash } from 'node:crypto';
+import { logger } from '../core/logger.js';
+// ---------------------------------------------------------------------------
+// InstinctStore
+// ---------------------------------------------------------------------------
+export class InstinctStore {
+    constructor(baseDir = join(process.cwd(), '.scale', 'instincts')) {
+        this.baseDir = baseDir;
+        if (!existsSync(baseDir))
+            mkdirSync(baseDir, { recursive: true });
+    }
+    /**
+     * Save an instinct to disk.
+     * Deduplication: if an instinct with the same trigger exists, only keep the higher-confidence one.
+     */
+    save(instinct) {
+        const existing = this.findByTrigger(instinct.trigger);
+        if (existing && existing.confidence >= instinct.confidence) {
+            // Keep existing. Increment observation count.
+            existing.observations += instinct.observations;
+            existing.updatedAt = new Date().toISOString();
+            this.writeInstinctFile(existing);
+            return existing.id;
+        }
+        // New or higher-confidence instinct replaces existing
+        if (existing) {
+            this.delete(existing.id);
+        }
+        instinct.updatedAt = new Date().toISOString();
+        this.writeInstinctFile(instinct);
+        return instinct.id;
+    }
+    /**
+     * Load all instincts from disk.
+     */
+    loadAll() {
+        const instincts = [];
+        if (!existsSync(this.baseDir))
+            return instincts;
+        try {
+            for (const domain of readdirSync(this.baseDir)) {
+                const domainDir = join(this.baseDir, domain);
+                if (!domain.endsWith('.yaml') && existsSync(domainDir) && !domain.startsWith('.')) {
+                    // Directory-based domain
+                    try {
+                        for (const file of readdirSync(domainDir)) {
+                            if (!file.endsWith('.yaml'))
+                                continue;
+                            const instinct = this.parseInstinctFile(join(domainDir, file));
+                            if (instinct)
+                                instincts.push(instinct);
+                        }
+                    }
+                    catch { /* skip unreadable domains */ }
+                }
+                else if (domain.endsWith('.yaml')) {
+                    // Flat file in root
+                    const instinct = this.parseInstinctFile(join(this.baseDir, domain));
+                    if (instinct)
+                        instincts.push(instinct);
+                }
+            }
+        }
+        catch (err) {
+            logger.warn({ err }, 'Failed to load instincts');
+        }
+        return instincts.sort((a, b) => b.confidence - a.confidence);
+    }
+    /**
+     * Get instincts filtered by confidence threshold and scope.
+     */
+    query(options) {
+        let instincts = this.loadAll();
+        if (options.minConfidence) {
+            instincts = instincts.filter(i => i.confidence >= options.minConfidence);
+        }
+        if (options.domain) {
+            instincts = instincts.filter(i => i.domain === options.domain);
+        }
+        if (options.scope) {
+            instincts = instincts.filter(i => i.scope === options.scope);
+        }
+        if (options.projectId) {
+            instincts = instincts.filter(i => !i.projectId || i.projectId === options.projectId);
+        }
+        return instincts;
+    }
+    /**
+     * Get high-confidence instincts for SessionStart injection (0.7+).
+     */
+    getInjectionInstincts(projectId) {
+        return this.query({ minConfidence: 0.7, projectId });
+    }
+    /**
+     * Find an instinct by trigger pattern.
+     */
+    findByTrigger(trigger) {
+        const hash = createHash('sha256').update(trigger).digest('hex').slice(0, 10);
+        const id = `instinct-${hash}`;
+        return this.findById(id);
+    }
+    /**
+     * Find an instinct by ID.
+     */
+    findById(id) {
+        // Search all domain directories
+        if (!existsSync(this.baseDir))
+            return null;
+        try {
+            for (const entry of readdirSync(this.baseDir)) {
+                const full = join(this.baseDir, entry);
+                if (existsSync(full) && !entry.startsWith('.')) {
+                    if (!entry.endsWith('.yaml')) {
+                        // Domain directory
+                        const filePath = join(full, `${id}.yaml`);
+                        if (existsSync(filePath))
+                            return this.parseInstinctFile(filePath);
+                    }
+                }
+            }
+        }
+        catch { /* skip */ }
+        // Flat file search
+        const flatPath = join(this.baseDir, `${id}.yaml`);
+        if (existsSync(flatPath))
+            return this.parseInstinctFile(flatPath);
+        return null;
+    }
+    /**
+     * Delete an instinct by ID.
+     */
+    delete(id) {
+        const instinct = this.findById(id);
+        if (!instinct)
+            return false;
+        const domainDir = join(this.baseDir, instinct.domain);
+        const filePath = join(domainDir, `${id}.yaml`);
+        try {
+            if (existsSync(filePath))
+                unlinkSync(filePath);
+            return true;
+        }
+        catch (err) {
+            logger.warn({ err, id }, 'Failed to delete instinct');
+            return false;
+        }
+    }
+    /**
+     * Record an instinct was applied (for hit rate tracking).
+     */
+    recordApplication(id, success) {
+        const instinct = this.findById(id);
+        if (!instinct)
+            return;
+        instinct.appliedCount++;
+        instinct.hitRate = instinct.observations > 0
+            ? instinct.appliedCount / instinct.observations
+            : 0;
+        instinct.updatedAt = new Date().toISOString();
+        this.writeInstinctFile(instinct);
+    }
+    /**
+     * Get store statistics.
+     */
+    stats() {
+        const all = this.loadAll();
+        const byDomain = {};
+        const byConfidence = {
+            'near-certain (0.9)': 0,
+            'strong (0.7)': 0,
+            'moderate (0.5)': 0,
+            'tentative (0.3)': 0,
+        };
+        for (const i of all) {
+            byDomain[i.domain] = (byDomain[i.domain] ?? 0) + 1;
+            if (i.confidence >= 0.9)
+                byConfidence['near-certain (0.9)']++;
+            else if (i.confidence >= 0.7)
+                byConfidence['strong (0.7)']++;
+            else if (i.confidence >= 0.5)
+                byConfidence['moderate (0.5)']++;
+            else
+                byConfidence['tentative (0.3)']++;
+        }
+        return { total: all.length, byDomain, byConfidence };
+    }
+    // -----------------------------------------------------------------------
+    // Internal
+    // -----------------------------------------------------------------------
+    writeInstinctFile(instinct) {
+        const domainDir = join(this.baseDir, instinct.domain);
+        if (!existsSync(domainDir))
+            mkdirSync(domainDir, { recursive: true });
+        const filePath = join(domainDir, `${instinct.id}.yaml`);
+        const yaml = this.serializeInstinct(instinct);
+        writeFileSync(filePath, yaml, 'utf-8');
+    }
+    serializeInstinct(instinct) {
+        const frontmatter = [
+            `id: ${instinct.id}`,
+            `trigger: "${instinct.trigger.replace(/"/g, '\\"')}"`,
+            `confidence: ${instinct.confidence}`,
+            `domain: ${instinct.domain}`,
+            `source: "${instinct.source}"`,
+            `scope: ${instinct.scope}`,
+            `project_id: ${instinct.projectId ?? ''}`,
+            `observations: ${instinct.observations}`,
+            `applied_count: ${instinct.appliedCount}`,
+            `hit_rate: ${instinct.hitRate.toFixed(2)}`,
+            `created_at: ${instinct.createdAt}`,
+            `updated_at: ${instinct.updatedAt}`,
+        ].join('\n');
+        const evidence = instinct.evidence.map(e => `  - "${e}"`).join('\n');
+        return [
+            '---',
+            frontmatter,
+            '---',
+            '',
+            instinct.action,
+            '',
+            '## Evidence',
+            evidence,
+            '',
+        ].join('\n');
+    }
+    parseInstinctFile(filePath) {
+        try {
+            const raw = readFileSync(filePath, 'utf-8');
+            const fmMatch = raw.match(/^---\n([\s\S]*?)\n---\n([\s\S]*)$/);
+            if (!fmMatch)
+                return null;
+            const frontmatter = fmMatch[1];
+            const body = fmMatch[2] ?? '';
+            const getYamlVal = (key) => {
+                const m = frontmatter.match(new RegExp(`^${key}:\\s*(.+?)$`, 'm'));
+                return m ? m[1].trim().replace(/^"(.*)"$/, '$1') : '';
+            };
+            return {
+                id: getYamlVal('id'),
+                trigger: getYamlVal('trigger'),
+                confidence: parseFloat(getYamlVal('confidence')) || 0.3,
+                domain: getYamlVal('domain') || 'general',
+                source: getYamlVal('source'),
+                scope: getYamlVal('scope') || 'project',
+                projectId: getYamlVal('project_id') || undefined,
+                action: body.trim(),
+                evidence: [],
+                observations: parseInt(getYamlVal('observations'), 10) || 0,
+                createdAt: getYamlVal('created_at') || new Date().toISOString(),
+                updatedAt: getYamlVal('updated_at') || new Date().toISOString(),
+                appliedCount: parseInt(getYamlVal('applied_count'), 10) || 0,
+                hitRate: parseFloat(getYamlVal('hit_rate')) || 0,
+            };
+        }
+        catch (err) {
+            logger.warn({ err, path: filePath }, 'Failed to parse instinct file');
+            return null;
+        }
+    }
+}
+//# sourceMappingURL=InstinctStore.js.map

package/dist/cortex/InstinctStore.js.map

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

@@ -0,0 +1,34 @@
+import type { Observation, Instinct } from './InstinctExtractor.js';
+export interface ReflexionResult {
+    rootCause: string;
+    confidence: number;
+    suggestedAction: string;
+    relatedFailures: string[];
+    instinct: Instinct | null;
+    modelUsed: string;
+    tokensUsed: number;
+}
+export declare class ReflexionEngine {
+    private modelEndpoint;
+    private modelName;
+    private enabled;
+    constructor(options?: {
+        endpoint?: string;
+        model?: string;
+    });
+    /**
+     * Reflect on a set of failed observations to produce root cause analysis.
+     */
+    reflect(observations: Observation[]): Promise<ReflexionResult>;
+    /**
+     * Reflect on gate failure patterns and generate improvement instincts.
+     */
+    reflectOnGate(gateName: string, failures: Observation[]): Promise<ReflexionResult>;
+    /**
+     * Batch reflect across all failing gates and merge results.
+     */
+    reflectAll(observations: Observation[]): Promise<ReflexionResult[]>;
+    private llmReflect;
+    private heuristicReflect;
+    private buildReflectionPrompt;
+}

package/dist/cortex/ReflexionEngine.js

@@ -0,0 +1,157 @@
+// SCALE Cortex — Reflexion Engine
+// 对齐 ECC: local LLM (Qwen/GLM/DeepSeek) reflection on failure evidence
+// Output: root cause analysis + improvement suggestions + actionable instincts
+// Cost: $0 API fees (local model)
+import { logger } from '../core/logger.js';
+// ---------------------------------------------------------------------------
+// ReflexionEngine
+// ---------------------------------------------------------------------------
+export class ReflexionEngine {
+    constructor(options) {
+        this.modelEndpoint = options?.endpoint ?? process.env.SCALE_LOCAL_BASE_URL ?? 'http://localhost:11434';
+        this.modelName = options?.model ?? process.env.SCALE_LOCAL_MODEL ?? 'qwen-2.5';
+        this.enabled = !!process.env.SCALE_LOCAL_MODEL || !!options?.model;
+    }
+    /**
+     * Reflect on a set of failed observations to produce root cause analysis.
+     */
+    async reflect(observations) {
+        if (observations.length === 0) {
+            return {
+                rootCause: 'No observations to reflect on',
+                confidence: 0,
+                suggestedAction: 'Collect more data',
+                relatedFailures: [],
+                instinct: null,
+                modelUsed: 'none',
+                tokensUsed: 0,
+            };
+        }
+        if (!this.enabled) {
+            return this.heuristicReflect(observations);
+        }
+        try {
+            return await this.llmReflect(observations);
+        }
+        catch (err) {
+            logger.warn({ err }, 'LLM reflection failed, falling back to heuristic');
+            return this.heuristicReflect(observations);
+        }
+    }
+    /**
+     * Reflect on gate failure patterns and generate improvement instincts.
+     */
+    async reflectOnGate(gateName, failures) {
+        const gateFailures = failures.filter(o => o.gateName === gateName && o.gateStatus === 'FAIL');
+        return this.reflect(gateFailures);
+    }
+    /**
+     * Batch reflect across all failing gates and merge results.
+     */
+    async reflectAll(observations) {
+        const failures = observations.filter(o => o.gateStatus === 'FAIL');
+        const byGate = new Map();
+        for (const obs of failures) {
+            if (!byGate.has(obs.gateName))
+                byGate.set(obs.gateName, []);
+            byGate.get(obs.gateName).push(obs);
+        }
+        const results = [];
+        for (const [gate, obs] of byGate) {
+            results.push(await this.reflectOnGate(gate, obs));
+        }
+        return results;
+    }
+    // -----------------------------------------------------------------------
+    // Internal
+    // -----------------------------------------------------------------------
+    async llmReflect(observations) {
+        const prompt = this.buildReflectionPrompt(observations);
+        const response = await fetch(`${this.modelEndpoint}/v1/chat/completions`, {
+            method: 'POST',
+            headers: { 'Content-Type': 'application/json' },
+            body: JSON.stringify({
+                model: this.modelName,
+                messages: [
+                    { role: 'system', content: 'You are a root cause analysis engine. Analyze the following gate failures and output structured JSON only.' },
+                    { role: 'user', content: prompt },
+                ],
+                temperature: 0.3,
+                max_tokens: 500,
+            }),
+            signal: AbortSignal.timeout(15000),
+        });
+        if (!response.ok)
+            throw new Error(`LLM endpoint returned ${response.status}`);
+        const data = await response.json();
+        const content = data.choices?.[0]?.message?.content ?? '';
+        try {
+            const parsed = JSON.parse(content);
+            return {
+                rootCause: parsed.rootCause ?? 'Unknown',
+                confidence: parsed.confidence ?? 0.5,
+                suggestedAction: parsed.suggestedAction ?? 'Manual investigation recommended',
+                relatedFailures: parsed.relatedFailures ?? [],
+                instinct: null, // Caller should create instinct from this
+                modelUsed: this.modelName,
+                tokensUsed: data.usage?.total_tokens ?? 0,
+            };
+        }
+        catch {
+            // If LLM didn't return valid JSON, use heuristic
+            return this.heuristicReflect(observations);
+        }
+    }
+    heuristicReflect(observations) {
+        const gateName = observations[0]?.gateName ?? 'unknown';
+        const errorPatterns = observations
+            .map(o => o.errorPattern)
+            .filter(Boolean);
+        // Most common error pattern
+        const patternCounts = new Map();
+        for (const p of errorPatterns) {
+            patternCounts.set(p, (patternCounts.get(p) ?? 0) + 1);
+        }
+        let dominantPattern = '';
+        let maxCount = 0;
+        for (const [p, c] of patternCounts) {
+            if (c > maxCount) {
+                maxCount = c;
+                dominantPattern = p;
+            }
+        }
+        const rootCause = dominantPattern
+            ? `Gate "${gateName}" recurring failure: "${dominantPattern}" (${maxCount}/${observations.length} occurrences)`
+            : `Gate "${gateName}" failed ${observations.length} time(s) — investigate patterns`;
+        return {
+            rootCause,
+            confidence: maxCount > 2 ? 0.7 : 0.4,
+            suggestedAction: dominantPattern
+                ? `Run 'scale auto-fix' targeting ${gateName} failures. Check the most recent evidence for resolution clues.`
+                : `Collect more failure data for gate "${gateName}" to identify patterns.`,
+            relatedFailures: errorPatterns.slice(0, 5),
+            instinct: null,
+            modelUsed: 'heuristic',
+            tokensUsed: 0,
+        };
+    }
+    buildReflectionPrompt(observations) {
+        const failures = observations
+            .map(o => `[${o.timestamp}] Gate: ${o.gateName} | Pattern: ${o.errorPattern ?? 'unknown'} | RC: ${o.rootCause ?? 'unknown'}`)
+            .join('\n');
+        return [
+            'Analyze these gate failures and output JSON:',
+            '',
+            failures,
+            '',
+            'Output format:',
+            '{',
+            '  "rootCause": "primary root cause",',
+            '  "confidence": 0.0-1.0,',
+            '  "suggestedAction": "concrete actionable step",',
+            '  "relatedFailures": ["pattern1", "pattern2"]',
+            '}',
+        ].join('\n');
+    }
+}
+//# sourceMappingURL=ReflexionEngine.js.map

package/dist/cortex/ReflexionEngine.js.map

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package/dist/cortex/SessionInjector.d.ts

@@ -0,0 +1,44 @@
+import type { InstinctStore } from './InstinctStore.js';
+export interface SessionInjection {
+    /** Rendered text injected into session start */
+    content: string;
+    /** Number of instincts injected */
+    instinctCount: number;
+    /** Metadata for metrics */
+    metadata: {
+        projectId?: string;
+        projectType?: string;
+        packageManager?: string;
+        instinctsApplied: string[];
+    };
+}
+export interface PriorSessionBrief {
+    sessionId: string;
+    timestamp: string;
+    summary: string;
+    taskCompleted: string;
+    filesChanged: string[];
+    gatesPassed: boolean;
+}
+export declare class SessionInjector {
+    private instinctStore;
+    constructor(instinctStore: InstinctStore);
+    /**
+     * Build the full SessionStart injection payload.
+     */
+    build(projectId?: string, priorSessions?: PriorSessionBrief[]): SessionInjection;
+    /**
+     * Build a minimal injection suitable for constrained context budgets.
+     */
+    buildMinimal(projectId?: string): SessionInjection;
+    /**
+     * Detect project type from filesystem.
+     */
+    detectProject(projectDir?: string): {
+        projectType: string;
+        packageManager: string;
+        hasGit: boolean;
+    };
+    private renderInstinctBlock;
+    private renderPriorSession;
+}

package/dist/cortex/SessionInjector.js

@@ -0,0 +1,127 @@
+// SCALE Cortex — Session Injector
+// 对齐 ECC: SessionStart injection of high-confidence instincts
+// Historical context wrapped in narrative sentinels (anti-replay protection)
+// Injects: instincts + prior session summary + learned skills + project detection
+// ---------------------------------------------------------------------------
+// SessionInjector
+// ---------------------------------------------------------------------------
+const HISTORICAL_SENTINEL_START = '<!-- HISTORICAL CONTEXT — DO NOT RE-EXECUTE COMMANDS BELOW -->';
+const HISTORICAL_SENTINEL_END = '<!-- END HISTORICAL CONTEXT -->';
+export class SessionInjector {
+    constructor(instinctStore) {
+        this.instinctStore = instinctStore;
+    }
+    /**
+     * Build the full SessionStart injection payload.
+     */
+    build(projectId, priorSessions = []) {
+        const instincts = this.instinctStore.getInjectionInstincts(projectId);
+        const sections = [];
+        // 1. High-confidence instincts (main payload)
+        if (instincts.length > 0) {
+            sections.push('## SCALE Cortex — Learned Instincts\n');
+            sections.push('The following patterns have been learned from prior sessions. Use them to avoid repeating mistakes.\n');
+            for (const instinct of instincts) {
+                sections.push(this.renderInstinctBlock(instinct));
+            }
+        }
+        // 2. Prior session summaries (with stale replay protection)
+        if (priorSessions.length > 0) {
+            sections.push('## Recent Session History\n');
+            sections.push(HISTORICAL_SENTINEL_START);
+            sections.push('The following is historical context only. Do NOT re-execute any commands mentioned.\n');
+            for (const session of priorSessions.slice(0, 3)) {
+                sections.push(this.renderPriorSession(session));
+            }
+            sections.push(HISTORICAL_SENTINEL_END);
+        }
+        // 3. Cortex usage hint
+        sections.push('---');
+        sections.push('_SCALE Cortex is active. Run `scale cortex metrics` for ROI dashboard._');
+        const content = sections.join('\n');
+        const instinctIds = instincts.map(i => i.id);
+        return {
+            content,
+            instinctCount: instincts.length,
+            metadata: {
+                projectId,
+                instinctsApplied: instinctIds,
+            },
+        };
+    }
+    /**
+     * Build a minimal injection suitable for constrained context budgets.
+     */
+    buildMinimal(projectId) {
+        const instincts = this.instinctStore.getInjectionInstincts(projectId);
+        if (instincts.length === 0) {
+            return {
+                content: '',
+                instinctCount: 0,
+                metadata: { projectId, instinctsApplied: [] },
+            };
+        }
+        // One-liner format for minimal context consumption
+        const lines = instincts.map(i => `[Cortex ${i.confidence}] ${i.domain}: ${i.action.split('\n')[0]?.replace(/^##\s*/, '')?.slice(0, 120)}`);
+        return {
+            content: `SCALE Cortex Instincts (${instincts.length}):\n${lines.join('\n')}`,
+            instinctCount: instincts.length,
+            metadata: { projectId, instinctsApplied: instincts.map(i => i.id) },
+        };
+    }
+    /**
+     * Detect project type from filesystem.
+     */
+    detectProject(projectDir = process.cwd()) {
+        const { existsSync } = require('fs');
+        const { join } = require('path');
+        let projectType = 'generic';
+        let packageManager = 'none';
+        if (existsSync(join(projectDir, 'package.json'))) {
+            projectType = 'node';
+            if (existsSync(join(projectDir, 'pnpm-lock.yaml')))
+                packageManager = 'pnpm';
+            else if (existsSync(join(projectDir, 'yarn.lock')))
+                packageManager = 'yarn';
+            else
+                packageManager = 'npm';
+        }
+        else if (existsSync(join(projectDir, 'go.mod'))) {
+            projectType = 'go';
+            packageManager = 'go modules';
+        }
+        else if (existsSync(join(projectDir, 'pyproject.toml'))) {
+            projectType = 'python';
+            packageManager = 'pip/poetry';
+        }
+        else if (existsSync(join(projectDir, 'Cargo.toml'))) {
+            projectType = 'rust';
+            packageManager = 'cargo';
+        }
+        const hasGit = existsSync(join(projectDir, '.git'));
+        return { projectType, packageManager, hasGit };
+    }
+    // -----------------------------------------------------------------------
+    // Internal
+    // -----------------------------------------------------------------------
+    renderInstinctBlock(instinct) {
+        const confidenceLabel = instinct.confidence >= 0.9 ? 'NEAR-CERTAIN' :
+            instinct.confidence >= 0.7 ? 'STRONG' :
+                instinct.confidence >= 0.5 ? 'MODERATE' : 'TENTATIVE';
+        return [
+            `### [${confidenceLabel}] ${instinct.domain}/${instinct.id}`,
+            `**Confidence:** ${(instinct.confidence * 100).toFixed(0)}% | **Observed:** ${instinct.observations} times | **Hit Rate:** ${(instinct.hitRate * 100).toFixed(0)}%`,
+            '',
+            instinct.action,
+            '',
+        ].join('\n');
+    }
+    renderPriorSession(session) {
+        return [
+            `- **${session.timestamp.slice(0, 10)}**: ${session.summary}`,
+            `  Files: ${session.filesChanged.slice(0, 5).join(', ')}${session.filesChanged.length > 5 ? '...' : ''}`,
+            `  Gates: ${session.gatesPassed ? 'PASS' : 'FAIL'} | Task: ${session.taskCompleted}`,
+        ].join('\n');
+    }
+}
+//# sourceMappingURL=SessionInjector.js.map

package/dist/cortex/SessionInjector.js.map

@@ -0,0 +1 @@
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