@nexus-cortex/core 4.26.0

package/dist/file-tracking/ContentAddressableStore.d.ts.map

@@ -0,0 +1 @@
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package/dist/file-tracking/ContentAddressableStore.js

@@ -0,0 +1,187 @@
+/**
+ * Content-Addressable File Storage
+ * Implements SHA-256 based checkpoint storage for Claude CLI
+ * Based on research: 02-claude-cli-analysis/FILE_CHECKPOINT_SYSTEM.md
+ */
+import * as crypto from 'crypto';
+import * as fs from 'fs/promises';
+import * as path from 'path';
+/**
+ * Content-addressable storage manager
+ * Uses SHA-256 hashing to deduplicate file content
+ */
+export class ContentAddressableStore {
+    baseDir;
+    sessionId;
+    // R10 (Opus parallel-bench): initialize() ran fs.mkdir(recursive) on every
+    // saveBackup. Memoize the promise so the syscall fires once per instance.
+    initPromise;
+    constructor(baseDir, sessionId) {
+        this.baseDir = baseDir;
+        this.sessionId = sessionId;
+    }
+    /**
+     * Get storage directory for current session
+     * Pattern: {baseDir}/file-history/{sessionId}/
+     */
+    getStorageDir() {
+        return path.join(this.baseDir, 'file-history', this.sessionId);
+    }
+    /**
+     * Initialize storage directory
+     * Creates directory if it doesn't exist
+     */
+    async initialize() {
+        if (!this.initPromise) {
+            const storageDir = this.getStorageDir();
+            this.initPromise = fs.mkdir(storageDir, { recursive: true }).then(() => undefined);
+        }
+        return this.initPromise;
+    }
+    /**
+     * Calculate SHA-256 hash of content
+     * Returns first 16 characters (matches Claude CLI behavior)
+     */
+    calculateHash(content) {
+        const hash = crypto.createHash('sha256');
+        hash.update(content, 'utf8');
+        return hash.digest('hex').substring(0, 16);
+    }
+    /**
+     * Generate backup filename
+     * Pattern: {hash}@v{version}
+     */
+    generateBackupFilename(hash, version) {
+        return `${hash}@v${version}`;
+    }
+    /**
+     * Save file content to content-addressable storage
+     * Returns backup file info
+     */
+    async saveBackup(content, version) {
+        await this.initialize();
+        const hash = this.calculateHash(content);
+        const backupFileName = this.generateBackupFilename(hash, version);
+        const fullPath = path.join(this.getStorageDir(), backupFileName);
+        // Write backup file
+        await fs.writeFile(fullPath, content, 'utf8');
+        // R10: size from the in-memory content — no redundant fs.stat syscall.
+        return {
+            backupFileName,
+            version,
+            hash,
+            fullPath,
+            timestamp: new Date().toISOString(),
+            size: Buffer.byteLength(content, 'utf8')
+        };
+    }
+    /**
+     * Load backup file content
+     */
+    async loadBackup(backupFileName) {
+        const fullPath = path.join(this.getStorageDir(), backupFileName);
+        return await fs.readFile(fullPath, 'utf8');
+    }
+    /**
+     * Check if backup file exists
+     */
+    async backupExists(backupFileName) {
+        const fullPath = path.join(this.getStorageDir(), backupFileName);
+        try {
+            await fs.access(fullPath);
+            return true;
+        }
+        catch {
+            return false;
+        }
+    }
+    /**
+     * List all backup files for this session
+     * Returns sorted by version number (newest first)
+     */
+    async listBackups() {
+        const storageDir = this.getStorageDir();
+        try {
+            const files = await fs.readdir(storageDir);
+            const backups = [];
+            for (const file of files) {
+                const match = file.match(/^([a-f0-9]{16})@v(\d+)$/);
+                if (match) {
+                    const [, hash, versionStr] = match;
+                    const version = parseInt(versionStr, 10);
+                    const fullPath = path.join(storageDir, file);
+                    const stats = await fs.stat(fullPath);
+                    backups.push({
+                        backupFileName: file,
+                        version,
+                        hash: hash,
+                        fullPath,
+                        timestamp: stats.mtime.toISOString(),
+                        size: stats.size
+                    });
+                }
+            }
+            // Sort by version descending (newest first)
+            backups.sort((a, b) => b.version - a.version);
+            return backups;
+        }
+        catch (error) {
+            // Directory doesn't exist yet
+            return [];
+        }
+    }
+    /**
+     * Find backups for a specific file (by hash prefix)
+     * Useful for finding all versions of same content
+     */
+    async findBackupsByHash(hashPrefix) {
+        const allBackups = await this.listBackups();
+        return allBackups.filter(b => b.hash.startsWith(hashPrefix));
+    }
+    /**
+     * Delete old backups
+     * Keeps only the N most recent versions
+     */
+    async pruneBackups(keepCount) {
+        const backups = await this.listBackups();
+        if (backups.length <= keepCount) {
+            return 0;
+        }
+        const toDelete = backups.slice(keepCount);
+        let deletedCount = 0;
+        for (const backup of toDelete) {
+            try {
+                await fs.unlink(backup.fullPath);
+                deletedCount++;
+            }
+            catch (error) {
+                console.warn(`Failed to delete backup ${backup.backupFileName}:`, error);
+            }
+        }
+        return deletedCount;
+    }
+    /**
+     * Get storage statistics
+     */
+    async getStats() {
+        const backups = await this.listBackups();
+        const totalSize = backups.reduce((sum, b) => sum + b.size, 0);
+        return {
+            totalFiles: backups.length,
+            totalSize
+        };
+    }
+    /**
+     * Clean up session storage (delete all backups)
+     */
+    async cleanup() {
+        const storageDir = this.getStorageDir();
+        try {
+            await fs.rm(storageDir, { recursive: true, force: true });
+        }
+        catch (error) {
+            console.warn(`Failed to cleanup storage directory ${storageDir}:`, error);
+        }
+    }
+}
+//# sourceMappingURL=ContentAddressableStore.js.map

package/dist/file-tracking/ContentAddressableStore.js.map

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package/dist/file-tracking/FileCheckpointManager.d.ts

@@ -0,0 +1,103 @@
+/**
+ * File Checkpoint Manager
+ * Tracks file modifications and creates automatic snapshots
+ * Based on research: 02-claude-cli-analysis/FILE_CHECKPOINT_SYSTEM.md
+ */
+import { FileHistorySnapshotMessage, FileBackupInfo } from '../session/MessageTypes.js';
+/**
+ * Tracked file state
+ */
+interface TrackedFile {
+    filePath: string;
+    currentVersion: number;
+    lastBackup: string | null;
+    lastModified: string;
+    modified: boolean;
+}
+/**
+ * Snapshot creation result
+ */
+export interface SnapshotResult {
+    success: boolean;
+    messageId: string;
+    snapshotMessage: FileHistorySnapshotMessage;
+    backedUpFiles: string[];
+    error?: string;
+}
+/**
+ * File restoration result
+ */
+export interface RestoreResult {
+    success: boolean;
+    filePath: string;
+    version: number;
+    error?: string;
+}
+/**
+ * Manages file checkpoint lifecycle
+ */
+export declare class FileCheckpointManager {
+    private store;
+    private trackedFiles;
+    constructor(baseDir: string, sessionId: string);
+    /**
+     * Initialize checkpoint manager
+     */
+    initialize(): Promise<void>;
+    /**
+     * Mark file as modified
+     * Called after Write or Edit tool usage
+     */
+    markModified(filePath: string): void;
+    /**
+     * Create snapshot for current message
+     * Backs up all modified files
+     */
+    createSnapshot(messageId: string): Promise<SnapshotResult>;
+    /**
+     * Create empty snapshot (no files tracked or modified)
+     */
+    private createEmptySnapshot;
+    /**
+     * Read file content
+     * Helper method for backup creation
+     */
+    private readFileContent;
+    /**
+     * Restore file from backup
+     */
+    restoreFile(filePath: string, version: number): Promise<RestoreResult>;
+    /**
+     * Get file version history
+     * Returns all versions for a tracked file
+     */
+    getFileHistory(filePath: string): FileBackupInfo[] | null;
+    /**
+     * Get all tracked files
+     */
+    getTrackedFiles(): string[];
+    /**
+     * Get tracked file info
+     */
+    getTrackedFileInfo(filePath: string): TrackedFile | null;
+    /**
+     * Load snapshots from session history
+     * Restores tracked file state from existing snapshots
+     */
+    loadFromSnapshots(snapshots: FileHistorySnapshotMessage[]): void;
+    /**
+     * Get checkpoint statistics
+     */
+    getStats(): Promise<{
+        trackedFiles: number;
+        totalBackups: number;
+        totalSize: number;
+        modifiedFiles: number;
+    }>;
+    /**
+     * Clean up checkpoint storage
+     */
+    cleanup(): Promise<void>;
+}
+export {};
+//# sourceMappingURL=FileCheckpointManager.d.ts.map

package/dist/file-tracking/FileCheckpointManager.d.ts.map

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package/dist/file-tracking/FileCheckpointManager.js

@@ -0,0 +1,269 @@
+/**
+ * File Checkpoint Manager
+ * Tracks file modifications and creates automatic snapshots
+ * Based on research: 02-claude-cli-analysis/FILE_CHECKPOINT_SYSTEM.md
+ */
+import { v4 as uuidv4 } from 'uuid';
+import * as fs from 'fs/promises';
+import { ContentAddressableStore } from './ContentAddressableStore.js';
+/**
+ * Manages file checkpoint lifecycle
+ */
+export class FileCheckpointManager {
+    store;
+    trackedFiles;
+    constructor(baseDir, sessionId) {
+        this.store = new ContentAddressableStore(baseDir, sessionId);
+        this.trackedFiles = new Map();
+    }
+    /**
+     * Initialize checkpoint manager
+     */
+    async initialize() {
+        await this.store.initialize();
+    }
+    /**
+     * Mark file as modified
+     * Called after Write or Edit tool usage
+     */
+    markModified(filePath) {
+        const tracked = this.trackedFiles.get(filePath);
+        if (tracked) {
+            tracked.modified = true;
+            tracked.lastModified = new Date().toISOString();
+        }
+        else {
+            // Start tracking new file
+            this.trackedFiles.set(filePath, {
+                filePath,
+                currentVersion: 0,
+                lastBackup: null,
+                lastModified: new Date().toISOString(),
+                modified: true
+            });
+        }
+    }
+    /**
+     * Create snapshot for current message
+     * Backs up all modified files
+     */
+    async createSnapshot(messageId) {
+        const backedUpFiles = [];
+        const trackedFileBackups = {};
+        try {
+            // Process each tracked file
+            for (const [filePath, tracked] of this.trackedFiles) {
+                if (tracked.modified) {
+                    // File was modified, create backup
+                    const content = await this.readFileContent(filePath);
+                    const nextVersion = tracked.currentVersion + 1;
+                    const backup = await this.store.saveBackup(content, nextVersion);
+                    // Update tracked state
+                    tracked.currentVersion = nextVersion;
+                    tracked.lastBackup = backup.backupFileName;
+                    tracked.modified = false;
+                    tracked.lastModified = backup.timestamp;
+                    trackedFileBackups[filePath] = {
+                        backupFileName: backup.backupFileName,
+                        version: nextVersion,
+                        backupTime: backup.timestamp
+                    };
+                    backedUpFiles.push(filePath);
+                }
+                else {
+                    // File not modified, keep existing backup info
+                    trackedFileBackups[filePath] = {
+                        backupFileName: tracked.lastBackup,
+                        version: tracked.currentVersion,
+                        backupTime: tracked.lastModified
+                    };
+                }
+            }
+            // Create snapshot message
+            const snapshotMessage = {
+                type: 'file-history-snapshot',
+                uuid: uuidv4(),
+                timestamp: new Date().toISOString(),
+                messageId,
+                snapshot: {
+                    messageId,
+                    trackedFileBackups,
+                    timestamp: new Date().toISOString()
+                },
+                isSnapshotUpdate: backedUpFiles.length > 0
+            };
+            return {
+                success: true,
+                messageId,
+                snapshotMessage,
+                backedUpFiles
+            };
+        }
+        catch (error) {
+            return {
+                success: false,
+                messageId,
+                snapshotMessage: this.createEmptySnapshot(messageId),
+                backedUpFiles,
+                error: error instanceof Error ? error.message : String(error)
+            };
+        }
+    }
+    /**
+     * Create empty snapshot (no files tracked or modified)
+     */
+    createEmptySnapshot(messageId) {
+        return {
+            type: 'file-history-snapshot',
+            uuid: uuidv4(),
+            timestamp: new Date().toISOString(),
+            messageId,
+            snapshot: {
+                messageId,
+                trackedFileBackups: {},
+                timestamp: new Date().toISOString()
+            },
+            isSnapshotUpdate: false
+        };
+    }
+    /**
+     * Read file content
+     * Helper method for backup creation
+     */
+    async readFileContent(filePath) {
+        try {
+            return await fs.readFile(filePath, 'utf8');
+        }
+        catch (error) {
+            throw new Error(`Failed to read file ${filePath}: ${error}`);
+        }
+    }
+    /**
+     * Restore file from backup
+     */
+    async restoreFile(filePath, version) {
+        const tracked = this.trackedFiles.get(filePath);
+        if (!tracked) {
+            return {
+                success: false,
+                filePath,
+                version,
+                error: `File ${filePath} is not being tracked`
+            };
+        }
+        if (version > tracked.currentVersion || version < 1) {
+            return {
+                success: false,
+                filePath,
+                version,
+                error: `Invalid version ${version}. Valid range: 1-${tracked.currentVersion}`
+            };
+        }
+        try {
+            // Find backup with this version
+            const allBackups = await this.store.listBackups();
+            const backup = allBackups.find(b => b.version === version);
+            if (!backup) {
+                return {
+                    success: false,
+                    filePath,
+                    version,
+                    error: `Backup for version ${version} not found`
+                };
+            }
+            // Load backup content
+            const content = await this.store.loadBackup(backup.backupFileName);
+            // Restore file
+            await fs.writeFile(filePath, content, 'utf8');
+            // Mark as modified (will be backed up on next snapshot)
+            this.markModified(filePath);
+            return {
+                success: true,
+                filePath,
+                version
+            };
+        }
+        catch (error) {
+            return {
+                success: false,
+                filePath,
+                version,
+                error: error instanceof Error ? error.message : String(error)
+            };
+        }
+    }
+    /**
+     * Get file version history
+     * Returns all versions for a tracked file
+     */
+    getFileHistory(filePath) {
+        const tracked = this.trackedFiles.get(filePath);
+        if (!tracked) {
+            return null;
+        }
+        // Build history from tracked state
+        const history = [];
+        for (let v = 1; v <= tracked.currentVersion; v++) {
+            history.push({
+                backupFileName: v === tracked.currentVersion ? tracked.lastBackup : `v${v}`,
+                version: v,
+                backupTime: v === tracked.currentVersion ? tracked.lastModified : 'unknown'
+            });
+        }
+        return history;
+    }
+    /**
+     * Get all tracked files
+     */
+    getTrackedFiles() {
+        return Array.from(this.trackedFiles.keys());
+    }
+    /**
+     * Get tracked file info
+     */
+    getTrackedFileInfo(filePath) {
+        return this.trackedFiles.get(filePath) || null;
+    }
+    /**
+     * Load snapshots from session history
+     * Restores tracked file state from existing snapshots
+     */
+    loadFromSnapshots(snapshots) {
+        // Process snapshots in chronological order
+        for (const snapshot of snapshots) {
+            if (!snapshot.isSnapshotUpdate) {
+                continue; // Skip empty snapshots
+            }
+            // Update tracked file state
+            for (const [filePath, backupInfo] of Object.entries(snapshot.snapshot.trackedFileBackups)) {
+                this.trackedFiles.set(filePath, {
+                    filePath,
+                    currentVersion: backupInfo.version,
+                    lastBackup: backupInfo.backupFileName,
+                    lastModified: backupInfo.backupTime,
+                    modified: false
+                });
+            }
+        }
+    }
+    /**
+     * Get checkpoint statistics
+     */
+    async getStats() {
+        const storeStats = await this.store.getStats();
+        return {
+            trackedFiles: this.trackedFiles.size,
+            totalBackups: storeStats.totalFiles,
+            totalSize: storeStats.totalSize,
+            modifiedFiles: Array.from(this.trackedFiles.values()).filter(f => f.modified).length
+        };
+    }
+    /**
+     * Clean up checkpoint storage
+     */
+    async cleanup() {
+        await this.store.cleanup();
+        this.trackedFiles.clear();
+    }
+}
+//# sourceMappingURL=FileCheckpointManager.js.map

package/dist/file-tracking/FileCheckpointManager.js.map

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package/dist/file-tracking/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * File checkpoint system
+ * Content-addressable storage for file version tracking
+ */
+export * from './ContentAddressableStore.js';
+export * from './FileCheckpointManager.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/file-tracking/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/file-tracking/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,8BAA8B,CAAC;AAC7C,cAAc,4BAA4B,CAAC"}

package/dist/file-tracking/index.js

@@ -0,0 +1,7 @@
+/**
+ * File checkpoint system
+ * Content-addressable storage for file version tracking
+ */
+export * from './ContentAddressableStore.js';
+export * from './FileCheckpointManager.js';
+//# sourceMappingURL=index.js.map

package/dist/file-tracking/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/file-tracking/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,8BAA8B,CAAC;AAC7C,cAAc,4BAA4B,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,54 @@
+/**
+ * @nexus-cortex/core - Core orchestration library implementing Claude CLI architecture
+ *
+ * This package provides:
+ * - Conversation compaction with 9-section summaries
+ * - Content-addressable file checkpoints
+ * - Deterministic system-reminder injection
+ * - JSONL-based session storage
+ * - Multi-provider LLM orchestration
+ * - Helper model middleware with automatic fallback
+ * - Timeline-based conversation tracking
+ * - Historical context retrieval tools
+ */
+export * from './adapters/index.js';
+export * from './models/index.js';
+export { ContextBudgetManager, StoredCompactionManager } from './conversation/index.js';
+export { HelperModelMiddleware, ErrorClassificationMiddleware, RetryMiddleware, PermissionsMiddleware, SystemMessageMiddleware, MentorshipMiddleware, WhitelistPolicy, BlacklistPolicy, FileOperationPolicy, BashCommandPolicy, CLIApprovalHandler, AutoApproveHandler, DenyAllHandler, IPCApprovalHandler, // For sub-agent permission forwarding
+PermissionAuditLogger, PermissionEvaluator, PermissionConfigLoader, PermissionPresets, resolvePermissionProfilePath, grantToolInProfile, revokeToolInProfile, listProfilePolicies, getApprovalHandlerFromProfile, setApprovalHandlerInProfile, readPermissionProfile, resolvePermissionWriteTarget } from './middleware/index.js';
+export type { CostTracking, PermissionPolicy, PermissionDecision, PermissionContext, PermissionAuditEntry, ApprovalHandler, FileOperationPolicyConfig, BashCommandPolicyConfig, PermissionsMiddlewareOptions } from './middleware/index.js';
+export { SessionTimeline, CheckpointManager, JSONLHistoryStore } from './session/index.js';
+export type { Message, UserMessage, AssistantMessage, SystemMessage } from './session/index.js';
+export * from './tools/index.js';
+export * from './mcp/index.js';
+export * from './config/index.js';
+export * from './orchestrator/index.js';
+export * from './file-tracking/index.js';
+export * from './system-messages/index.js';
+export * from './agents/index.js';
+export * from './commands/index.js';
+export * from './utils/index.js';
+export * from './ui/index.js';
+export { ModelRouterMatrix, estimateCost as estimateModelCost, resolveMaxMatrixBytes } from './training/ModelRouterMatrix.js';
+export type { BenchmarkRecord, ModelScore, CostEfficiencyProfile, ScoringMatrix } from './training/ModelRouterMatrix.js';
+export { classifyTask } from './training/TaskClassifier.js';
+export type { TaskType } from './training/TaskClassifier.js';
+export { ResearchBacklog, computePriority as computeDeficiencyPriority } from './training/ResearchBacklog.js';
+export type { DeficiencyRecord, DeficiencyStatus, Severity, NewDeficiency } from './training/ResearchBacklog.js';
+export { ExperimentLedger } from './training/ExperimentLedger.js';
+export type { ExperimentRecord, ExperimentTaskResult, ExperimentDecision, NewExperiment, DecisionUpdate } from './training/ExperimentLedger.js';
+export { compareVersions, regressionScan, toTaskResult } from './training/VersionComparison.js';
+export type { TaskComparison, CompareOptions, RegressionReport } from './training/VersionComparison.js';
+export { decideExperiment, bootstrapCI, permutationPValue, sidakThreshold, mcFwerThreshold, aggregateEffect, mulberry32, } from './training/AutoResearchStats.js';
+export type { RNG, TaskArms, GateOptions, ExperimentVerdict } from './training/AutoResearchStats.js';
+export { evaluateExperiment as evaluateAutoResearchExperiment, verifyOnHoldout } from './training/AutoResearchGate.js';
+export type { EvaluateInput, EvaluateResult } from './training/AutoResearchGate.js';
+export { thompsonSelect } from './training/ThompsonRouter.js';
+export type { ThompsonOptions } from './training/ThompsonRouter.js';
+export { gradeRun, runBench, parseTaskSet } from './training/BenchRunner.js';
+export type { Verifier, TaskSpec, JudgeFn, GradeResult, HarnessRunner, HarnessRunResult, RunBenchOptions, BenchSummary, BenchTaskSummary, } from './training/BenchRunner.js';
+export { runExperiment } from './training/ExperimentRunner.js';
+export type { ExperimentArms, RunExperimentOptions, ExperimentResult, ExperimentBenchSummaries, } from './training/ExperimentRunner.js';
+export * as RuntimeInterfaces from './interfaces/index.js';
+export { NodeConfigProvider, NodeHistoryStoreAdapter, NodeToolExecutorAdapter, NodePermissionAdapter } from './adapters/node/index.js';
+//# sourceMappingURL=index.d.ts.map