@hongmaple0820/med-scale-research-os 0.43.0

package/dist/workflow/WorkspaceSafety.js

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+import { execFileSync } from 'node:child_process';
+export function inspectWorkspaceSafety(projectDir) {
+    try {
+        execFileSync('git', ['-C', projectDir, 'rev-parse', '--show-toplevel'], { encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore'] });
+    }
+    catch {
+        return {
+            checked: true,
+            gitRepository: false,
+            blocked: false,
+            conflicts: [],
+            message: 'Project directory is not a git repository; workspace conflict check skipped.',
+        };
+    }
+    try {
+        const porcelain = execFileSync('git', ['-C', projectDir, 'status', '--porcelain=v1', '--untracked-files=no'], {
+            encoding: 'utf-8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+        });
+        const conflicts = porcelain
+            .split(/\r?\n/)
+            .map(line => line.trimEnd())
+            .filter(Boolean)
+            .filter(line => isUnmergedPorcelainStatus(line.slice(0, 2)))
+            .map(line => line.slice(3).trim());
+        return {
+            checked: true,
+            gitRepository: true,
+            blocked: conflicts.length > 0,
+            conflicts,
+            message: conflicts.length > 0
+                ? `Unresolved git conflicts: ${conflicts.join(', ')}`
+                : 'No unresolved git conflicts detected.',
+        };
+    }
+    catch (error) {
+        return {
+            checked: true,
+            gitRepository: true,
+            blocked: true,
+            conflicts: [],
+            message: `Git workspace conflict check failed: ${error instanceof Error ? error.message : String(error)}`,
+        };
+    }
+}
+export function isUnmergedPorcelainStatus(status) {
+    return ['DD', 'AU', 'UD', 'UA', 'DU', 'AA', 'UU'].includes(status);
+}
+//# sourceMappingURL=WorkspaceSafety.js.map

package/dist/workflow/WorkspaceSafety.js.map

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package/dist/workflow/WorkspaceTopology.d.ts

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+export type WorkspaceTopologyKind = 'single' | 'monorepo' | 'polyrepo' | 'submodule-workspace' | 'moe';
+export type WorkspaceRepositoryRole = 'root' | 'service' | 'package' | 'submodule' | 'nested-repo' | 'external';
+export interface WorkspaceRepositoryConfig {
+    name: string;
+    path: string;
+    role: WorkspaceRepositoryRole;
+    required?: boolean;
+    services?: string[];
+    branchPattern?: string;
+    remote?: string;
+    dependsOn?: string[];
+    pointerFile?: string;
+}
+export interface WorkspaceBranchPolicy {
+    mode?: 'gitlab-flow';
+    integrationBranch?: string;
+    productionBranch?: string;
+    protectedBranches?: string[];
+    featurePrefixes?: string[];
+    releasePrefixes?: string[];
+    hotfixPrefixes?: string[];
+    requireAuthorScopeDate?: boolean;
+}
+export interface WorkspaceFinishPolicy {
+    requireCleanRepositories?: boolean;
+    requirePushedBranches?: boolean;
+    requireRootPointerUpdate?: boolean;
+    requireReviewArtifacts?: boolean;
+}
+export interface WorkspaceTopologyConfig {
+    version?: number;
+    topology: WorkspaceTopologyKind;
+    repositories: WorkspaceRepositoryConfig[];
+    branchPolicy?: WorkspaceBranchPolicy;
+    finishPolicy?: WorkspaceFinishPolicy;
+}
+export interface ResolvedWorkspaceTopology extends WorkspaceTopologyConfig {
+    version: number;
+    configured: boolean;
+    configPath: string;
+    branchPolicy: Required<WorkspaceBranchPolicy>;
+    finishPolicy: Required<WorkspaceFinishPolicy>;
+    warnings: string[];
+}
+export interface WorkspaceTopologyOptions {
+    projectDir?: string;
+    scaleDir?: string;
+}
+export interface WorkspaceTopologyTemplateOptions {
+    topology?: WorkspaceTopologyKind;
+    projectName?: string;
+}
+export declare function loadWorkspaceTopology(projectDir?: string, scaleDir?: string): ResolvedWorkspaceTopology | null;
+export declare function resolveWorkspaceTopology(options?: WorkspaceTopologyOptions): ResolvedWorkspaceTopology;
+export declare function writeWorkspaceTopologyTemplate(projectDir?: string, options?: WorkspaceTopologyTemplateOptions, scaleDir?: string): string;
+export declare function workspaceTopologyTemplate(options?: WorkspaceTopologyTemplateOptions): string;
+export declare function workspaceTopologyPath(projectDir?: string, scaleDir?: string): string;
+export declare function resolveRepositoryPath(projectDir: string, repo: WorkspaceRepositoryConfig): string;

package/dist/workflow/WorkspaceTopology.js

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+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { isAbsolute, join, resolve } from 'node:path';
+export function loadWorkspaceTopology(projectDir = process.cwd(), scaleDir = '.scale') {
+    const path = workspaceTopologyPath(projectDir, scaleDir);
+    if (!existsSync(path))
+        return null;
+    const raw = JSON.parse(readFileSync(path, 'utf-8'));
+    return normalizeWorkspaceTopology(raw, {
+        configured: true,
+        configPath: path,
+    });
+}
+export function resolveWorkspaceTopology(options = {}) {
+    const projectDir = resolve(options.projectDir ?? process.cwd());
+    const scaleDir = options.scaleDir ?? '.scale';
+    const loaded = loadWorkspaceTopology(projectDir, scaleDir);
+    if (loaded)
+        return loaded;
+    return normalizeWorkspaceTopology({
+        version: 1,
+        topology: 'single',
+        repositories: [
+            { name: 'root', path: '.', role: 'root', required: true },
+        ],
+    }, {
+        configured: false,
+        configPath: workspaceTopologyPath(projectDir, scaleDir),
+        warnings: [`No workspace topology found at ${workspaceTopologyPath(projectDir, scaleDir)}; using single-repository defaults.`],
+    });
+}
+export function writeWorkspaceTopologyTemplate(projectDir = process.cwd(), options = {}, scaleDir = '.scale') {
+    const path = workspaceTopologyPath(projectDir, scaleDir);
+    const dir = path.split(/[\\/]/).slice(0, -1).join('/');
+    if (dir && !existsSync(dir))
+        mkdirSync(dir, { recursive: true });
+    writeFileSync(path, workspaceTopologyTemplate(options), 'utf-8');
+    return path;
+}
+export function workspaceTopologyTemplate(options = {}) {
+    const topology = options.topology ?? 'moe';
+    const repositories = [
+        {
+            name: 'root',
+            path: '.',
+            role: 'root',
+            required: true,
+        },
+    ];
+    if (topology === 'monorepo') {
+        repositories.push({
+            name: 'example-service',
+            path: 'services/example',
+            role: 'service',
+            required: false,
+            services: ['example'],
+        });
+    }
+    else if (topology === 'moe' || topology === 'polyrepo') {
+        repositories.push({
+            name: 'example-service',
+            path: '../example-service',
+            role: 'external',
+            required: false,
+            services: ['example'],
+            branchPattern: 'codex/*',
+            remote: 'origin',
+            dependsOn: [],
+            pointerFile: 'repos/example-service.ref',
+        });
+    }
+    else if (topology === 'submodule-workspace') {
+        repositories.push({
+            name: 'example-service',
+            path: 'services/example',
+            role: 'submodule',
+            required: false,
+            services: ['example'],
+            remote: 'origin',
+        });
+    }
+    const config = {
+        version: 1,
+        topology,
+        repositories,
+        branchPolicy: defaultBranchPolicy(),
+        finishPolicy: defaultFinishPolicy(topology),
+    };
+    return `${JSON.stringify(config, null, 2)}\n`;
+}
+export function workspaceTopologyPath(projectDir = process.cwd(), scaleDir = '.scale') {
+    const root = isAbsolute(scaleDir) ? scaleDir : join(projectDir, scaleDir);
+    return join(root, 'workspace.json');
+}
+export function resolveRepositoryPath(projectDir, repo) {
+    return isAbsolute(repo.path) ? repo.path : resolve(projectDir, repo.path);
+}
+function normalizeWorkspaceTopology(raw, meta) {
+    const topology = normalizeTopology(raw.topology);
+    const repositories = normalizeRepositories(raw.repositories);
+    const warnings = [
+        ...(meta.warnings ?? []),
+        ...topologyWarnings(topology, repositories),
+    ];
+    return {
+        version: raw.version ?? 1,
+        topology,
+        repositories,
+        branchPolicy: {
+            ...defaultBranchPolicy(),
+            ...(raw.branchPolicy ?? {}),
+        },
+        finishPolicy: {
+            ...defaultFinishPolicy(topology),
+            ...(raw.finishPolicy ?? {}),
+        },
+        configured: meta.configured,
+        configPath: meta.configPath,
+        warnings,
+    };
+}
+function normalizeTopology(value) {
+    if (value === 'single'
+        || value === 'monorepo'
+        || value === 'polyrepo'
+        || value === 'submodule-workspace'
+        || value === 'moe') {
+        return value;
+    }
+    return 'single';
+}
+function normalizeRepositories(repositories) {
+    const normalized = (repositories ?? [])
+        .filter(repo => Boolean(repo.name && repo.path))
+        .map(repo => ({
+        ...repo,
+        path: normalizeRelative(repo.path),
+        required: repo.required !== false,
+    }));
+    if (!normalized.some(repo => repo.role === 'root' || repo.path === '.')) {
+        normalized.unshift({ name: 'root', path: '.', role: 'root', required: true });
+    }
+    return normalized.length > 0
+        ? normalized
+        : [{ name: 'root', path: '.', role: 'root', required: true }];
+}
+function defaultFinishPolicy(topology) {
+    return {
+        requireCleanRepositories: true,
+        requirePushedBranches: true,
+        requireRootPointerUpdate: topology === 'moe' || topology === 'submodule-workspace',
+        requireReviewArtifacts: topology === 'moe',
+    };
+}
+function defaultBranchPolicy() {
+    return {
+        mode: 'gitlab-flow',
+        integrationBranch: 'dev',
+        productionBranch: 'master',
+        protectedBranches: ['dev', 'master', 'main'],
+        featurePrefixes: ['feature/', 'feat/', 'fix/', 'chore/', 'docs/', 'codex/'],
+        releasePrefixes: ['release/'],
+        hotfixPrefixes: ['hotfix/'],
+        requireAuthorScopeDate: true,
+    };
+}
+function normalizeRelative(path) {
+    return path.replace(/\\/g, '/');
+}
+function topologyWarnings(topology, repositories) {
+    if (topology !== 'moe' && topology !== 'polyrepo')
+        return [];
+    return repositories
+        .filter(repo => repo.path !== '.' && !isAbsolute(repo.path) && !repo.path.startsWith('../'))
+        .map(repo => `${topology} repository "${repo.name}" uses path "${repo.path}" under the root checkout; prefer a sibling or absolute path to avoid nested git conflicts.`);
+}
+//# sourceMappingURL=WorkspaceTopology.js.map

package/dist/workflow/WorkspaceTopology.js.map

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package/dist/workflow/autofix/AutoFixEngine.d.ts

@@ -0,0 +1,37 @@
+import type { IEventBus } from '../../core/eventBus.js';
+export interface AutoFixOptions {
+    scope: 'lint' | 'test' | 'security' | 'all';
+    maxAttempts: number;
+    escalateModel: boolean;
+    dryRun: boolean;
+}
+export interface FixAttempt {
+    attempt: number;
+    category: string;
+    diagnosticCommand: string;
+    fixAction: string;
+    fixOutput: string;
+    success: boolean;
+    verifierCommand: string;
+    verifierOutput: string;
+    durationMs: number;
+}
+export interface AutoFixReport {
+    totalFailures: number;
+    fixed: number;
+    unfixed: number;
+    attempts: FixAttempt[];
+    summary: string;
+    recommendation: string;
+}
+export declare class AutoFixEngine {
+    private eventBus;
+    private attempts;
+    constructor(eventBus: IEventBus);
+    run(options: AutoFixOptions): Promise<AutoFixReport>;
+    private scan;
+    private diagnose;
+    private applyFix;
+    private reVerify;
+    private escalateCommand;
+}

package/dist/workflow/autofix/AutoFixEngine.js

@@ -0,0 +1,169 @@
+import { logger } from '../../core/logger.js';
+import { execSync } from 'node:child_process';
+export class AutoFixEngine {
+    constructor(eventBus) {
+        this.eventBus = eventBus;
+        this.attempts = [];
+    }
+    async run(options) {
+        const report = {
+            totalFailures: 0,
+            fixed: 0,
+            unfixed: 0,
+            attempts: [],
+            summary: '',
+            recommendation: '',
+        };
+        logger.info({ scope: options.scope }, 'AutoFix engine starting');
+        // Step 1: Scan for failures
+        const failures = await this.scan(options.scope);
+        report.totalFailures = failures.length;
+        if (failures.length === 0) {
+            report.summary = 'No failures detected. All gates passing.';
+            report.recommendation = 'No action needed.';
+            return report;
+        }
+        // Step 2: For each failure, diagnose → fix → re-verify
+        for (let i = 0; i < failures.length; i++) {
+            const failure = failures[i];
+            logger.info({ failure, index: i }, `Processing failure ${i + 1}/${failures.length}`);
+            let fixed = false;
+            for (let attempt = 1; attempt <= options.maxAttempts; attempt++) {
+                const start = Date.now();
+                // Diagnose
+                const diagnosis = await this.diagnose(failure, attempt);
+                // Fix
+                const fixOutput = options.dryRun
+                    ? `[DRY RUN] Would fix: ${failure.category}`
+                    : await this.applyFix(failure, attempt);
+                // Re-verify
+                const verifierOutput = options.dryRun
+                    ? { passed: false, output: `[DRY RUN] Would re-verify: ${failure.category}` }
+                    : await this.reVerify(failure);
+                const success = !options.dryRun && verifierOutput.passed;
+                const fa = {
+                    attempt,
+                    category: failure.category,
+                    diagnosticCommand: diagnosis,
+                    fixAction: failure.fixStrategy ?? 'auto-detect',
+                    fixOutput,
+                    success,
+                    verifierCommand: failure.verifyCommand ?? '',
+                    verifierOutput: verifierOutput.output ?? '',
+                    durationMs: Date.now() - start,
+                };
+                this.attempts.push(fa);
+                this.eventBus.emit('autofix.attempt', fa);
+                if (success) {
+                    fixed = true;
+                    report.fixed++;
+                    break;
+                }
+                // Escalate model tier on retry
+                if (options.escalateModel) {
+                    const escalatedCommand = await this.escalateCommand(failure, attempt);
+                    logger.info({ attempt, escalatedCommand }, 'Model escalated for retry');
+                }
+            }
+            if (!fixed) {
+                report.unfixed++;
+                logger.warn({ failure }, `Failed to fix after ${options.maxAttempts} attempts`);
+            }
+        }
+        report.summary = `AutoFix complete: ${report.fixed}/${report.totalFailures} fixed, ${report.unfixed} unresolved.`;
+        report.recommendation = report.unfixed > 0
+            ? `Manual intervention needed for ${report.unfixed} failure(s). Review evidence at .scale/evidence/autofix/`
+            : 'All failures resolved. Proceed with gate verification.';
+        report.attempts = this.attempts;
+        this.eventBus.emit('autofix.complete', report);
+        return report;
+    }
+    async scan(scope) {
+        const failures = [];
+        try {
+            if (scope === 'all' || scope === 'lint') {
+                try {
+                    execSync('npm run lint', { encoding: 'utf-8', stdio: 'pipe' });
+                }
+                catch (e) {
+                    failures.push({
+                        category: 'lint',
+                        command: 'npm run lint',
+                        description: e.stderr?.slice(0, 500) ?? 'Lint failure detected',
+                        fixStrategy: 'eslint --fix',
+                        verifyCommand: 'npm run lint',
+                    });
+                }
+            }
+            if (scope === 'all' || scope === 'test') {
+                try {
+                    execSync('npm test', { encoding: 'utf-8', stdio: 'pipe' });
+                }
+                catch (e) {
+                    failures.push({
+                        category: 'test',
+                        command: 'npm test',
+                        description: e.stderr?.slice(0, 500) ?? 'Test failure detected',
+                        fixStrategy: 'run-and-inspect',
+                        verifyCommand: 'npm test',
+                    });
+                }
+            }
+            if (scope === 'all' || scope === 'security') {
+                // Use existing security gate patterns from src/workflow/gates/GateSystem.ts
+                failures.push({
+                    category: 'security',
+                    command: 'scale preflight --profile security --json',
+                    description: 'Security gate scan requested',
+                    fixStrategy: 'manual-review',
+                    verifyCommand: 'scale preflight --profile security --json',
+                });
+            }
+        }
+        catch (err) {
+            logger.error({ err }, 'Error during scan');
+        }
+        return failures;
+    }
+    async diagnose(failure, attempt) {
+        // Generate a diagnostic command based on failure type and attempt
+        const commands = {
+            lint: `Analyze lint errors (attempt ${attempt}): ${failure.description.slice(0, 200)}`,
+            test: `Analyze test failures (attempt ${attempt}): ${failure.description.slice(0, 200)}`,
+            security: `Analyze security findings (attempt ${attempt}): ${failure.description.slice(0, 200)}`,
+        };
+        return commands[failure.category] ?? `Diagnose: ${failure.description.slice(0, 200)}`;
+    }
+    async applyFix(failure, attempt) {
+        switch (failure.fixStrategy) {
+            case 'eslint --fix':
+                try {
+                    return execSync('npx eslint --fix .', { encoding: 'utf-8', stdio: 'pipe' });
+                }
+                catch (e) {
+                    return e.stdout ?? e.stderr ?? 'eslint --fix ran with warnings';
+                }
+            case 'run-and-inspect':
+                return `Test fix attempt ${attempt}: re-run and inspect failures`;
+            case 'manual-review':
+                return `Security fix attempt ${attempt}: review and apply mitigations`;
+            default:
+                return `Auto-fix attempt ${attempt} using strategy: ${failure.fixStrategy}`;
+        }
+    }
+    async reVerify(failure) {
+        try {
+            const output = execSync(failure.verifyCommand, { encoding: 'utf-8', stdio: 'pipe' });
+            return { passed: true, output };
+        }
+        catch (e) {
+            return { passed: false, output: e.stderr ?? e.stdout ?? 'Re-verification failed' };
+        }
+    }
+    async escalateCommand(failure, attempt) {
+        const tiers = ['fast', 'balanced', 'powerful'];
+        const tier = tiers[Math.min(attempt, tiers.length - 1)];
+        return `${failure.category} fix attempt ${attempt} → escalated to ${tier} model tier`;
+    }
+}
+//# sourceMappingURL=AutoFixEngine.js.map

package/dist/workflow/autofix/AutoFixEngine.js.map

@@ -0,0 +1 @@
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package/dist/workflow/autonomous/AutonomousDevLoop.d.ts

@@ -0,0 +1,88 @@
+import type { IEventBus } from '../../core/eventBus.js';
+import { WorklogManager, type WorklogState } from './WorklogManager.js';
+export interface DevLoopConfig {
+    /** Base directory for .scale artifacts */
+    scaleDir: string;
+    /** Path to worklog markdown file */
+    worklogPath: string;
+    /** Path to baton directory for cross-session persistence */
+    batonPath: string;
+    /** Max defects to fix per run (prevents session timeout) */
+    maxDefectsPerRun: number;
+    /** Max features to develop per run */
+    maxFeaturesPerRun: number;
+    /** Command to run QA tests */
+    qaCommand: string;
+    /** Working directory for QA command execution */
+    cwd: string;
+}
+export interface QAResult {
+    passed: boolean;
+    totalTests: number;
+    passedTests: number;
+    failedTests: number;
+    failures: QAFailure[];
+    duration: number;
+    rawOutput: string;
+}
+export interface QAFailure {
+    testName: string;
+    file: string;
+    error: string;
+}
+export interface FixResult {
+    entryId: string;
+    success: boolean;
+    description: string;
+    filesChanged: string[];
+}
+export interface DevResult {
+    entryId: string;
+    success: boolean;
+    description: string;
+    filesChanged: string[];
+}
+export interface LoopState {
+    runId: string;
+    startedAt: string;
+    phase: 'read_worklog' | 'run_qa' | 'fix_defects' | 'develop_features' | 'update_worklog' | 'write_baton' | 'complete';
+    worklogState?: WorklogState;
+    qaResult?: QAResult;
+    fixResults: FixResult[];
+    devResult?: DevResult;
+    errors: string[];
+}
+export interface LoopResult {
+    runId: string;
+    success: boolean;
+    duration: number;
+    phase: LoopState['phase'];
+    qaPassed: boolean;
+    defectsFixed: number;
+    featureProgressed: boolean;
+    errors: string[];
+    nextAction: string;
+}
+export declare function createDefaultConfig(overrides?: Partial<DevLoopConfig>): DevLoopConfig;
+export declare class AutonomousDevLoop {
+    private config;
+    private eventBus;
+    private worklogManager;
+    constructor(eventBus: IEventBus, config?: Partial<DevLoopConfig>);
+    /** Execute the autonomous development loop */
+    run(): Promise<LoopResult>;
+    private readWorklog;
+    private runQA;
+    /** Parse QA output into structured result */
+    private parseQAOutput;
+    private fixDefects;
+    private developFeatures;
+    private updateWorklogState;
+    private writeBaton;
+    private buildBatonSession;
+    private buildNextPrompt;
+    private determineNextAction;
+    private buildResult;
+    getConfig(): DevLoopConfig;
+    getWorklogManager(): WorklogManager;
+}