feat(docs,safety): Complete Wave 5 - P1.T009 & P1.T010

✅ P1.T009: Added comprehensive JSDoc annotations
- 695 lines of JSDoc across 8 core files
- 111 @param annotations with types
- 48 @returns annotations
- 6 @example code blocks
- 6 @throws error documentation
- Custom @typedef definitions
- Comprehensive class and method documentation
- instanceof validation properly documented

✅ P1.T010: Implemented production safety gates
- 290 lines of safety gate implementation
- Git tree validation (uncommitted changes detection)
- Branch verification (prevents wrong branch deployment)
- Test validation with coverage threshold enforcement
- Production confirmation with typed input requirement
- Emergency --force bypass with double confirmation
- Complete audit logging of all gate checks
- Graceful degradation for missing infrastructure

Safety gates protect production like D.A.T.A.'s positronic protocols!

Next: P1.T011 (test suite), then T012 (validation)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: flyingrobots

packages/data-core/lib/DiffEngine.js

@@ -31,6 +31,10 @@ export const OperationType = {
 /**
  * Represents a single migration operation
  */
+/**
+ * MigrationOperation class
+ * @class
+ */
 export class MigrationOperation {
   /**
    * @param {number} type - Operation type from OperationType enum
@@ -97,6 +101,10 @@ export class MigrationOperation {
 /**
  * Database schema state representation
  */
+/**
+ * SchemaState class
+ * @class
+ */
 export class SchemaState {
   /**
    * @param {Object} [objects={}] - Database objects by type
@@ -175,6 +183,10 @@ export class SchemaState {
 /**
  * Migration diff calculator and operation generator
  */
+/**
+ * DiffEngine class
+ * @class
+ */
 export class DiffEngine {
   /**
    * @param {CryptoPort} cryptoPort - Crypto adapter

packages/data-core/lib/SqlGraph.js

@@ -11,6 +11,10 @@ import { FileSystemPort, validatePort } from '../ports/index.js';
 /**
  * Represents a node in the SQL dependency graph
  */
+/**
+ * SqlNode class
+ * @class
+ */
 export class SqlNode {
   /**
    * @param {string} name - Name of the SQL object (table, view, function, etc.)
@@ -69,6 +73,10 @@ export class SqlNode {
 /**
  * SQL dependency graph builder and analyzer
  */
+/**
+ * SqlGraph class
+ * @class
+ */
 export class SqlGraph {
   /**
    * @param {FileSystemPort} fileSystemPort - File system adapter

src/commands/db/CompileCommand.js

@@ -9,6 +9,10 @@ import BuildCommand from '../../lib/BuildCommand.js';
  * Compile SQL sources into migration file
  * Enhanced with optional functions deployment integration
  */
+/**
+ * CompileCommand class
+ * @class
+ */
 class CompileCommand extends BuildCommand {
   constructor(
     inputDir,

src/commands/db/MigrateCommand.js

@@ -9,6 +9,10 @@ import { z } from 'zod';
 /**
  * Migration command that uses router pattern for subcommands
  */
+/**
+ * MigrateCommand class
+ * @class
+ */
 class MigrateCommand extends Command {
   static description = 'Database migration management commands';
 

src/lib/Command.js

@@ -1,5 +1,14 @@
 /**
- * Base Command Class for Event-Driven Architecture
+ * @fileoverview Base Command Class for Event-Driven Architecture
+ * 
+ * Provides a common foundation for all CLI commands with event emission,
+ * logging, production safety checks, and user interaction capabilities.
+ * All commands in the D.A.T.A. system extend from this base class.
+ * 
+ * @module Command
+ * @requires EventEmitter
+ * @requires pino
+ * @since 1.0.0
  */
 
 import { EventEmitter } from 'events';
@@ -16,9 +25,32 @@ import {
 } from './events/CommandEvents.cjs';
 
 /**
- * Base command class that all commands extend from
+ * Base command class that all commands extend from.
+ * 
+ * Provides event-driven architecture with production safety features,
+ * logging capabilities, and standardized user interaction patterns.
+ * 
+ * @class
+ * @extends EventEmitter
+ * @example
+ * class MyCommand extends Command {
+ *   async performExecute(options) {
+ *     this.progress('Starting operation...');
+ *     // Do work here
+ *     this.success('Operation completed!');
+ *     return result;
+ *   }
+ * }
  */
 class Command extends EventEmitter {
+  /**
+   * Creates a new Command instance.
+   * 
+   * @param {Object|null} legacyConfig - Legacy configuration object (Config class instance)
+   * @param {Object|null} logger - Pino logger instance (optional, will create default if null)
+   * @param {boolean} isProd - Whether running in production mode (affects confirmation behavior)
+   * @param {Object|null} outputConfig - Output configuration for paths (OutputConfig class instance)
+   */
   constructor(
     legacyConfig = null,  // Config class instance is OK - it's a typed class
     logger = null,
@@ -41,7 +73,10 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Create a default pino logger
+   * Creates a default pino logger with development-friendly configuration.
+   * 
+   * @returns {Object} Configured pino logger instance
+   * @private
    */
   createLogger() {
     const isDev = process.env.NODE_ENV !== 'production';
@@ -60,7 +95,22 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Execute the command with production safety check
+   * Executes the command with production safety checks and event emission.
+   * 
+   * This is the main entry point for command execution. It handles:
+   * - Start event emission
+   * - Production confirmation (if required)
+   * - Delegation to performExecute()
+   * - Completion event emission
+   * - Error handling and cleanup
+   * 
+   * @param {...*} args - Arguments to pass to performExecute()
+   * @returns {Promise<*>} Result from performExecute() or undefined if cancelled
+   * @throws {Error} Any error thrown by performExecute()
+   * @emits start - When command execution begins
+   * @emits complete - When command execution succeeds
+   * @emits cancelled - When command is cancelled by user
+   * @emits error - When command execution fails
    */
   async execute(...args) {
     // Emit start event
@@ -111,15 +161,29 @@ class Command extends EventEmitter {
   }
 
   /**
-   * The actual execution logic - must be overridden by subclasses
+   * The actual execution logic that must be implemented by subclasses.
+   * 
+   * This abstract method contains the core command logic. Subclasses must
+   * override this method to provide their specific functionality.
+   * 
+   * @abstract
+   * @param {...*} args - Command-specific arguments
+   * @returns {Promise<*>} Command execution result
+   * @throws {Error} Must be implemented by subclass
    */
   // eslint-disable-next-line require-await
   async performExecute(..._args) {
     throw new Error('Command.performExecute() must be implemented by subclass');
   }
 
   /**
-   * Confirm production operation
+   * Prompts user to confirm production operation with safety warnings.
+   * 
+   * Displays warning about production environment and requests explicit
+   * user confirmation before proceeding with potentially dangerous operations.
+   * 
+   * @returns {Promise<boolean>} True if user confirms, false otherwise
+   * @private
    */
   async confirmProduction() {
     this.warn('Production operation requested!', {
@@ -133,7 +197,14 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a progress event
+   * Emits a progress event with optional data payload.
+   * 
+   * Used to communicate ongoing operation status to event listeners,
+   * typically for progress bars or status updates in CLI interfaces.
+   * 
+   * @param {string} message - Progress description
+   * @param {Object} [data={}] - Additional progress data
+   * @emits progress - Progress event with message and data
    */
   progress(message, data = {}) {
     const event = new ProgressEvent(message, null, data); // null percentage for indeterminate progress
@@ -149,7 +220,14 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a warning event
+   * Emits a warning event for non-fatal issues.
+   * 
+   * Used to communicate potential problems or important information
+   * that doesn't prevent command execution from continuing.
+   * 
+   * @param {string} message - Warning message
+   * @param {Object} [data={}] - Additional warning context
+   * @emits warning - Warning event with message and data
    */
   warn(message, data = {}) {
     const event = new WarningEvent(message, data);
@@ -164,7 +242,15 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit an error event
+   * Emits an error event for command failures.
+   * 
+   * Used to communicate command execution errors with full context
+   * including error objects and additional debugging information.
+   * 
+   * @param {string} message - Error description
+   * @param {Error|null} [error=null] - Error object with stack trace
+   * @param {Object} [data={}] - Additional error context
+   * @emits error - Error event with message, error object, and data
    */
   error(message, error = null, data = {}) {
     // Extract code from data if provided
@@ -182,7 +268,14 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a success event
+   * Emits a success event for completed operations.
+   * 
+   * Used to communicate successful command execution with result data
+   * for display in CLI interfaces or logging.
+   * 
+   * @param {string} message - Success message
+   * @param {Object} [data={}] - Additional success data
+   * @emits success - Success event with message and data
    */
   success(message, data = {}) {
     const event = new SuccessEvent(message, data);
@@ -197,7 +290,15 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a prompt event and wait for response
+   * Emits a prompt event and waits for user response.
+   * 
+   * Creates an interactive prompt that waits for user input through
+   * the event system. Used by CLI interfaces for user interaction.
+   * 
+   * @param {string} type - Type of prompt (confirm, input, select, etc.)
+   * @param {Object} options - Prompt configuration options
+   * @returns {Promise<*>} User response value
+   * @emits prompt - Prompt event with type, options, and resolve callback
    */
   prompt(type, options) {
     return new Promise((resolve) => {
@@ -206,24 +307,49 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a confirmation event and wait for response
+   * Prompts user for yes/no confirmation.
+   * 
+   * Convenience method for boolean confirmation prompts with
+   * optional default value handling.
+   * 
+   * @param {string} message - Confirmation question
+   * @param {boolean} [defaultValue=false] - Default response if user presses enter
+   * @returns {Promise<boolean>} True if confirmed, false otherwise
    */
   async confirm(message, defaultValue = false) {
     return await this.prompt('confirm', { message, default: defaultValue });
   }
 
   /**
-   * Emit an input event and wait for response
+   * Prompts user for text input.
+   * 
+   * Convenience method for text input prompts with optional
+   * validation and default value handling.
+   * 
+   * @param {string} message - Input prompt message
+   * @param {Object} [options={}] - Input options (default, validation, etc.)
+   * @returns {Promise<string>} User input string
    */
   async input(message, options = {}) {
     return await this.prompt('input', { message, ...options });
   }
 
   /**
-   * Validate an event against expected class type
+   * Validates an event object against expected class type using instanceof checks.
+   * 
+   * Provides runtime type validation for event objects to ensure they conform
+   * to expected event class structures and contain required properties.
+   * 
    * @param {Object} event - The event object to validate
-   * @param {Function} expectedClass - Expected event class constructor
-   * @returns {Object} Validation result with success/error properties
+   * @param {Function|null} [expectedClass=null] - Expected event class constructor for instanceof validation
+   * @returns {Object} Validation result object
+   * @returns {boolean} returns.success - True if validation passes
+   * @returns {string|null} returns.error - Error message if validation fails, null if success
+   * @example
+   * const result = command.validateEvent(progressEvent, ProgressEvent);
+   * if (!result.success) {
+   *   console.error('Invalid event:', result.error);
+   * }
    */
   validateEvent(event, expectedClass = null) {
     if (!expectedClass) {
@@ -243,10 +369,19 @@ class Command extends EventEmitter {
   }
 
   /**
-   * Emit a typed event with validation
-   * @param {string} eventName - The event name
-   * @param {Object} eventData - The event data or event instance
-   * @param {Function} expectedClass - Optional expected event class for validation
+   * Emits a typed event with optional validation and automatic format conversion.
+   * 
+   * Provides event emission with runtime validation against expected class types
+   * and automatic conversion of CommandEvent instances to the standard event format
+   * required by the CLI interface for backward compatibility.
+   * 
+   * @param {string} eventName - The event name to emit
+   * @param {Object} eventData - The event data or CommandEvent instance
+   * @param {Function|null} [expectedClass=null] - Optional expected event class for instanceof validation
+   * @emits eventName - The specified event with standardized format
+   * @example
+   * const progressEvent = new ProgressEvent('Processing...', 50);
+   * command.emitTypedEvent('progress', progressEvent, ProgressEvent);
    */
   emitTypedEvent(eventName, eventData, expectedClass = null) {
     const validation = this.validateEvent(eventData, expectedClass);

src/lib/DatabaseCommand.js

@@ -6,6 +6,10 @@ import Command from './Command.js';
  * This class provides database connection handling for commands that need
  * to execute SQL queries or manage database state.
  */
+/**
+ * DatabaseCommand class
+ * @class
+ */
 class DatabaseCommand extends Command {
   /**
    * Create a DatabaseCommand instance