sqlew 2.1.4 → 3.0.2

package/dist/index.js

@@ -8,12 +8,13 @@ import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
 import { CallToolRequestSchema, ListToolsRequestSchema, } from '@modelcontextprotocol/sdk/types.js';
 import { initializeDatabase, closeDatabase, setConfigValue, getAllConfig } from './database.js';
 import { CONFIG_KEYS } from './constants.js';
-import { setDecision, getContext, getDecision, searchByTags, getVersions, searchByLayer, quickSetDecision, searchAdvanced, setDecisionBatch, hasUpdates, setFromTemplate, createTemplate, listTemplates } from './tools/context.js';
+import { setDecision, getContext, getDecision, searchByTags, getVersions, searchByLayer, quickSetDecision, searchAdvanced, setDecisionBatch, hasUpdates, setFromTemplate, createTemplate, listTemplates, hardDeleteDecision } from './tools/context.js';
 import { sendMessage, getMessages, markRead, sendMessageBatch } from './tools/messaging.js';
 import { recordFileChange, getFileChanges, checkFileLock, recordFileChangeBatch } from './tools/files.js';
 import { addConstraint, getConstraints, deactivateConstraint } from './tools/constraints.js';
-import { getLayerSummary, clearOldData, getStats, getActivityLog } from './tools/utils.js';
+import { getLayerSummary, clearOldData, getStats, getActivityLog, flushWAL } from './tools/utils.js';
 import { getConfig, updateConfig } from './tools/config.js';
+import { createTask, updateTask, getTask, listTasks, moveTask, linkTask, archiveTask, batchCreateTasks, taskHelp } from './tools/tasks.js';
 // Parse command-line arguments
 const args = process.argv.slice(2);
 const parsedArgs = {};
@@ -80,8 +81,8 @@ catch (error) {
 }
 // Create MCP server
 const server = new Server({
-    name: 'mcp-sklew',
-    version: '2.1.4',
+    name: 'mcp-sqlew',
+    version: '3.0.0',
 }, {
     capabilities: {
         tools: {},
@@ -93,52 +94,19 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
         tools: [
             {
                 name: 'decision',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-Context Management - Store decisions with metadata (tags, layers, versions, scopes)
-
-## Quick Examples
-- Set decision: {action: "set", key: "auth_method", value: "jwt", layer: "business", tags: ["security"]}
-- Get decision: {action: "get", key: "auth_method"}
-- List decisions: {action: "list", status: "active", layer: "business"}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| set | action, key, value, layer | agent, version, status, tags, scopes |
-| get | action, key | version |
-| list | action | status, layer, tags, scope, tag_match, limit, offset |
-| search_tags | action, tags | match_mode, status, layer |
-| search_layer | action, layer | status, include_tags |
-| versions | action, key | - |
-| quick_set | action, key, value | agent, layer, version, status, tags, scopes |
-| search_advanced | action | layers, tags_all, tags_any, exclude_tags, scopes, updated_after, updated_before, decided_by, statuses, search_text, sort_by, sort_order, limit, offset |
-| set_batch | action, decisions | atomic |
-| has_updates | action, agent_name, since_timestamp | - |
-| set_from_template | action, template, key, value, layer | agent, version, status, tags, scopes |
-| create_template | action, name, defaults | required_fields, created_by |
-| list_templates | action | - |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "Parameter \\"value\\" is required" → Provide value parameter directly (not nested in defaults)
-- "Invalid layer" → Use: presentation, business, data, infrastructure, cross-cutting
-- "Invalid status" → Use: active, deprecated, draft
-
-## Valid Values
-- **layer**: presentation | business | data | infrastructure | cross-cutting
-- **status**: active | deprecated | draft
-- **tag_match**: AND | OR
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Context Management - Store decisions with metadata (tags, layers, versions, scopes)
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
                         action: {
                             type: 'string',
                             description: 'Action',
-                            enum: ['set', 'get', 'list', 'search_tags', 'search_layer', 'versions', 'quick_set', 'search_advanced', 'set_batch', 'has_updates', 'set_from_template', 'create_template', 'list_templates', 'help']
+                            enum: ['set', 'get', 'list', 'search_tags', 'search_layer', 'versions', 'quick_set', 'search_advanced', 'set_batch', 'has_updates', 'set_from_template', 'create_template', 'list_templates', 'hard_delete', 'help', 'example']
                         },
                         key: { type: 'string' },
                         value: { type: ['string', 'number'] },
@@ -179,41 +147,16 @@ Use action: "help" for detailed documentation.`,
             },
             {
                 name: 'message',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-Agent Messaging - Send messages between agents with priority levels and read tracking
-
-## Quick Examples
-- Send message: {action: "send", from_agent: "bot1", msg_type: "info", message: "Task complete"}
-- Get messages: {action: "get", agent_name: "bot1", unread_only: true}
-- Mark as read: {action: "mark_read", agent_name: "bot1", message_ids: [1, 2, 3]}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| send | action, from_agent, msg_type, message | to_agent, priority, payload |
-| get | action, agent_name | unread_only, priority_filter, msg_type_filter, limit |
-| mark_read | action, agent_name, message_ids | - |
-| send_batch | action, messages | atomic |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "Invalid msg_type" → Use: decision, warning, request, info
-- "Invalid priority" → Use: low, medium, high, critical
-- "message_ids array cannot be empty" → Provide at least one message ID
-
-## Valid Values
-- **msg_type**: decision | warning | request | info
-- **priority**: low | medium | high | critical (default: medium)
-- **to_agent**: agent name or null for broadcast
-- **atomic** (batch): true (all-or-nothing) | false (best-effort, recommended for AI agents)
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Agent Messaging - Send messages between agents with priority levels and read tracking
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
-                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['send', 'get', 'mark_read', 'send_batch', 'help'] },
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['send', 'get', 'mark_read', 'send_batch', 'help', 'example'] },
                         agent_name: { type: 'string' },
                         from_agent: { type: 'string' },
                         to_agent: { type: ['string', 'null'] },
@@ -235,41 +178,16 @@ Use action: "help" for detailed documentation.`,
             },
             {
                 name: 'file',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-File Change Tracking - Track file changes with layer classification and lock detection
-
-## Quick Examples
-- Record change: {action: "record", file_path: "src/index.ts", agent_name: "bot1", change_type: "modified", layer: "infrastructure"}
-- Get changes: {action: "get", agent_name: "bot1", layer: "infrastructure", limit: 10}
-- Check lock: {action: "check_lock", file_path: "src/index.ts", lock_duration: 300}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| record | action, file_path, agent_name, change_type | layer, description |
-| get | action | file_path, agent_name, layer, change_type, since, limit |
-| check_lock | action, file_path | lock_duration |
-| record_batch | action, file_changes | atomic |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "Invalid change_type" → Use: created, modified, deleted
-- "Invalid layer" → Use: presentation, business, data, infrastructure, cross-cutting
-- "Parameter \\"file_changes\\" must contain at least one item" → Provide non-empty array
-
-## Valid Values
-- **change_type**: created | modified | deleted
-- **layer**: presentation | business | data | infrastructure | cross-cutting
-- **lock_duration**: seconds (default: 300 = 5 minutes)
-- **atomic** (batch): true (all-or-nothing) | false (best-effort, recommended for AI agents)
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+File Change Tracking - Track file changes with layer classification and lock detection
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
-                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['record', 'get', 'check_lock', 'record_batch', 'help'] },
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['record', 'get', 'check_lock', 'record_batch', 'help', 'example'] },
                         file_path: { type: 'string' },
                         agent_name: { type: 'string' },
                         change_type: { type: 'string', enum: ['created', 'modified', 'deleted'] },
@@ -287,44 +205,16 @@ Use action: "help" for detailed documentation.`,
             },
             {
                 name: 'constraint',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-Constraint Management - Manage architectural rules and requirements
-
-## What are Constraints vs Decisions?
-- **Decision**: Documents a choice that was made ("We chose JWT over sessions")
-- **Constraint**: Enforces a rule that must be followed ("API response time must be <100ms")
-
-## Quick Examples
-- Add constraint: {action: "add", category: "performance", constraint_text: "API response <100ms", priority: "high", layer: "business"}
-- Get constraints: {action: "get", category: "performance", active_only: true}
-- Deactivate: {action: "deactivate", constraint_id: 5}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| add | action, category, constraint_text | priority, layer, tags, created_by |
-| get | action | category, layer, priority, tags, active_only, limit |
-| deactivate | action, constraint_id | - |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "Invalid category" → Use: performance, architecture, security
-- "category and constraint_text are required" → Provide both required fields
-- "constraint_id is required" → Provide valid constraint ID number
-
-## Valid Values
-- **category**: performance | architecture | security
-- **priority**: low | medium | high | critical (default: medium)
-- **layer**: presentation | business | data | infrastructure | cross-cutting
-- **active_only**: true (default) | false
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Constraint Management - Manage architectural rules and requirements
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
-                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['add', 'get', 'deactivate', 'help'] },
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['add', 'get', 'deactivate', 'help', 'example'] },
                         constraint_id: { type: 'number' },
                         category: { type: 'string', enum: ['performance', 'architecture', 'security'] },
                         constraint_text: { type: 'string' },
@@ -340,43 +230,16 @@ Use action: "help" for detailed documentation.`,
             },
             {
                 name: 'stats',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-Statistics & Utilities - View stats, activity logs, and manage data cleanup
-
-## Quick Examples
-- Layer summary: {action: "layer_summary"}
-- DB statistics: {action: "db_stats"}
-- Clear old data: {action: "clear", messages_older_than_hours: 48, file_changes_older_than_days: 14}
-- Activity log: {action: "activity_log", since: "1h", agent_names: ["bot1"], limit: 50}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| layer_summary | action | - |
-| db_stats | action | - |
-| clear | action | messages_older_than_hours, file_changes_older_than_days |
-| activity_log | action | since, agent_names, actions, limit |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "Invalid 'since' parameter" → Use relative format (5m, 1h, 2d) or ISO timestamp
-
-## Valid Values
-- **since**: Relative time (5m, 1h, 2d) or ISO 8601 timestamp
-- **agent_names**: Array of agent names or ["*"] for all
-- **limit**: Number (default: 100 for activity_log)
-
-## Clear Action Behavior
-- **Without parameters**: Uses config-based weekend-aware retention
-- **With parameters**: Overrides config, no weekend-awareness
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Statistics & Utilities - View stats, activity logs, manage data cleanup, and WAL checkpoints
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
-                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['layer_summary', 'db_stats', 'clear', 'activity_log', 'help'] },
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['layer_summary', 'db_stats', 'clear', 'activity_log', 'flush', 'help', 'example'] },
                         messages_older_than_hours: { type: 'number' },
                         file_changes_older_than_days: { type: 'number' },
                         since: { type: 'string', description: 'Time filter (e.g., "5m", "1h", "2d" or ISO timestamp)' },
@@ -389,40 +252,16 @@ Use action: "help" for detailed documentation.`,
             },
             {
                 name: 'config',
-                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
-
-Configuration - Manage auto-deletion settings with weekend-aware retention
-
-## Quick Examples
-- Get config: {action: "get"}
-- Update config: {action: "update", ignoreWeekend: true, messageRetentionHours: 48, fileHistoryRetentionDays: 10}
-
-## Parameter Requirements by Action
-
-| Action | Required Parameters | Optional Parameters |
-|--------|-------------------|---------------------|
-| get | action | - |
-| update | action | ignoreWeekend, messageRetentionHours, fileHistoryRetentionDays |
-
-## Common Errors & Fixes
-- "Unknown action: undefined" → Add action parameter (REQUIRED!)
-- "messageRetentionHours must be between 1 and 168" → Use value 1-168 (1 week max)
-- "fileHistoryRetentionDays must be between 1 and 90" → Use value 1-90
-
-## Valid Values
-- **ignoreWeekend**: true (skip weekends in retention calculation) | false (standard time-based)
-- **messageRetentionHours**: 1-168 (default: 24)
-- **fileHistoryRetentionDays**: 1-90 (default: 7)
-
-## Weekend-Aware Behavior
-- **ignoreWeekend=false**: 24h = 24 hours ago (standard)
-- **ignoreWeekend=true**: 24h on Monday = Friday (skips Sat/Sun)
-
-Use action: "help" for detailed documentation.`,
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Configuration - Manage auto-deletion settings with weekend-aware retention
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
                 inputSchema: {
                     type: 'object',
                     properties: {
-                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['get', 'update', 'help'] },
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['get', 'update', 'help', 'example'] },
                         ignoreWeekend: { type: 'boolean' },
                         messageRetentionHours: { type: 'number', minimum: 1, maximum: 168 },
                         fileHistoryRetentionDays: { type: 'number', minimum: 1, maximum: 90 },
@@ -430,6 +269,42 @@ Use action: "help" for detailed documentation.`,
                     required: ['action'],
                 },
             },
+            {
+                name: 'task',
+                description: `**REQUIRED PARAMETER**: action (must be specified in ALL calls)
+
+Kanban Task Watcher - AI-optimized task management with auto-stale detection
+
+Use action: "help" for detailed documentation.
+Use action: "example" for comprehensive usage examples.`,
+                inputSchema: {
+                    type: 'object',
+                    properties: {
+                        action: { type: 'string', description: 'Action (use "help" for usage)', enum: ['create', 'update', 'get', 'list', 'move', 'link', 'archive', 'batch_create', 'help', 'example'] },
+                        task_id: { type: 'number' },
+                        title: { type: 'string' },
+                        description: { type: 'string' },
+                        acceptance_criteria: { type: 'string' },
+                        notes: { type: 'string' },
+                        priority: { type: 'number', minimum: 1, maximum: 4 },
+                        assigned_agent: { type: 'string' },
+                        created_by_agent: { type: 'string' },
+                        layer: { type: 'string', enum: ['presentation', 'business', 'data', 'infrastructure', 'cross-cutting'] },
+                        tags: { type: 'array', items: { type: 'string' } },
+                        status: { type: 'string', enum: ['todo', 'in_progress', 'waiting_review', 'blocked', 'done', 'archived'] },
+                        new_status: { type: 'string', enum: ['todo', 'in_progress', 'waiting_review', 'blocked', 'done', 'archived'] },
+                        link_type: { type: 'string', enum: ['decision', 'constraint', 'file'] },
+                        target_id: { type: ['string', 'number'] },
+                        link_relation: { type: 'string' },
+                        limit: { type: 'number', default: 50 },
+                        offset: { type: 'number', default: 0 },
+                        // batch_create parameters
+                        tasks: { type: 'array', description: 'Array of tasks for batch operation (max: 50)' },
+                        atomic: { type: 'boolean', description: 'Atomic mode - all succeed or all fail (default: true)' },
+                    },
+                    required: ['action'],
+                },
+            },
         ],
     };
 });
@@ -496,10 +371,59 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                     case 'list_templates':
                         result = listTemplates(params);
                         break;
+                    case 'hard_delete':
+                        result = hardDeleteDecision(params);
+                        break;
                     case 'help':
                         result = {
                             tool: 'decision',
                             description: 'Manage decisions with metadata (tags, layers, versions, scopes)',
+                            purpose: {
+                                title: '⚠️ CRITICAL: Store WHY and REASON, Not WHAT',
+                                principle: 'Decisions table is for ARCHITECTURAL CONTEXT and REASONING, NOT implementation logs or task completion status',
+                                what_to_store: {
+                                    correct: [
+                                        'WHY a design choice was made (e.g., "Chose JWT over sessions because stateless auth scales better for our microservice architecture")',
+                                        'REASONING behind architecture decisions (e.g., "Moved oscillator_type to MonophonicSynthConfig to separate synthesis methods - FM operators use different config")',
+                                        'PROBLEM ANALYSIS and solution rationale (e.g., "Nested transaction bug: setDecision wraps in transaction, batch also wraps → solution: extract internal helper without transaction wrapper")',
+                                        'DESIGN TRADE-OFFS and alternatives considered (e.g., "Query builder limited to simple filters, kept domain-specific logic inline for maintainability")',
+                                        'CONSTRAINTS and requirements reasoning (e.g., "API response must be <100ms because mobile clients timeout at 200ms")',
+                                        'BREAKING CHANGES with migration rationale (e.g., "Removed /v1/users endpoint - clients must use /v2/users with pagination for scalability")'
+                                    ],
+                                    incorrect: [
+                                        '❌ Task completion logs (e.g., "Task 5 completed", "Refactoring done", "Tests passing") → Use tasks tool instead',
+                                        '❌ Implementation status (e.g., "Added validators.ts", "Fixed bug in batch_create", "Updated README") → These are WHAT, not WHY',
+                                        '❌ Test results (e.g., "All tests passing", "Integration tests complete", "v3.0.2 testing verified") → Temporary status, not architectural context',
+                                        '❌ Git commit summaries (e.g., "Released v3.0.2", "Created git commit 2bf55a0") → Belongs in git history',
+                                        '❌ Documentation updates (e.g., "README reorganized", "Help actions enhanced") → Implementation logs, not decisions',
+                                        '❌ Build status (e.g., "Build succeeded", "TypeScript compiled with zero errors") → Temporary status'
+                                    ]
+                                },
+                                analogy: {
+                                    git_history: 'WHAT changed (files, lines, commits)',
+                                    code_comments: 'HOW it works (implementation details, algorithms)',
+                                    sqlew_decisions: 'WHY it was changed (reasoning, trade-offs, context)',
+                                    sqlew_tasks: 'WHAT needs to be done (work items, status, completion)'
+                                },
+                                examples: [
+                                    {
+                                        key: 'api/auth/jwt-choice',
+                                        value: 'Chose JWT over session-based auth because: (1) Stateless design scales horizontally, (2) Mobile clients can cache tokens, (3) Microservice architecture requires distributed auth. Trade-off: Revocation requires token blacklist, but acceptable for 15-min token lifetime.',
+                                        explanation: 'Explains WHY JWT was chosen, considers trade-offs, provides architectural context'
+                                    },
+                                    {
+                                        key: 'database/postgresql-choice',
+                                        value: 'Selected PostgreSQL over MongoDB because: (1) Complex relational queries required for reporting, (2) ACID compliance critical for financial data, (3) Team has strong SQL expertise. Trade-off: Less flexible schema, but data integrity more important than schema flexibility for our use case.',
+                                        explanation: 'Documents database choice with reasoning, alternatives considered, and trade-offs'
+                                    },
+                                    {
+                                        key: 'security/encryption-at-rest',
+                                        value: 'Implementing AES-256 encryption for all PII in database because: (1) GDPR compliance requires encryption at rest, (2) Recent security audit identified unencrypted sensitive data, (3) Performance impact <5ms per query acceptable. Alternative considered: Database-level encryption rejected due to backup/restore complexity.',
+                                        explanation: 'Explains security decision with compliance reasoning and performance considerations'
+                                    }
+                                ],
+                                cleanup_rule: 'Delete decisions that start with "COMPLETED:", contain task status, test results, or implementation logs. Keep only architectural reasoning and design rationale.'
+                            },
                             actions: {
                                 set: 'Set/update a decision. Params: key (required), value (required), agent, layer, version, status, tags, scopes',
                                 get: 'Get specific decision by key. Params: key (required)',
@@ -513,7 +437,8 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 has_updates: 'Check for updates since timestamp (FR-003 Phase A - Lightweight Polling). Params: agent_name (required), since_timestamp (required, ISO 8601 format like "2025-10-14T08:00:00Z"). Returns: {has_updates: boolean, counts: {decisions: N, messages: N, files: N}}. Token cost: ~5-10 tokens per check. Uses COUNT queries on t_decisions, t_agent_messages, t_file_changes with timestamp filtering. Enables efficient polling without full data retrieval.',
                                 set_from_template: 'Set decision using template (FR-006). Params: template (required, template name), key (required), value (required), agent, layer (override), version, status (override), tags (override), scopes, plus any template-required fields. Applies template defaults (layer, status, tags) while allowing overrides. Validates required fields if specified by template. Returns: {success, key, key_id, version, template_used, applied_defaults, message}. Built-in templates: breaking_change, security_vulnerability, performance_optimization, deprecation, architecture_decision.',
                                 create_template: 'Create new decision template (FR-006). Params: name (required, unique), defaults (required, object with layer/status/tags/priority), required_fields (optional, array of field names), created_by (optional, agent name). Returns: {success, template_id, template_name, message}. Example defaults: {"layer":"business","status":"active","tags":["breaking"]}. Validates layer/status values.',
-                                list_templates: 'List all decision templates (FR-006). No params required. Returns: {templates: [{id, name, defaults, required_fields, created_by, created_at}], count}. Shows both built-in and custom templates.'
+                                list_templates: 'List all decision templates (FR-006). No params required. Returns: {templates: [{id, name, defaults, required_fields, created_by, created_at}], count}. Shows both built-in and custom templates.',
+                                hard_delete: 'Permanently delete a decision (hard delete). Params: key (required). WARNING: IRREVERSIBLE - removes all records including version history, tags, scopes. Use cases: manual cleanup after decision-to-task migration, remove test/debug decisions, purge sensitive data. Unlike soft delete (status=deprecated), this completely removes from database. Idempotent - safe to call even if already deleted. Returns: {success, key, message}.'
                             },
                             examples: {
                                 set: '{ action: "set", key: "auth_method", value: "jwt", tags: ["security"] }',
@@ -526,7 +451,146 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 has_updates: '{ action: "has_updates", agent_name: "my-agent", since_timestamp: "2025-10-14T08:00:00Z" }',
                                 set_from_template: '{ action: "set_from_template", template: "breaking_change", key: "oscillator-type-moved", value: "oscillator_type moved to MonophonicSynthConfig" }',
                                 create_template: '{ action: "create_template", name: "bug_fix", defaults: {"layer":"business","tags":["bug","fix"],"status":"active"}, created_by: "my-agent" }',
-                                list_templates: '{ action: "list_templates" }'
+                                list_templates: '{ action: "list_templates" }',
+                                hard_delete: '{ action: "hard_delete", key: "task_old_authentication_refactor" }'
+                            },
+                            documentation: {
+                                tool_selection: 'docs/TOOL_SELECTION.md - Decision tree, tool comparison, when to use each tool (236 lines, ~12k tokens)',
+                                tool_reference: 'docs/TOOL_REFERENCE.md - Parameter requirements, batch operations, templates (471 lines, ~24k tokens)',
+                                workflows: 'docs/WORKFLOWS.md - Multi-step workflow examples, multi-agent coordination (602 lines, ~30k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - Common errors, best practices, troubleshooting (345 lines, ~17k tokens)',
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Layer definitions, enum values (status/layer/priority), atomic mode (339 lines, ~17k tokens)'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'decision',
+                            description: 'Comprehensive decision tool examples without needing WebFetch access',
+                            scenarios: {
+                                basic_usage: {
+                                    title: 'Basic Decision Management',
+                                    examples: [
+                                        {
+                                            scenario: 'Record API design decision',
+                                            request: '{ action: "set", key: "api_auth_method", value: "JWT with refresh tokens", layer: "business", tags: ["api", "security", "authentication"] }',
+                                            explanation: 'Documents the choice of authentication method for the API'
+                                        },
+                                        {
+                                            scenario: 'Retrieve a decision',
+                                            request: '{ action: "get", key: "api_auth_method" }',
+                                            response_structure: '{ key, value, layer, status, version, tags, scopes, decided_by, updated_at }'
+                                        },
+                                        {
+                                            scenario: 'List all active decisions',
+                                            request: '{ action: "list", status: "active", limit: 20 }',
+                                            explanation: 'Returns active decisions with metadata for browsing'
+                                        }
+                                    ]
+                                },
+                                advanced_filtering: {
+                                    title: 'Advanced Search and Filtering',
+                                    examples: [
+                                        {
+                                            scenario: 'Find all security-related decisions in business layer',
+                                            request: '{ action: "search_advanced", layers: ["business"], tags_any: ["security", "authentication"], status: ["active"], sort_by: "updated", sort_order: "desc" }',
+                                            explanation: 'Combines layer filtering, tag matching, and sorting'
+                                        },
+                                        {
+                                            scenario: 'Search within API scope with multiple tags',
+                                            request: '{ action: "search_advanced", scopes: ["api/*"], tags_all: ["breaking", "v2.0"], updated_after: "2025-01-01" }',
+                                            explanation: 'Uses scope wildcards and timestamp filtering for recent breaking changes'
+                                        }
+                                    ]
+                                },
+                                versioning_workflow: {
+                                    title: 'Version Management',
+                                    steps: [
+                                        {
+                                            step: 1,
+                                            action: 'Create initial decision',
+                                            request: '{ action: "set", key: "database_choice", value: "PostgreSQL", layer: "data", version: "1.0.0", tags: ["database"] }'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'Update decision (creates new version)',
+                                            request: '{ action: "set", key: "database_choice", value: "PostgreSQL with read replicas", layer: "data", version: "1.1.0", tags: ["database", "scaling"] }'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'View version history',
+                                            request: '{ action: "versions", key: "database_choice" }',
+                                            result: 'Returns all versions with timestamps and changes'
+                                        }
+                                    ]
+                                },
+                                batch_operations: {
+                                    title: 'Batch Decision Management',
+                                    examples: [
+                                        {
+                                            scenario: 'Record multiple related decisions atomically',
+                                            request: '{ action: "set_batch", decisions: [{"key": "cache_layer", "value": "Redis", "layer": "infrastructure"}, {"key": "cache_ttl", "value": "3600", "layer": "infrastructure"}], atomic: true }',
+                                            explanation: 'All decisions succeed or all fail together (atomic mode)'
+                                        },
+                                        {
+                                            scenario: 'Best-effort batch insert',
+                                            request: '{ action: "set_batch", decisions: [{...}, {...}, {...}], atomic: false }',
+                                            explanation: 'Each decision processed independently - partial success allowed'
+                                        }
+                                    ]
+                                },
+                                templates: {
+                                    title: 'Using Decision Templates',
+                                    examples: [
+                                        {
+                                            scenario: 'Use built-in breaking_change template',
+                                            request: '{ action: "set_from_template", template: "breaking_change", key: "api_remove_legacy_endpoint", value: "Removed /v1/users endpoint - migrate to /v2/users" }',
+                                            explanation: 'Automatically applies layer=business, tags=["breaking"], status=active'
+                                        },
+                                        {
+                                            scenario: 'Create custom template',
+                                            request: '{ action: "create_template", name: "feature_flag", defaults: {"layer": "presentation", "tags": ["feature-flag"], "status": "draft"}, created_by: "backend-team" }',
+                                            explanation: 'Define reusable templates for common decision patterns'
+                                        }
+                                    ]
+                                },
+                                quick_set_inference: {
+                                    title: 'Quick Set with Smart Defaults',
+                                    examples: [
+                                        {
+                                            scenario: 'Auto-infer layer from key prefix',
+                                            request: '{ action: "quick_set", key: "api/instruments/oscillator-refactor", value: "Moved oscillator_type to MonophonicSynthConfig" }',
+                                            inferred: 'layer=presentation (from api/*), tags=["instruments", "oscillator-refactor"], scope=api/instruments'
+                                        },
+                                        {
+                                            scenario: 'Database decision with auto-inference',
+                                            request: '{ action: "quick_set", key: "db/users/add-email-index", value: "Added index on email column" }',
+                                            inferred: 'layer=data (from db/*), tags=["users", "add-email-index"]'
+                                        }
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                key_naming: [
+                                    'Use hierarchical keys: "api/users/authentication"',
+                                    'Prefix with layer hint: api/* → presentation, db/* → data, service/* → business',
+                                    'Use descriptive names that explain the decision context'
+                                ],
+                                tagging: [
+                                    'Tag with relevant categories: security, performance, breaking, etc.',
+                                    'Include version tags for release-specific decisions',
+                                    'Use consistent tag naming conventions across team'
+                                ],
+                                versioning: [
+                                    'Use semantic versioning: 1.0.0, 1.1.0, 2.0.0',
+                                    'Increment major version for breaking changes',
+                                    'Document rationale in decision value text'
+                                ],
+                                cleanup: [
+                                    'Mark deprecated decisions with status="deprecated"',
+                                    'Use hard_delete only for sensitive data or migration cleanup',
+                                    'Link related decisions using scopes'
+                                ]
                             }
                         };
                         break;
@@ -562,6 +626,115 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 get: '{ action: "get", agent_name: "bot1", unread_only: true }',
                                 mark_read: '{ action: "mark_read", agent_name: "bot1", message_ids: [1, 2, 3] }',
                                 send_batch: '{ action: "send_batch", messages: [{"from_agent": "bot1", "msg_type": "info", "message": "Task 1 done"}, {"from_agent": "bot1", "msg_type": "info", "message": "Task 2 done"}], atomic: true }'
+                            },
+                            documentation: {
+                                workflows: 'docs/WORKFLOWS.md - Multi-agent coordination, messaging patterns, cross-session handoffs (602 lines, ~30k tokens)',
+                                tool_reference: 'docs/TOOL_REFERENCE.md - Message tool parameters, batch operations (471 lines, ~24k tokens)',
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Enum values (msg_type/priority), atomic mode (339 lines, ~17k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - Common errors, messaging best practices (345 lines, ~17k tokens)'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'message',
+                            description: 'Comprehensive messaging examples for multi-agent coordination',
+                            scenarios: {
+                                basic_messaging: {
+                                    title: 'Basic Agent Communication',
+                                    examples: [
+                                        {
+                                            scenario: 'Send info message between agents',
+                                            request: '{ action: "send", from_agent: "backend-agent", to_agent: "frontend-agent", msg_type: "info", message: "API endpoint /users is ready" }',
+                                            explanation: 'Direct message from one agent to another'
+                                        },
+                                        {
+                                            scenario: 'Broadcast message to all agents',
+                                            request: '{ action: "send", from_agent: "coordinator", to_agent: null, msg_type: "info", message: "Deployment starting in 5 minutes", priority: "high" }',
+                                            explanation: 'null to_agent broadcasts to all agents'
+                                        },
+                                        {
+                                            scenario: 'Get unread messages',
+                                            request: '{ action: "get", agent_name: "frontend-agent", unread_only: true }',
+                                            explanation: 'Retrieve only unread messages for an agent'
+                                        }
+                                    ]
+                                },
+                                priority_messaging: {
+                                    title: 'Priority-Based Communication',
+                                    examples: [
+                                        {
+                                            scenario: 'Critical error notification',
+                                            request: '{ action: "send", from_agent: "monitoring-agent", msg_type: "warning", message: "Database connection lost", priority: "critical" }',
+                                            explanation: 'High-priority messages for urgent issues'
+                                        },
+                                        {
+                                            scenario: 'Filter by priority',
+                                            request: '{ action: "get", agent_name: "ops-agent", priority_filter: "critical" }',
+                                            explanation: 'Get only critical priority messages'
+                                        }
+                                    ]
+                                },
+                                workflow_coordination: {
+                                    title: 'Multi-Step Workflow',
+                                    steps: [
+                                        {
+                                            step: 1,
+                                            action: 'Agent A requests work from Agent B',
+                                            request: '{ action: "send", from_agent: "agent-a", to_agent: "agent-b", msg_type: "request", message: "Please process user data batch-123" }'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'Agent B checks messages',
+                                            request: '{ action: "get", agent_name: "agent-b", msg_type_filter: "request", unread_only: true }'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'Agent B marks as read and processes',
+                                            request: '{ action: "mark_read", agent_name: "agent-b", message_ids: [123] }'
+                                        },
+                                        {
+                                            step: 4,
+                                            action: 'Agent B sends completion notification',
+                                            request: '{ action: "send", from_agent: "agent-b", to_agent: "agent-a", msg_type: "info", message: "Batch-123 processing complete" }'
+                                        }
+                                    ]
+                                },
+                                batch_messaging: {
+                                    title: 'Batch Message Operations',
+                                    examples: [
+                                        {
+                                            scenario: 'Send multiple status updates atomically',
+                                            request: '{ action: "send_batch", messages: [{"from_agent": "worker-1", "msg_type": "info", "message": "Task 1 done"}, {"from_agent": "worker-1", "msg_type": "info", "message": "Task 2 done"}], atomic: true }',
+                                            explanation: 'All messages sent or none (atomic mode)'
+                                        },
+                                        {
+                                            scenario: 'Best-effort batch sending',
+                                            request: '{ action: "send_batch", messages: [{...}, {...}], atomic: false }',
+                                            explanation: 'Each message sent independently - partial success allowed'
+                                        }
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                message_types: [
+                                    'Use "decision" for recording important choices',
+                                    'Use "warning" for errors or issues requiring attention',
+                                    'Use "request" for work requests between agents',
+                                    'Use "info" for status updates and notifications'
+                                ],
+                                priority_usage: [
+                                    'critical: System failures, data loss, security breaches',
+                                    'high: Important but not emergency (deployment notifications)',
+                                    'medium: Regular coordination messages (default)',
+                                    'low: Optional information, logging'
+                                ],
+                                coordination_patterns: [
+                                    'Always mark messages as read after processing',
+                                    'Use broadcast (to_agent=null) for system-wide announcements',
+                                    'Filter by msg_type when checking for specific message categories',
+                                    'Include context in message text or payload for debugging'
+                                ]
                             }
                         };
                         break;
@@ -597,6 +770,106 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 get: '{ action: "get", agent_name: "refactor-bot", layer: "infrastructure", limit: 10 }',
                                 check_lock: '{ action: "check_lock", file_path: "src/index.ts", lock_duration: 300 }',
                                 record_batch: '{ action: "record_batch", file_changes: [{"file_path": "src/types.ts", "agent_name": "bot1", "change_type": "modified", "layer": "data"}, {"file_path": "src/index.ts", "agent_name": "bot1", "change_type": "modified", "layer": "infrastructure"}], atomic: true }'
+                            },
+                            documentation: {
+                                workflows: 'docs/WORKFLOWS.md - File locking patterns, concurrent file access workflows (602 lines, ~30k tokens)',
+                                tool_reference: 'docs/TOOL_REFERENCE.md - File tool parameters, batch operations (471 lines, ~24k tokens)',
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Layer definitions, enum values (change_type), atomic mode (339 lines, ~17k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - File tracking best practices (345 lines, ~17k tokens)'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'file',
+                            description: 'Comprehensive file tracking examples for multi-agent coordination',
+                            scenarios: {
+                                basic_tracking: {
+                                    title: 'Basic File Change Tracking',
+                                    examples: [
+                                        {
+                                            scenario: 'Record file modification',
+                                            request: '{ action: "record", file_path: "src/api/users.ts", agent_name: "refactor-agent", change_type: "modified", layer: "business", description: "Added email validation" }',
+                                            explanation: 'Track changes with layer and description'
+                                        },
+                                        {
+                                            scenario: 'Get recent changes by agent',
+                                            request: '{ action: "get", agent_name: "refactor-agent", limit: 10 }',
+                                            explanation: 'View what an agent has been working on'
+                                        },
+                                        {
+                                            scenario: 'Track changes to specific file',
+                                            request: '{ action: "get", file_path: "src/api/users.ts" }',
+                                            explanation: 'See all modifications to a particular file'
+                                        }
+                                    ]
+                                },
+                                file_locking: {
+                                    title: 'Concurrent Access Prevention',
+                                    workflow: [
+                                        {
+                                            step: 1,
+                                            action: 'Check if file is locked',
+                                            request: '{ action: "check_lock", file_path: "src/database/schema.sql", lock_duration: 300 }',
+                                            result: '{ locked: false } or { locked: true, locked_by: "agent-name", locked_at: "timestamp" }'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'If not locked, record change (creates lock)',
+                                            request: '{ action: "record", file_path: "src/database/schema.sql", agent_name: "migration-agent", change_type: "modified" }'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'Lock expires after 5 minutes (default) or specified duration'
+                                        }
+                                    ]
+                                },
+                                layer_organization: {
+                                    title: 'Tracking by Architecture Layer',
+                                    examples: [
+                                        {
+                                            scenario: 'Get all presentation layer changes',
+                                            request: '{ action: "get", layer: "presentation", limit: 20 }',
+                                            explanation: 'View frontend/UI changes across agents'
+                                        },
+                                        {
+                                            scenario: 'Track infrastructure changes',
+                                            request: '{ action: "get", layer: "infrastructure", change_type: "modified" }',
+                                            explanation: 'Monitor config and deployment file changes'
+                                        }
+                                    ]
+                                },
+                                batch_tracking: {
+                                    title: 'Batch File Operations',
+                                    examples: [
+                                        {
+                                            scenario: 'Record multiple file changes atomically',
+                                            request: '{ action: "record_batch", file_changes: [{"file_path": "src/api.ts", "agent_name": "bot1", "change_type": "modified", "layer": "presentation"}, {"file_path": "src/types.ts", "agent_name": "bot1", "change_type": "modified", "layer": "data"}], atomic: true }',
+                                            explanation: 'All changes recorded or none (transaction)'
+                                        }
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                change_tracking: [
+                                    'Always specify layer for better organization',
+                                    'Include description for non-obvious changes',
+                                    'Use check_lock before modifying shared files',
+                                    'Track both creation and deletion of files'
+                                ],
+                                lock_management: [
+                                    'Default lock duration is 300 seconds (5 minutes)',
+                                    'Locks prevent concurrent modifications',
+                                    'Locks auto-expire - no manual unlock needed',
+                                    'Use appropriate lock_duration for operation complexity'
+                                ],
+                                layer_assignment: [
+                                    'presentation: UI components, API controllers',
+                                    'business: Services, domain logic',
+                                    'data: Models, repositories, migrations',
+                                    'infrastructure: Config, deployment, CI/CD',
+                                    'cross-cutting: Utilities used across layers'
+                                ]
                             }
                         };
                         break;
@@ -627,6 +900,148 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 add: '{ action: "add", category: "performance", constraint_text: "API response time <100ms", priority: "high", tags: ["api"] }',
                                 get: '{ action: "get", category: "performance", active_only: true }',
                                 deactivate: '{ action: "deactivate", constraint_id: 5 }'
+                            },
+                            documentation: {
+                                tool_selection: 'docs/TOOL_SELECTION.md - Decision tree, constraint vs decision comparison (236 lines, ~12k tokens)',
+                                workflows: 'docs/WORKFLOWS.md - Constraint validation workflows, requirement tracking (602 lines, ~30k tokens)',
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Layer definitions, enum values (category/priority) (339 lines, ~17k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - When to use constraints, common patterns (345 lines, ~17k tokens)'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'constraint',
+                            description: 'Comprehensive constraint examples for various use cases',
+                            categories: {
+                                performance: {
+                                    description: 'Performance-related constraints for response times, throughput, resource usage',
+                                    examples: [
+                                        {
+                                            scenario: 'API Response Time',
+                                            example: '{ action: "add", category: "performance", constraint_text: "All API endpoints must respond within 100ms for 95th percentile", priority: "high", layer: "business", tags: ["api", "latency"] }',
+                                            rationale: 'Ensures fast user experience and prevents timeout issues'
+                                        },
+                                        {
+                                            scenario: 'Database Query Performance',
+                                            example: '{ action: "add", category: "performance", constraint_text: "Database queries must complete within 50ms", priority: "high", layer: "data", tags: ["database", "query"] }',
+                                            rationale: 'Prevents database bottlenecks and ensures scalability'
+                                        },
+                                        {
+                                            scenario: 'Memory Usage',
+                                            example: '{ action: "add", category: "performance", constraint_text: "Peak memory usage must not exceed 512MB per instance", priority: "critical", layer: "infrastructure", tags: ["memory", "resource"] }',
+                                            rationale: 'Prevents out-of-memory errors in containerized environments'
+                                        }
+                                    ]
+                                },
+                                architecture: {
+                                    description: 'Architectural constraints for code structure, dependencies, patterns',
+                                    examples: [
+                                        {
+                                            scenario: 'Layer Dependency Rules',
+                                            example: '{ action: "add", category: "architecture", constraint_text: "Presentation layer must not directly access data layer - use business layer only", priority: "critical", layer: "cross-cutting", tags: ["layering", "separation"] }',
+                                            rationale: 'Enforces clean architecture and separation of concerns'
+                                        },
+                                        {
+                                            scenario: 'Dependency Injection',
+                                            example: '{ action: "add", category: "architecture", constraint_text: "All service classes must use constructor-based dependency injection", priority: "medium", layer: "business", tags: ["di", "testability"] }',
+                                            rationale: 'Improves testability and reduces coupling'
+                                        },
+                                        {
+                                            scenario: 'API Versioning',
+                                            example: '{ action: "add", category: "architecture", constraint_text: "All public APIs must include version prefix (e.g., /v1/, /v2/)", priority: "high", layer: "presentation", tags: ["api", "versioning"] }',
+                                            rationale: 'Enables backward compatibility and smooth API evolution'
+                                        }
+                                    ]
+                                },
+                                security: {
+                                    description: 'Security constraints for authentication, authorization, data protection',
+                                    examples: [
+                                        {
+                                            scenario: 'Authentication Required',
+                                            example: '{ action: "add", category: "security", constraint_text: "All non-public endpoints must require JWT authentication", priority: "critical", layer: "presentation", tags: ["auth", "jwt"] }',
+                                            rationale: 'Prevents unauthorized access to protected resources'
+                                        },
+                                        {
+                                            scenario: 'Data Encryption',
+                                            example: '{ action: "add", category: "security", constraint_text: "All PII (Personally Identifiable Information) must be encrypted at rest using AES-256", priority: "critical", layer: "data", tags: ["encryption", "pii"] }',
+                                            rationale: 'Protects sensitive data and ensures compliance'
+                                        },
+                                        {
+                                            scenario: 'Input Validation',
+                                            example: '{ action: "add", category: "security", constraint_text: "All user inputs must be validated and sanitized before processing", priority: "critical", layer: "presentation", tags: ["validation", "injection-prevention"] }',
+                                            rationale: 'Prevents injection attacks (SQL, XSS, etc.)'
+                                        }
+                                    ]
+                                }
+                            },
+                            workflows: {
+                                constraint_validation: {
+                                    description: 'Workflow for validating code against constraints',
+                                    steps: [
+                                        {
+                                            step: 1,
+                                            action: 'Retrieve active constraints for layer',
+                                            example: '{ action: "get", layer: "business", active_only: true }'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'Check code changes against constraints',
+                                            example: 'Review file changes and verify compliance with each constraint'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'Report violations',
+                                            example: 'Use message tool to send warnings for constraint violations'
+                                        },
+                                        {
+                                            step: 4,
+                                            action: 'Link violations to tasks',
+                                            example: 'Create tasks to fix violations and link to relevant constraints'
+                                        }
+                                    ]
+                                },
+                                requirement_tracking: {
+                                    description: 'Workflow for tracking requirements as constraints',
+                                    steps: [
+                                        {
+                                            step: 1,
+                                            action: 'Add requirement as constraint',
+                                            example: '{ action: "add", category: "performance", constraint_text: "System must handle 1000 concurrent users", priority: "high", tags: ["requirement", "load"] }'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'Link related decisions',
+                                            example: 'Use decision tool to record architectural decisions that address the constraint'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'Create implementation tasks',
+                                            example: 'Use task tool to break down implementation and link to constraint'
+                                        },
+                                        {
+                                            step: 4,
+                                            action: 'Validate compliance',
+                                            example: 'Test implementation against constraint criteria'
+                                        }
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                writing_constraints: [
+                                    'Be specific and measurable (use numbers, percentages, time limits)',
+                                    'Include rationale in tags or separate documentation',
+                                    'Use appropriate priority (critical for must-have, high for important, medium/low for nice-to-have)',
+                                    'Assign to correct layer (where constraint is enforced)',
+                                    'Tag comprehensively for easy retrieval'
+                                ],
+                                managing_constraints: [
+                                    'Review constraints regularly and deactivate outdated ones',
+                                    'Link constraints to related decisions and tasks',
+                                    'Use constraints for both technical and business requirements',
+                                    'Validate code changes against active constraints',
+                                    'Document constraint violations and remediation plans'
+                                ]
                             }
                         };
                         break;
@@ -652,21 +1067,132 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                             limit: params.limit,
                         });
                         break;
+                    case 'flush':
+                        result = flushWAL();
+                        break;
                     case 'help':
                         result = {
                             tool: 'stats',
-                            description: 'View database statistics, activity logs, and manage data cleanup',
+                            description: 'View database statistics, activity logs, manage data cleanup, and WAL checkpoints',
                             actions: {
                                 layer_summary: 'Get summary by layer. No params required',
                                 db_stats: 'Get database statistics. No params required',
                                 clear: 'Clear old data. Params: messages_older_than_hours, file_changes_older_than_days',
-                                activity_log: 'Get activity log (v3.0.0). Params: since (e.g., "5m", "1h", "2d"), agent_names (array or ["*"]), actions (filter by action types), limit (default: 100)'
+                                activity_log: 'Get activity log (v3.0.0). Params: since (e.g., "5m", "1h", "2d"), agent_names (array or ["*"]), actions (filter by action types), limit (default: 100)',
+                                flush: 'Force WAL checkpoint to flush pending transactions to main database file. No params required. Uses TRUNCATE mode for complete flush. Useful before git commits to ensure database file is up-to-date.'
                             },
                             examples: {
                                 layer_summary: '{ action: "layer_summary" }',
                                 db_stats: '{ action: "db_stats" }',
                                 clear: '{ action: "clear", messages_older_than_hours: 48, file_changes_older_than_days: 14 }',
-                                activity_log: '{ action: "activity_log", since: "1h", agent_names: ["bot1", "bot2"], limit: 50 }'
+                                activity_log: '{ action: "activity_log", since: "1h", agent_names: ["bot1", "bot2"], limit: 50 }',
+                                flush: '{ action: "flush" }'
+                            },
+                            documentation: {
+                                workflows: 'docs/WORKFLOWS.md - Activity monitoring, automatic cleanup workflows (602 lines, ~30k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - Database health, cleanup strategies (345 lines, ~17k tokens)',
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Layer definitions for layer_summary (339 lines, ~17k tokens)',
+                                architecture: 'docs/ARCHITECTURE.md - Database schema, views, statistics tables'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'stats',
+                            description: 'Database statistics and maintenance examples',
+                            scenarios: {
+                                layer_analysis: {
+                                    title: 'Architecture Layer Summary',
+                                    example: {
+                                        request: '{ action: "layer_summary" }',
+                                        response_structure: '{ layer: string, decision_count: number, file_changes: number, active_constraints: number }[]',
+                                        use_case: 'Understand which layers have most activity and decisions'
+                                    }
+                                },
+                                database_health: {
+                                    title: 'Database Statistics',
+                                    example: {
+                                        request: '{ action: "db_stats" }',
+                                        response_structure: '{ decisions: N, messages: N, file_changes: N, constraints: N, db_size_mb: N }',
+                                        use_case: 'Monitor database growth and table sizes'
+                                    }
+                                },
+                                activity_monitoring: {
+                                    title: 'Activity Log Queries',
+                                    examples: [
+                                        {
+                                            scenario: 'Recent activity (last hour)',
+                                            request: '{ action: "activity_log", since: "1h", limit: 50 }',
+                                            explanation: 'View all agent activity in the past hour'
+                                        },
+                                        {
+                                            scenario: 'Specific agent activity',
+                                            request: '{ action: "activity_log", since: "24h", agent_names: ["backend-agent", "frontend-agent"] }',
+                                            explanation: 'Track what specific agents have been doing'
+                                        },
+                                        {
+                                            scenario: 'Filter by action type',
+                                            request: '{ action: "activity_log", since: "2d", actions: ["set_decision", "create_task"] }',
+                                            explanation: 'See only specific types of actions'
+                                        }
+                                    ]
+                                },
+                                data_cleanup: {
+                                    title: 'Maintenance and Cleanup',
+                                    examples: [
+                                        {
+                                            scenario: 'Manual cleanup with specific retention',
+                                            request: '{ action: "clear", messages_older_than_hours: 48, file_changes_older_than_days: 14 }',
+                                            explanation: 'Override config and delete old data'
+                                        },
+                                        {
+                                            scenario: 'Config-based automatic cleanup',
+                                            request: '{ action: "clear" }',
+                                            explanation: 'Use configured retention settings (respects weekend-aware mode)'
+                                        }
+                                    ]
+                                },
+                                wal_management: {
+                                    title: 'WAL Checkpoint (Git Workflow)',
+                                    workflow: [
+                                        {
+                                            step: 1,
+                                            action: 'Make changes to context (decisions, tasks, etc.)',
+                                            explanation: 'SQLite WAL mode keeps changes in separate file'
+                                        },
+                                        {
+                                            step: 2,
+                                            action: 'Before git commit, flush WAL',
+                                            request: '{ action: "flush" }',
+                                            explanation: 'Merges WAL changes into main .db file'
+                                        },
+                                        {
+                                            step: 3,
+                                            action: 'Commit database file',
+                                            explanation: 'Database file now contains all changes for version control'
+                                        }
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                monitoring: [
+                                    'Check layer_summary regularly to identify hotspots',
+                                    'Monitor db_stats to prevent database bloat',
+                                    'Use activity_log for debugging multi-agent issues',
+                                    'Set appropriate retention periods based on project needs'
+                                ],
+                                cleanup: [
+                                    'Run periodic cleanup to manage database size',
+                                    'Use weekend-aware mode for business hour retention',
+                                    'Consider longer retention for important decisions',
+                                    'Test cleanup with manual parameters before automating'
+                                ],
+                                wal_checkpoints: [
+                                    'Always flush before git commits for clean diffs',
+                                    'WAL mode improves concurrent access performance',
+                                    'Checkpoint automatically happens on shutdown',
+                                    'Manual flush ensures immediate persistence'
+                                ]
                             }
                         };
                         break;
@@ -692,6 +1218,291 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                             examples: {
                                 get: '{ action: "get" }',
                                 update: '{ action: "update", ignoreWeekend: true, messageRetentionHours: 48 }'
+                            },
+                            documentation: {
+                                shared_concepts: 'docs/SHARED_CONCEPTS.md - Weekend-aware retention behavior explained (339 lines, ~17k tokens)',
+                                best_practices: 'docs/BEST_PRACTICES.md - Retention strategies, cleanup timing (345 lines, ~17k tokens)',
+                                architecture: 'docs/ARCHITECTURE.md - Auto-cleanup architecture, configuration system'
+                            }
+                        };
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'config',
+                            description: 'Configuration management examples',
+                            scenarios: {
+                                view_config: {
+                                    title: 'Current Configuration',
+                                    example: {
+                                        request: '{ action: "get" }',
+                                        response: '{ ignoreWeekend: boolean, messageRetentionHours: number, fileHistoryRetentionDays: number }',
+                                        explanation: 'View current auto-deletion settings'
+                                    }
+                                },
+                                standard_retention: {
+                                    title: 'Standard Time-Based Retention',
+                                    example: {
+                                        request: '{ action: "update", ignoreWeekend: false, messageRetentionHours: 24, fileHistoryRetentionDays: 7 }',
+                                        explanation: 'Messages deleted after 24 hours, file history after 7 days (strict time-based)'
+                                    }
+                                },
+                                weekend_aware: {
+                                    title: 'Weekend-Aware Retention',
+                                    example: {
+                                        request: '{ action: "update", ignoreWeekend: true, messageRetentionHours: 24, fileHistoryRetentionDays: 7 }',
+                                        explanation: 'On Monday, 24h retention = Friday (skips weekend)',
+                                        scenario: 'Useful for business-hour contexts where weekend messages should persist'
+                                    }
+                                },
+                                extended_retention: {
+                                    title: 'Long-Term Project Retention',
+                                    example: {
+                                        request: '{ action: "update", messageRetentionHours: 168, fileHistoryRetentionDays: 90 }',
+                                        explanation: '1 week message retention, 90 days file history (max allowed)',
+                                        use_case: 'Long-running projects needing extended context'
+                                    }
+                                }
+                            },
+                            retention_behavior: {
+                                ignoreWeekend_false: {
+                                    description: 'Standard time-based retention',
+                                    examples: [
+                                        '24h on Monday = 24 hours ago (Sunday)',
+                                        '24h on Friday = 24 hours ago (Thursday)',
+                                        'Straightforward chronological deletion'
+                                    ]
+                                },
+                                ignoreWeekend_true: {
+                                    description: 'Business-hours retention (skips Sat/Sun)',
+                                    examples: [
+                                        '24h on Monday = Friday (skips Sat/Sun)',
+                                        '24h on Tuesday = Monday',
+                                        '24h on Friday = Thursday',
+                                        '24h on Saturday/Sunday = Friday',
+                                        'Preserves weekend messages until Monday cleanup'
+                                    ]
+                                }
+                            },
+                            best_practices: {
+                                choosing_retention: [
+                                    'Short projects: 24h messages, 7d file history',
+                                    'Medium projects: 72h messages, 14d file history',
+                                    'Long projects: 168h (1 week) messages, 30-90d file history',
+                                    'Use ignoreWeekend=true for business-hour focused work'
+                                ],
+                                limits: [
+                                    'messageRetentionHours: 1-168 (1 hour to 1 week)',
+                                    'fileHistoryRetentionDays: 1-90',
+                                    'Choose based on your projects needs and database size constraints'
+                                ],
+                                cli_override: [
+                                    'Can override config at server startup via CLI args',
+                                    '--autodelete-ignore-weekend, --autodelete-message-hours, --autodelete-file-history-days',
+                                    'Runtime updates via config tool take precedence over CLI'
+                                ]
+                            }
+                        };
+                        break;
+                    default: throw new Error(`Unknown action: ${params.action}`);
+                }
+                break;
+            case 'task':
+                switch (params.action) {
+                    case 'create':
+                        result = createTask(params);
+                        break;
+                    case 'update':
+                        result = updateTask(params);
+                        break;
+                    case 'get':
+                        result = getTask(params);
+                        break;
+                    case 'list':
+                        result = listTasks(params);
+                        break;
+                    case 'move':
+                        result = moveTask(params);
+                        break;
+                    case 'link':
+                        result = linkTask(params);
+                        break;
+                    case 'archive':
+                        result = archiveTask(params);
+                        break;
+                    case 'batch_create':
+                        result = batchCreateTasks({ tasks: params.tasks, atomic: params.atomic });
+                        break;
+                    case 'help':
+                        result = taskHelp();
+                        break;
+                    case 'example':
+                        result = {
+                            tool: 'task',
+                            description: 'Comprehensive task management examples for Kanban-style workflow',
+                            scenarios: {
+                                basic_task_management: {
+                                    title: 'Creating and Managing Tasks',
+                                    examples: [
+                                        {
+                                            scenario: 'Create a new task',
+                                            request: '{ action: "create", title: "Implement user authentication", description: "Add JWT-based auth to API", priority: 3, assigned_agent: "backend-agent", layer: "business", tags: ["authentication", "security"] }',
+                                            explanation: 'Creates task in todo status with high priority'
+                                        },
+                                        {
+                                            scenario: 'Get task details',
+                                            request: '{ action: "get", task_id: 5 }',
+                                            response: 'Full task details including metadata, links, and timestamps'
+                                        },
+                                        {
+                                            scenario: 'List tasks by status',
+                                            request: '{ action: "list", status: "in_progress", limit: 20 }',
+                                            explanation: 'View all in-progress tasks'
+                                        }
+                                    ]
+                                },
+                                status_workflow: {
+                                    title: 'Task Lifecycle (Status Transitions)',
+                                    workflow: [
+                                        {
+                                            step: 1,
+                                            status: 'todo',
+                                            action: '{ action: "create", title: "...", status: "todo" }',
+                                            description: 'Task created and waiting to be started'
+                                        },
+                                        {
+                                            step: 2,
+                                            status: 'in_progress',
+                                            action: '{ action: "move", task_id: 1, new_status: "in_progress" }',
+                                            description: 'Agent starts working on task'
+                                        },
+                                        {
+                                            step: 3,
+                                            status: 'waiting_review',
+                                            action: '{ action: "move", task_id: 1, new_status: "waiting_review" }',
+                                            description: 'Work complete, awaiting review/approval'
+                                        },
+                                        {
+                                            step: 4,
+                                            status: 'done',
+                                            action: '{ action: "move", task_id: 1, new_status: "done" }',
+                                            description: 'Task reviewed and completed'
+                                        },
+                                        {
+                                            step: 5,
+                                            status: 'archived',
+                                            action: '{ action: "archive", task_id: 1 }',
+                                            description: 'Task archived for historical record'
+                                        }
+                                    ],
+                                    blocked_status: {
+                                        description: 'Use "blocked" when task cannot proceed due to dependencies',
+                                        example: '{ action: "move", task_id: 1, new_status: "blocked" }'
+                                    }
+                                },
+                                auto_stale_detection: {
+                                    title: 'Automatic Stale Task Management',
+                                    behavior: [
+                                        {
+                                            rule: 'in_progress > 2 hours → waiting_review',
+                                            explanation: 'Tasks stuck in progress auto-move to waiting_review',
+                                            rationale: 'Prevents tasks from being forgotten while in progress'
+                                        },
+                                        {
+                                            rule: 'waiting_review > 24 hours → todo',
+                                            explanation: 'Unreviewed tasks return to todo queue',
+                                            rationale: 'Ensures waiting tasks dont accumulate indefinitely'
+                                        }
+                                    ],
+                                    configuration: {
+                                        keys: ['task_stale_hours_in_progress', 'task_stale_hours_waiting_review', 'task_auto_stale_enabled'],
+                                        note: 'Configure via config table in database'
+                                    }
+                                },
+                                task_linking: {
+                                    title: 'Linking Tasks to Context',
+                                    examples: [
+                                        {
+                                            scenario: 'Link task to decision',
+                                            request: '{ action: "link", task_id: 5, link_type: "decision", target_id: "api_auth_method", link_relation: "implements" }',
+                                            explanation: 'Track which tasks implement specific decisions'
+                                        },
+                                        {
+                                            scenario: 'Link task to constraint',
+                                            request: '{ action: "link", task_id: 5, link_type: "constraint", target_id: 3, link_relation: "addresses" }',
+                                            explanation: 'Show task addresses a performance/architecture/security constraint'
+                                        },
+                                        {
+                                            scenario: 'Link task to file',
+                                            request: '{ action: "link", task_id: 5, link_type: "file", target_id: "src/api/auth.ts", link_relation: "modifies" }',
+                                            explanation: 'Indicate which files the task will modify'
+                                        }
+                                    ]
+                                },
+                                batch_operations: {
+                                    title: 'Batch Task Creation',
+                                    examples: [
+                                        {
+                                            scenario: 'Create multiple related tasks',
+                                            request: '{ action: "batch_create", tasks: [{"title": "Design API", "priority": 3}, {"title": "Implement API", "priority": 3}, {"title": "Write tests", "priority": 2}], atomic: false }',
+                                            explanation: 'Create task breakdown - use atomic:false for best-effort'
+                                        }
+                                    ]
+                                },
+                                filtering_queries: {
+                                    title: 'Advanced Task Queries',
+                                    examples: [
+                                        {
+                                            scenario: 'Find high-priority tasks for agent',
+                                            request: '{ action: "list", assigned_agent: "backend-agent", priority: 3, status: "todo" }',
+                                            note: 'Priority is numeric: 1=low, 2=medium, 3=high, 4=critical'
+                                        },
+                                        {
+                                            scenario: 'Get all security-related tasks',
+                                            request: '{ action: "list", tags: ["security"], limit: 50 }',
+                                            explanation: 'Filter by tags for topic-based views'
+                                        },
+                                        {
+                                            scenario: 'View infrastructure layer tasks',
+                                            request: '{ action: "list", layer: "infrastructure" }',
+                                            explanation: 'See all DevOps/config related tasks'
+                                        }
+                                    ]
+                                }
+                            },
+                            valid_transitions: {
+                                from_todo: ['in_progress', 'blocked', 'done', 'archived'],
+                                from_in_progress: ['waiting_review', 'blocked', 'todo'],
+                                from_waiting_review: ['done', 'in_progress', 'todo'],
+                                from_blocked: ['todo', 'in_progress'],
+                                from_done: ['archived', 'todo'],
+                                from_archived: []
+                            },
+                            best_practices: {
+                                task_creation: [
+                                    'Use descriptive titles (200 char max)',
+                                    'Set appropriate priority: 1=low, 2=medium (default), 3=high, 4=critical',
+                                    'Assign to layer where work will be done',
+                                    'Tag comprehensively for easy filtering',
+                                    'Include acceptance_criteria for complex tasks'
+                                ],
+                                status_management: [
+                                    'Move to in_progress when starting work',
+                                    'Use waiting_review for completed but unverified work',
+                                    'Set to blocked with notes explaining dependency',
+                                    'Archive done tasks periodically for cleaner views'
+                                ],
+                                linking: [
+                                    'Link tasks to decisions they implement',
+                                    'Link to constraints they address',
+                                    'Link to files they will modify',
+                                    'Use descriptive link_relation values'
+                                ],
+                                coordination: [
+                                    'Use assigned_agent for clear ownership',
+                                    'Filter by status for Kanban board views',
+                                    'Monitor auto-stale transitions for stuck work',
+                                    'Use tags for cross-cutting concerns (security, performance, etc.)'
+                                ]
                             }
                         };
                         break;