@hongmaple0820/med-scale-research-os 0.43.0

package/dist/codegraph/CodeIntelligence.js.map

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

@@ -0,0 +1,64 @@
+export interface ConfigProfile {
+    id: string;
+    name: string;
+    description: string;
+    /** Which config sections are visible/relevant at this level */
+    sections: ConfigSection[];
+    /** Default values for this profile */
+    defaults: ProfileDefaults;
+}
+export type ConfigSection = 'basic' | 'guardrails' | 'knowledge' | 'evolution' | 'models' | 'advanced';
+export type DependencyBootstrapPackId = 'ui' | 'memory' | 'knowledge' | 'external-cli';
+export interface ProfileBootstrapPlan {
+    profileId: string;
+    governancePack?: string;
+    packs: DependencyBootstrapPackId[];
+    inspectCommand: string;
+    applyCommand: string;
+}
+export interface ProfileDefaults {
+    scenario: 'sandbox' | 'standard' | 'critical';
+    guardrails: {
+        enabled: boolean;
+        detectors: string[];
+        autoLint: boolean;
+        beforeStop: boolean;
+    };
+    knowledge: {
+        enabled: boolean;
+        vectorSearch: boolean;
+    };
+    evolution: {
+        enabled: boolean;
+        autoApprove: boolean;
+    };
+    models: {
+        routing: 'simple' | 'advanced';
+    };
+}
+export declare const PROFILES: Record<string, ConfigProfile>;
+/**
+ * Get profile by ID, falling back to 'standard' if not found.
+ */
+export declare function getProfile(id: string): ConfigProfile;
+/**
+ * List all available profiles for display.
+ */
+export declare function listProfiles(): Array<{
+    id: string;
+    name: string;
+    description: string;
+    bootstrapPacks: DependencyBootstrapPackId[];
+    dependencyBootstrapCommand: string;
+}>;
+export declare function getRecommendedBootstrapPacks(profileId: string, governancePack?: string): DependencyBootstrapPackId[];
+export declare function getBootstrapPlanForProfile(profileId: string, governancePack?: string): ProfileBootstrapPlan;
+/**
+ * Generate config.yaml content for a given profile.
+ * Returns only the sections relevant to the profile level.
+ */
+export declare function generateConfigForProfile(profileId: string, projectInfo: {
+    name: string;
+    type?: string;
+    agents?: string[];
+}): string;

package/dist/config/profiles.js

@@ -0,0 +1,223 @@
+// SCALE Engine — Configuration Profiles
+// Pre-defined profiles that bundle common settings into simple choices.
+// Users select a profile during `scale init`, then customize only what they need.
+export const PROFILES = {
+    minimal: {
+        id: 'minimal',
+        name: 'Minimal',
+        description: 'Basic artifact management. No guardrails, no knowledge, no evolution. Good for trying SCALE.',
+        sections: ['basic'],
+        defaults: {
+            scenario: 'sandbox',
+            guardrails: { enabled: false, detectors: [], autoLint: false, beforeStop: false },
+            knowledge: { enabled: false, vectorSearch: false },
+            evolution: { enabled: false, autoApprove: false },
+            models: { routing: 'simple' },
+        },
+    },
+    standard: {
+        id: 'standard',
+        name: 'Standard',
+        description: 'Guardrails + lint + test verification. Recommended for most projects.',
+        sections: ['basic', 'guardrails'],
+        defaults: {
+            scenario: 'standard',
+            guardrails: {
+                enabled: true,
+                detectors: ['dangerous-command', 'role-permission', 'brute-retry', 'premature-done'],
+                autoLint: true,
+                beforeStop: true,
+            },
+            knowledge: { enabled: false, vectorSearch: false },
+            evolution: { enabled: false, autoApprove: false },
+            models: { routing: 'simple' },
+        },
+    },
+    advanced: {
+        id: 'advanced',
+        name: 'Advanced',
+        description: 'Full governance: guardrails + graphify knowledge recall + gbrain memory routing + evolution + model routing.',
+        sections: ['basic', 'guardrails', 'knowledge', 'evolution', 'models', 'advanced'],
+        defaults: {
+            scenario: 'standard',
+            guardrails: {
+                enabled: true,
+                detectors: ['dangerous-command', 'role-permission', 'brute-retry', 'premature-done', 'blame-shift', 'idle-tool', 'busy-loop'],
+                autoLint: true,
+                beforeStop: true,
+            },
+            knowledge: { enabled: true, vectorSearch: true },
+            evolution: { enabled: true, autoApprove: false },
+            models: { routing: 'advanced' },
+        },
+    },
+    'china-local': {
+        id: 'china-local',
+        name: 'China Local',
+        description: 'Optimized for local model deployment in China (Qwen/GLM/DeepSeek compatible). Reduced guardrails for local model contexts.',
+        sections: ['basic', 'guardrails', 'models'],
+        defaults: {
+            scenario: 'standard',
+            guardrails: {
+                enabled: true,
+                detectors: ['dangerous-command', 'role-permission', 'brute-retry', 'premature-done'],
+                autoLint: true,
+                beforeStop: false,
+            },
+            knowledge: { enabled: false, vectorSearch: false },
+            evolution: { enabled: false, autoApprove: false },
+            models: { routing: 'advanced' },
+        },
+    },
+};
+const PROFILE_BOOTSTRAP_PACKS = {
+    minimal: ['external-cli'],
+    standard: ['external-cli'],
+    advanced: ['external-cli', 'memory', 'knowledge'],
+    'china-local': ['external-cli'],
+};
+const GOVERNANCE_PACK_BOOTSTRAP_PACKS = {
+    'frontend-app': ['ui'],
+};
+/**
+ * Get profile by ID, falling back to 'standard' if not found.
+ */
+export function getProfile(id) {
+    return PROFILES[id] ?? PROFILES.standard;
+}
+/**
+ * List all available profiles for display.
+ */
+export function listProfiles() {
+    return Object.values(PROFILES).map(p => ({
+        id: p.id,
+        name: p.name,
+        description: p.description,
+        bootstrapPacks: getRecommendedBootstrapPacks(p.id),
+        dependencyBootstrapCommand: getBootstrapPlanForProfile(p.id).inspectCommand,
+    }));
+}
+export function getRecommendedBootstrapPacks(profileId, governancePack) {
+    const profile = getProfile(profileId);
+    const selected = [
+        ...(PROFILE_BOOTSTRAP_PACKS[profile.id] ?? PROFILE_BOOTSTRAP_PACKS.standard),
+        ...(governancePack ? (GOVERNANCE_PACK_BOOTSTRAP_PACKS[governancePack] ?? []) : []),
+    ];
+    return unique(selected);
+}
+export function getBootstrapPlanForProfile(profileId, governancePack) {
+    const profile = getProfile(profileId);
+    const packs = getRecommendedBootstrapPacks(profile.id, governancePack);
+    const packArg = packs.join(',');
+    return {
+        profileId: profile.id,
+        governancePack,
+        packs,
+        inspectCommand: `scale bootstrap deps --pack ${packArg} --json`,
+        applyCommand: `scale bootstrap deps --pack ${packArg} --apply`,
+    };
+}
+/**
+ * Generate config.yaml content for a given profile.
+ * Returns only the sections relevant to the profile level.
+ */
+export function generateConfigForProfile(profileId, projectInfo) {
+    const profile = getProfile(profileId);
+    const d = profile.defaults;
+    const lines = [];
+    lines.push(`# SCALE Engine Configuration`);
+    lines.push(`# Profile: ${profile.name} — ${profile.description}`);
+    lines.push(`# Customize below, or change profile with: scale config profile <id>`);
+    lines.push(``);
+    lines.push(`version: 1`);
+    lines.push(`profile: ${profileId}`);
+    lines.push(``);
+    lines.push(`project:`);
+    lines.push(`  name: ${projectInfo.name}`);
+    if (projectInfo.type)
+        lines.push(`  type: ${projectInfo.type}`);
+    lines.push(``);
+    lines.push(`storage:`);
+    lines.push(`  db: .scale/scale.db`);
+    lines.push(`  events: .scale/events`);
+    lines.push(`  artifacts: .scale/artifacts`);
+    if (d.knowledge.vectorSearch) {
+        lines.push(`  knowledge:`);
+        lines.push(`    backend: graphify`);
+        lines.push(`    graph: graphify-out/graph.json`);
+        lines.push(`  memory:`);
+        lines.push(`    provider: gbrain`);
+    }
+    lines.push(``);
+    if (projectInfo.agents && projectInfo.agents.length > 0) {
+        lines.push(`agents:`);
+        for (const agent of projectInfo.agents) {
+            lines.push(`  - name: ${agent}`);
+        }
+        lines.push(``);
+    }
+    if (profile.sections.includes('guardrails')) {
+        lines.push(`guardrails:`);
+        lines.push(`  preTool:`);
+        lines.push(`    enabled: ${d.guardrails.enabled}`);
+        if (d.guardrails.detectors.length > 0) {
+            lines.push(`    detectors:`);
+            for (const det of d.guardrails.detectors) {
+                lines.push(`      - ${det}`);
+            }
+        }
+        lines.push(`  postTool:`);
+        lines.push(`    enabled: ${d.guardrails.enabled}`);
+        lines.push(`    autoLint:`);
+        lines.push(`      enabled: ${d.guardrails.autoLint}`);
+        lines.push(`  beforeStop:`);
+        lines.push(`    enabled: ${d.guardrails.beforeStop}`);
+        lines.push(`    requireVerification: true`);
+        lines.push(``);
+    }
+    if (profile.sections.includes('knowledge')) {
+        lines.push(`knowledge:`);
+        lines.push(`  extraction:`);
+        lines.push(`    enabled: ${d.knowledge.enabled}`);
+        lines.push(`  recall:`);
+        lines.push(`    topK: 3`);
+        lines.push(`    minRelevance: 0.4`);
+        lines.push(``);
+    }
+    if (profile.sections.includes('evolution')) {
+        lines.push(`evolution:`);
+        lines.push(`  enabled: ${d.evolution.enabled}`);
+        lines.push(`  autoApprove: ${d.evolution.autoApprove}`);
+        lines.push(``);
+    }
+    if (profile.sections.includes('models')) {
+        lines.push(`models:`);
+        lines.push(`  defaults:`);
+        if (d.models.routing === 'simple') {
+            lines.push(`    all: claude-sonnet-4-5`);
+        }
+        else if (profileId === 'china-local') {
+            lines.push(`    explore: qwen-2.5-72b`);
+            lines.push(`    plan: deepseek-v3`);
+            lines.push(`    implement: qwen-2.5-72b`);
+            lines.push(`    verify: qwen-2.5-7b`);
+            lines.push(`    architect: glm-4-plus`);
+        }
+        else {
+            lines.push(`    explore: claude-haiku`);
+            lines.push(`    plan: claude-sonnet-4-5`);
+            lines.push(`    implement: claude-sonnet-4-5`);
+            lines.push(`    verify: claude-haiku`);
+            lines.push(`    architect: claude-opus-4-5`);
+        }
+        lines.push(``);
+    }
+    lines.push(`logging:`);
+    lines.push(`  level: info`);
+    lines.push(`  file: .scale/scale.log`);
+    return lines.join('\n');
+}
+function unique(values) {
+    return [...new Set(values)];
+}
+//# sourceMappingURL=profiles.js.map

package/dist/config/profiles.js.map

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package/dist/context/AntiPatternRegistry.d.ts

@@ -0,0 +1,38 @@
+import type { IEventBus } from '../core/eventBus.js';
+export interface AntiPattern {
+    id: string;
+    principle: 'think-before-coding' | 'simplicity-first' | 'surgical-changes' | 'goal-driven-execution';
+    category: string;
+    title: string;
+    userRequest: string;
+    wrongCode: string;
+    wrongDescription: string;
+    correctApproach: string | string[];
+    correctCode?: string;
+    correctDescription: string;
+    testQuestion?: string;
+    tags: string[];
+}
+export interface AntiPatternMatch {
+    patternId: string;
+    detectedIn: string;
+    severity: 'high' | 'medium' | 'low';
+    suggestion: string;
+}
+export interface IAntiPatternRegistry {
+    getAntiPatterns(principle?: string): AntiPattern[];
+    searchAntiPatterns(query: string): AntiPattern[];
+    detectInCode(code: string): AntiPatternMatch[];
+    getExample(principle: string, category: string): AntiPattern | undefined;
+}
+export declare class AntiPatternRegistry implements IAntiPatternRegistry {
+    private patterns;
+    private eventBus;
+    constructor(eventBus?: IEventBus);
+    getAntiPatterns(principle?: string): AntiPattern[];
+    searchAntiPatterns(query: string): AntiPattern[];
+    detectInCode(code: string): AntiPatternMatch[];
+    getExample(principle: string, category: string): AntiPattern | undefined;
+    register(pattern: AntiPattern): void;
+}
+export declare function createAntiPatternRegistry(eventBus?: IEventBus): IAntiPatternRegistry;

package/dist/context/AntiPatternRegistry.js

@@ -0,0 +1,203 @@
+// SCALE Engine - Anti-Pattern Registry (andrej-karpathy-skills style)
+// Repository of common LLM coding mistakes with corrections
+import { logger } from '../core/logger.js';
+// ============================================================================
+// Anti-Pattern Database (from Karpathy EXAMPLES.md)
+// ============================================================================
+const KARPATHY_ANTIPATTERNS = [
+    // === Think Before Coding ===
+    {
+        id: 'AP-001',
+        principle: 'think-before-coding',
+        category: 'hidden-assumptions',
+        title: 'Hidden Assumptions',
+        userRequest: 'Add a feature to export user data',
+        wrongCode: `def export_users(format='json'):
+    users = User.query.all()
+    if format == 'json':
+        with open('users.json', 'w') as f:
+            json.dump([u.to_dict() for u in users], f)
+    return f"Exported {len(users)} users"`,
+        wrongDescription: 'Assumed export ALL users, assumed file location, assumed no pagination or privacy concerns',
+        correctApproach: ['Before implementing, clarify: 1. Scope: Export all or filtered? 2. Format: Download/API/background? 3. Fields: Which user fields? 4. Volume: How many users?'],
+        correctDescription: 'Surface assumptions explicitly, ask for clarification on ambiguous requirements',
+        testQuestion: 'Did you clarify scope, format, fields, and volume before implementing?',
+        tags: ['assumptions', 'privacy', 'scope', 'requirements']
+    },
+    {
+        id: 'AP-002',
+        principle: 'think-before-coding',
+        category: 'multiple-interpretations',
+        title: 'Multiple Interpretations Picked Silently',
+        userRequest: 'Make the search faster',
+        wrongCode: `@lru_cache(maxsize=1000)
+async def search(query: str) -> List[Result]:
+    # 200 lines of optimization without asking which "faster" matters`,
+        wrongDescription: 'Picked one interpretation of "faster" silently - could mean response time, throughput, or perceived UX',
+        correctApproach: ['"Make search faster" could mean: 1. Response time (< 100ms) 2. Throughput (more concurrent) 3. Perceived UX (partial results). Present all, let user choose.'],
+        correctDescription: 'Present multiple interpretations when ambiguity exists, do not pick silently',
+        testQuestion: 'Did you list all possible interpretations of the request?',
+        tags: ['ambiguity', 'interpretations', 'optimization']
+    },
+    // === Simplicity First ===
+    {
+        id: 'AP-003',
+        principle: 'simplicity-first',
+        category: 'over-abstraction',
+        title: 'Over-Abstraction',
+        userRequest: 'Add a function to calculate discount',
+        wrongCode: `class DiscountStrategy(ABC):
+    @abstractmethod
+    def calculate(self, amount: float) -> float: pass
+class PercentageDiscount(DiscountStrategy): ...
+class FixedDiscount(DiscountStrategy): ...
+class DiscountCalculator:
+    def __init__(self, config: DiscountConfig): ...`,
+        wrongDescription: 'Created Strategy pattern, abstract base class, config class for a simple percentage calculation',
+        correctApproach: 'Write a single function first. Add classes/abstractions only when multiple discount types are actually required.',
+        correctCode: `def calculate_discount(amount: float, percent: float) -> float:
+    return amount * (percent / 100)`,
+        correctDescription: 'One function until complexity is actually needed. Add classes when multiple discount types are required.',
+        testQuestion: 'Would a senior engineer say this is overcomplicated?',
+        tags: ['abstraction', 'design-patterns', 'overengineering']
+    },
+    {
+        id: 'AP-004',
+        principle: 'simplicity-first',
+        category: 'speculative-features',
+        title: 'Speculative Features',
+        userRequest: 'Save user preferences to database',
+        wrongCode: `class PreferenceManager:
+    def save(self, user_id, prefs, merge=True, validate=True, notify=False):
+        # Added caching, validation, merging, notifications - nobody asked`,
+        wrongDescription: 'Added caching, validation, merging, notifications - features nobody asked for',
+        correctApproach: 'Just save the preferences. Add caching when performance matters, validation when bad data appears, notifications when needed.',
+        correctCode: `def save_preferences(db, user_id: int, preferences: dict):
+    db.execute("UPDATE users SET preferences = ? WHERE id = ?", (json.dumps(preferences), user_id))`,
+        correctDescription: 'Add later if needed: caching (when performance matters), validation (when bad data appears)',
+        testQuestion: 'Did you add features beyond what was asked?',
+        tags: ['speculative', 'features', 'yagni']
+    },
+    // === Surgical Changes ===
+    {
+        id: 'AP-005',
+        principle: 'surgical-changes',
+        category: 'drive-by-refactoring',
+        title: 'Drive-by Refactoring',
+        userRequest: 'Fix the bug where empty emails crash the validator',
+        wrongCode: `# Changed comments, added docstring, improved email validation beyond bug,
+# added username validation nobody asked for`,
+        wrongDescription: 'Improved email validation beyond the bug, added username validation, changed comments, added docstring',
+        correctApproach: 'Only fix the empty email handling. Do not change comments, add docstrings, or improve adjacent code.',
+        correctDescription: 'Only changed the specific lines that fix empty email handling. No style changes, no extra validation.',
+        testQuestion: 'Does every changed line trace directly to the user request?',
+        tags: ['refactoring', 'surgical', 'minimal']
+    },
+    {
+        id: 'AP-006',
+        principle: 'surgical-changes',
+        category: 'style-drift',
+        title: 'Style Drift',
+        userRequest: 'Add logging to the upload function',
+        wrongCode: `# Changed quote style (' to "), added type hints, added docstring,
+# reformatted whitespace, changed boolean return logic`,
+        wrongDescription: 'Changed quote style, added type hints, added docstring, reformatted whitespace',
+        correctApproach: 'Match existing code style. Only add the logging statements without changing quotes, types, or formatting.',
+        correctDescription: 'Match existing style: single quotes, no type hints, existing boolean pattern, spacing style',
+        testQuestion: 'Did you match existing code style?',
+        tags: ['style', 'formatting', 'consistency']
+    },
+    // === Goal-Driven Execution ===
+    {
+        id: 'AP-007',
+        principle: 'goal-driven-execution',
+        category: 'vague-approach',
+        title: 'Vague Approach Without Success Criteria',
+        userRequest: 'Fix the authentication system',
+        wrongCode: `I'll fix auth by: 1. Review code 2. Identify issues 3. Make improvements 4. Test
+[Proceeds without clear success criteria]`,
+        wrongDescription: 'No verifiable success criteria, no reproduction test, vague steps',
+        correctApproach: ['Plan: 1. Write test: Change password -> verify session invalidated (Verify: test fails). 2. Implement (Verify: test passes). 3. Check edge cases (Verify: additional tests pass). 4. No regression (Verify: full suite green)'],
+        correctDescription: 'Transform vague tasks into verifiable goals with success criteria',
+        testQuestion: 'Can each step be independently verified?',
+        tags: ['goals', 'verification', 'success-criteria']
+    },
+    {
+        id: 'AP-008',
+        principle: 'goal-driven-execution',
+        category: 'fix-without-reproducing',
+        title: 'Fix Without Reproducing',
+        userRequest: 'The sorting breaks when there are duplicate scores',
+        wrongCode: `# Immediately changes sort logic without writing a reproduction test first`,
+        wrongDescription: 'Fixed without writing a test that reproduces the issue first',
+        correctApproach: ['1. Write test: sort_scores with duplicates -> verify consistent ordering. 2. Verify: run 10 times -> fails inconsistently. 3. Now fix with stable sort'],
+        correctDescription: 'Write test first that reproduces bug, verify test fails, then fix',
+        testQuestion: 'Did you write a test that reproduces the bug before fixing?',
+        tags: ['testing', 'tdd', 'reproduction']
+    }
+];
+// ============================================================================
+// AntiPatternRegistry Implementation
+// ============================================================================
+export class AntiPatternRegistry {
+    constructor(eventBus) {
+        this.patterns = new Map();
+        this.eventBus = eventBus ?? null;
+        for (const pattern of KARPATHY_ANTIPATTERNS) {
+            this.patterns.set(pattern.id, pattern);
+        }
+        logger.info({ count: this.patterns.size }, 'AntiPatternRegistry initialized');
+    }
+    getAntiPatterns(principle) {
+        const all = Array.from(this.patterns.values());
+        if (!principle)
+            return all;
+        return all.filter(p => p.principle === principle);
+    }
+    searchAntiPatterns(query) {
+        const lowerQuery = query.toLowerCase();
+        return Array.from(this.patterns.values()).filter(p => p.title.toLowerCase().includes(lowerQuery) ||
+            p.category.toLowerCase().includes(lowerQuery) ||
+            p.tags.some(t => t.includes(lowerQuery)) ||
+            p.userRequest.toLowerCase().includes(lowerQuery));
+    }
+    detectInCode(code) {
+        const matches = [];
+        const detectionRules = [
+            { pattern: 'AP-003', check: /class\s+\w+Strategy\s*\(/ },
+            { pattern: 'AP-003', check: /@abstractmethod/ },
+            { pattern: 'AP-004', check: /merge:\s*bool\s*=/ },
+            { pattern: 'AP-004', check: /validate:\s*bool\s*=/ },
+            { pattern: 'AP-004', check: /notify:\s*bool\s*=/ },
+        ];
+        for (const rule of detectionRules) {
+            if (rule.check.test(code)) {
+                const pattern = this.patterns.get(rule.pattern);
+                if (pattern) {
+                    matches.push({
+                        patternId: rule.pattern,
+                        detectedIn: 'code-structure',
+                        severity: 'high',
+                        suggestion: `Potential ${pattern.title}: ${pattern.correctDescription}`
+                    });
+                }
+            }
+        }
+        if (matches.length > 0) {
+            this.eventBus?.emit('antipattern.detected', { matches });
+        }
+        return matches;
+    }
+    getExample(principle, category) {
+        return Array.from(this.patterns.values()).find(p => p.principle === principle && p.category === category);
+    }
+    register(pattern) {
+        this.patterns.set(pattern.id, pattern);
+        this.eventBus?.emit('antipattern.registered', { patternId: pattern.id });
+        logger.info({ patternId: pattern.id }, 'Custom anti-pattern registered');
+    }
+}
+export function createAntiPatternRegistry(eventBus) {
+    return new AntiPatternRegistry(eventBus);
+}
+//# sourceMappingURL=AntiPatternRegistry.js.map

package/dist/context/AntiPatternRegistry.js.map

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

@@ -0,0 +1,20 @@
+export interface CavemanConfig {
+    enabled: boolean;
+    preserveTerms: string[];
+    symbolMap: Record<string, string>;
+    maxCompressionRatio: number;
+}
+export declare const DEFAULT_SYMBOL_MAP: Record<string, string>;
+export declare const DEFAULT_PRESERVE_TERMS: string[];
+export interface ICavemanCompressor {
+    compress(text: string, config: CavemanConfig): string;
+    shouldActivate(tokenUsage: number, tokenLimit: number): boolean;
+}
+export declare class CavemanCompressor implements ICavemanCompressor {
+    compress(text: string, config: CavemanConfig): string;
+    shouldActivate(tokenUsage: number, tokenLimit: number): boolean;
+    private removeFillerWords;
+    private applySymbols;
+}
+export declare function createCavemanCompressor(): ICavemanCompressor;
+export declare const DEFAULT_CAVEMAN_CONFIG: CavemanConfig;