diff --git a/ccw/src/core/routes/claude-routes.ts b/ccw/src/core/routes/claude-routes.ts
index 36adcec2..8561a382 100644
--- a/ccw/src/core/routes/claude-routes.ts
+++ b/ccw/src/core/routes/claude-routes.ts
@@ -314,7 +314,7 @@ TASK: • Analyze module's purpose and responsibilities • Document public APIs
 MODE: analysis
 CONTEXT: @${modulePath}/**/* | Memory: Project conventions from .claude/CLAUDE.md
 EXPECTED: Module-level CLAUDE.md with: - Module purpose (1-2 sentences) - Key files and their roles - Public API documentation - Integration points - Testing approach
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/planning/02-design-component-spec.txt) | Module-level perspective only | Concrete examples | analysis=READ-ONLY`;
+RULES: $PROTO $TMPL | Module-level perspective only | Concrete examples | analysis=READ-ONLY`;
   } else {
     // User/Project level prompt
     const contextPath = level === 'user' ? '~/.claude' : '.claude';
@@ -323,7 +323,7 @@ TASK: • Analyze ${level} configuration and conventions • Identify common pat
 MODE: analysis
 CONTEXT: @${contextPath}/**/*
 EXPECTED: Updated CLAUDE.md content with: - Preserved existing sections - New insights appended to relevant sections - Timestamp header - Focus on ${level}-level concerns
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-patterns.txt) | Maintain existing CLAUDE.md structure | Focus on actionable rules | analysis=READ-ONLY`;
+RULES: $PROTO $TMPL | Maintain existing CLAUDE.md structure | Focus on actionable rules | analysis=READ-ONLY`;
   }
 }
 
@@ -559,6 +559,7 @@ export async function handleClaudeRoutes(ctx: RouteContext): Promise<boolean> {
         // Import CLI executor and content formatter
         const { executeCliTool } = await import('../../tools/cli-executor.js');
         const { SmartContentFormatter } = await import('../../tools/cli-output-converter.js');
+        const { loadProtocol, loadTemplate } = await import('../../tools/template-discovery.js');
 
         // Determine file path based on level
         let filePath: string;
@@ -617,6 +618,15 @@ export async function handleClaudeRoutes(ctx: RouteContext): Promise<boolean> {
           });
         };
 
+        // Build rulesEnv for $PROTO and $TMPL injection
+        const templateName = level === 'module'
+          ? 'planning-design-component-spec'
+          : 'analysis-analyze-code-patterns';
+        const rulesEnv = {
+          PROTO: loadProtocol('analysis'),
+          TMPL: loadTemplate(templateName)
+        };
+
         const startTime = Date.now();
         const result = await executeCliTool({
           tool: tool === 'qwen' ? 'qwen' : 'gemini',
@@ -627,7 +637,8 @@ export async function handleClaudeRoutes(ctx: RouteContext): Promise<boolean> {
           timeout: 600000, // 10 minutes
           stream: false,
           category: 'internal',
-          id: syncId
+          id: syncId,
+          rulesEnv
         }, (unit) => {
           // CliOutputUnit handler: use SmartContentFormatter for intelligent formatting (never returns null)
           const content = SmartContentFormatter.format(unit.content, unit.type);
diff --git a/ccw/src/core/routes/rules-routes.ts b/ccw/src/core/routes/rules-routes.ts
index 95b4bdbb..03ccd5c4 100644
--- a/ccw/src/core/routes/rules-routes.ts
+++ b/ccw/src/core/routes/rules-routes.ts
@@ -7,6 +7,7 @@ import { join } from 'path';
 import { homedir } from 'os';
 import { executeCliTool } from '../../tools/cli-executor.js';
 import { SmartContentFormatter } from '../../tools/cli-output-converter.js';
+import { loadProtocol, loadTemplate } from '../../tools/template-discovery.js';
 import type { RouteContext } from './types.js';
 
 interface ParsedRuleFrontmatter {
@@ -445,7 +446,7 @@ FILE NAME: ${fileName}
 ${subdirectory ? `SUBDIRECTORY: ${subdirectory}` : ''}
 ${reviewInstruction}
 
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/universal/00-universal-rigorous-style.txt) | Generate ONLY the rule content in markdown | No additional commentary | Do NOT use any tools | Output raw markdown text directly | write=CREATE`;
+RULES: $PROTO $TMPL | Generate ONLY the rule content in markdown | No additional commentary | Do NOT use any tools | Output raw markdown text directly | write=CREATE`;
 }
 
 /**
@@ -516,7 +517,7 @@ FILE NAME: ${fileName}
 ${subdirectory ? `SUBDIRECTORY: ${subdirectory}` : ''}
 INFERRED CATEGORY: ${context.category}
 
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-patterns.txt) | Extract REAL patterns from code | Include actual code snippets as examples | Do NOT use any tools | Output raw markdown text directly | analysis=READ-ONLY`;
+RULES: $PROTO $TMPL | Extract REAL patterns from code | Include actual code snippets as examples | Do NOT use any tools | Output raw markdown text directly | analysis=READ-ONLY`;
 }
 
 /**
@@ -567,7 +568,7 @@ EXPECTED OUTPUT:
 - If the original is already high quality, return it unchanged
 - Preserve any frontmatter (---paths---) if present
 
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/universal/00-universal-rigorous-style.txt) | Output ONLY improved markdown content | No additional text | Do NOT use any tools | Output raw markdown text directly | write=CREATE`;
+RULES: $PROTO $TMPL | Output ONLY improved markdown content | No additional text | Do NOT use any tools | Output raw markdown text directly | write=CREATE`;
 }
 
 /**
@@ -628,7 +629,7 @@ async function generateRuleViaCLI(params: RuleGenerateParams): Promise<Record<st
 TASK: • Create rule based on ${templateType} template • Generate structured markdown content
 MODE: write
 EXPECTED: Complete rule content in markdown format following template structure
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/universal/00-universal-rigorous-style.txt) | Follow Claude Code rule format | Use ${templateType} template patterns | Do NOT use any tools | Output raw markdown text directly | write=CREATE
+RULES: $PROTO $TMPL | Follow Claude Code rule format | Use ${templateType} template patterns | Do NOT use any tools | Output raw markdown text directly | write=CREATE
 
 TEMPLATE TYPE: ${templateType}
 FILE NAME: ${fileName}`;
@@ -676,6 +677,15 @@ FILE NAME: ${fileName}`;
         }
       : undefined;
 
+    // Build rulesEnv for $PROTO and $TMPL injection
+    const templateName = generationType === 'extract'
+      ? 'analysis-analyze-code-patterns'
+      : 'universal-universal-rigorous-style';
+    const rulesEnv = {
+      PROTO: loadProtocol(mode),
+      TMPL: loadTemplate(templateName)
+    };
+
     // Execute CLI tool (Claude) with at least 10 minutes timeout
     const startTime = Date.now();
     const result = await executeCliTool({
@@ -685,7 +695,8 @@ FILE NAME: ${fileName}`;
       cd: workingDir,
       timeout: 600000, // 10 minutes
       category: 'internal',
-      id: executionId
+      id: executionId,
+      rulesEnv
     }, onOutput);
 
     // Broadcast CLI_EXECUTION_COMPLETED event
@@ -763,6 +774,12 @@ FILE NAME: ${fileName}`;
           }
         : undefined;
 
+      // Build rulesEnv for review step
+      const reviewRulesEnv = {
+        PROTO: loadProtocol('write'),
+        TMPL: loadTemplate('universal-universal-rigorous-style')
+      };
+
       const reviewStartTime = Date.now();
       const reviewExecution = await executeCliTool({
         tool: 'claude',
@@ -771,7 +788,8 @@ FILE NAME: ${fileName}`;
         cd: workingDir,
         timeout: 300000, // 5 minutes for review
         category: 'internal',
-        id: reviewExecutionId
+        id: reviewExecutionId,
+        rulesEnv: reviewRulesEnv
       }, reviewOnOutput);
 
       // Broadcast review CLI_EXECUTION_COMPLETED event
diff --git a/ccw/src/tools/claude-cli-tools.ts b/ccw/src/tools/claude-cli-tools.ts
index e4c8e3ad..b8776ac9 100644
--- a/ccw/src/tools/claude-cli-tools.ts
+++ b/ccw/src/tools/claude-cli-tools.ts
@@ -15,6 +15,18 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 
+// ========== Debug Logging ==========
+// Only output logs when DEBUG is enabled (via --debug flag or DEBUG env var)
+function isDebugEnabled(): boolean {
+  return process.env.DEBUG === 'true' || process.env.DEBUG === '1' || process.env.CCW_DEBUG === 'true';
+}
+
+function debugLog(message: string): void {
+  if (isDebugEnabled()) {
+    console.log(message);
+  }
+}
+
 // ========== Types ==========
 
 export interface ClaudeCliTool {
@@ -264,7 +276,7 @@ function migrateConfig(config: any, projectDir: string): ClaudeCliToolsConfig {
     return config as ClaudeCliToolsConfig;
   }
 
-  console.log(`[claude-cli-tools] Migrating config from v${config.version || '1.0'} to v3.2.0`);
+  debugLog(`[claude-cli-tools] Migrating config from v${config.version || '1.0'} to v3.2.0`);
 
   // Try to load legacy cli-config.json for model data
   let legacyCliConfig: any = null;
@@ -274,7 +286,7 @@ function migrateConfig(config: any, projectDir: string): ClaudeCliToolsConfig {
     const fs = require('fs');
     if (fs.existsSync(legacyPath)) {
       legacyCliConfig = JSON.parse(fs.readFileSync(legacyPath, 'utf-8'));
-      console.log(`[claude-cli-tools] Found legacy cli-config.json, merging model data`);
+      debugLog(`[claude-cli-tools] Found legacy cli-config.json, merging model data`);
     }
   } catch {
     // Ignore errors loading legacy config
@@ -321,7 +333,7 @@ function migrateConfig(config: any, projectDir: string): ClaudeCliToolsConfig {
           tags: ep.tags.filter((t: string) => t !== 'cli-wrapper'),
           type: 'cli-wrapper'
         };
-        console.log(`[claude-cli-tools] Migrated cli-wrapper "${ep.name}" to tools`);
+        debugLog(`[claude-cli-tools] Migrated cli-wrapper "${ep.name}" to tools`);
       }
     } else {
       // Pure API endpoint becomes a tool with type: 'api-endpoint'
@@ -332,7 +344,7 @@ function migrateConfig(config: any, projectDir: string): ClaudeCliToolsConfig {
           type: 'api-endpoint',
           id: ep.id  // Store endpoint ID for settings lookup
         };
-        console.log(`[claude-cli-tools] Migrated API endpoint "${ep.name}" to tools`);
+        debugLog(`[claude-cli-tools] Migrated API endpoint "${ep.name}" to tools`);
       }
     }
   }
@@ -347,7 +359,7 @@ function migrateConfig(config: any, projectDir: string): ClaudeCliToolsConfig {
         type: 'api-endpoint',
         id: ep.id  // Store endpoint ID for settings lookup
       };
-      console.log(`[claude-cli-tools] Migrated API endpoint "${ep.name}" to tools`);
+      debugLog(`[claude-cli-tools] Migrated API endpoint "${ep.name}" to tools`);
     }
   }
 
@@ -375,7 +387,7 @@ export function ensureClaudeCliTools(projectDir: string, createInProject: boolea
   }
 
   // Config doesn't exist - create in global directory only
-  console.log('[claude-cli-tools] Config not found, creating default cli-tools.json in ~/.claude');
+  debugLog('[claude-cli-tools] Config not found, creating default cli-tools.json in ~/.claude');
 
   const defaultConfig: ClaudeCliToolsConfig = { ...DEFAULT_TOOLS_CONFIG };
 
@@ -387,7 +399,7 @@ export function ensureClaudeCliTools(projectDir: string, createInProject: boolea
   const globalPath = getGlobalConfigPath();
   try {
     fs.writeFileSync(globalPath, JSON.stringify(defaultConfig, null, 2), 'utf-8');
-    console.log(`[claude-cli-tools] Created default config at: ${globalPath}`);
+    debugLog(`[claude-cli-tools] Created default config at: ${globalPath}`);
     return { ...defaultConfig, _source: 'global' };
   } catch (err) {
     console.error('[claude-cli-tools] Failed to create global config:', err);
@@ -438,13 +450,13 @@ export function loadClaudeCliTools(projectDir: string): ClaudeCliToolsConfig & {
     if (needsSave) {
       try {
         saveClaudeCliTools(projectDir, config);
-        console.log(`[claude-cli-tools] Saved migrated config to: ${resolved.path}`);
+        debugLog(`[claude-cli-tools] Saved migrated config to: ${resolved.path}`);
       } catch (err) {
         console.warn('[claude-cli-tools] Failed to save migrated config:', err);
       }
     }
 
-    console.log(`[claude-cli-tools] Loaded tools config from ${resolved.source}: ${resolved.path}`);
+    debugLog(`[claude-cli-tools] Loaded tools config from ${resolved.source}: ${resolved.path}`);
     return config;
   } catch (err) {
     console.error('[claude-cli-tools] Error loading tools config:', err);
@@ -468,7 +480,7 @@ export function saveClaudeCliTools(projectDir: string, config: ClaudeCliToolsCon
 
   try {
     fs.writeFileSync(configPath, JSON.stringify(configToSave, null, 2), 'utf-8');
-    console.log(`[claude-cli-tools] Saved tools config to: ${configPath}`);
+    debugLog(`[claude-cli-tools] Saved tools config to: ${configPath}`);
   } catch (err) {
     console.error('[claude-cli-tools] Error saving tools config:', err);
     throw new Error(`Failed to save CLI tools config: ${err}`);
@@ -504,7 +516,7 @@ export function loadClaudeCliSettings(projectDir: string): ClaudeCliSettingsConf
       _source: resolved.source
     };
 
-    console.log(`[claude-cli-tools] Loaded settings from ${resolved.source}: ${resolved.path}`);
+    debugLog(`[claude-cli-tools] Loaded settings from ${resolved.source}: ${resolved.path}`);
     return config;
   } catch (err) {
     console.error('[claude-cli-tools] Error loading settings:', err);
@@ -528,7 +540,7 @@ export function saveClaudeCliSettings(projectDir: string, config: ClaudeCliSetti
 
   try {
     fs.writeFileSync(settingsPath, JSON.stringify(configToSave, null, 2), 'utf-8');
-    console.log(`[claude-cli-tools] Saved settings to: ${settingsPath}`);
+    debugLog(`[claude-cli-tools] Saved settings to: ${settingsPath}`);
   } catch (err) {
     console.error('[claude-cli-tools] Error saving settings:', err);
     throw new Error(`Failed to save CLI settings: ${err}`);
@@ -744,7 +756,7 @@ export function updateCodeIndexMcp(
         content = content.replace(nonePattern, targetFile);
 
         fs.writeFileSync(projectClaudeMdPath, content, 'utf-8');
-        console.log(`[claude-cli-tools] Updated project CLAUDE.md to use ${provider} (no global CLAUDE.md found)`);
+        debugLog(`[claude-cli-tools] Updated project CLAUDE.md to use ${provider} (no global CLAUDE.md found)`);
       }
     } else {
       // Update global CLAUDE.md (primary target)
@@ -756,7 +768,7 @@ export function updateCodeIndexMcp(
       content = content.replace(nonePattern, targetFile);
 
       fs.writeFileSync(globalClaudeMdPath, content, 'utf-8');
-      console.log(`[claude-cli-tools] Updated global CLAUDE.md to use ${provider}`);
+      debugLog(`[claude-cli-tools] Updated global CLAUDE.md to use ${provider}`);
     }
 
     return { success: true, settings };
diff --git a/ccw/src/tools/cli-executor-core.ts b/ccw/src/tools/cli-executor-core.ts
index 3738c6b3..87c6fad7 100644
--- a/ccw/src/tools/cli-executor-core.ts
+++ b/ccw/src/tools/cli-executor-core.ts
@@ -1149,7 +1149,7 @@ async function executeCliTool(
         duration_ms: duration,
         output: newTurnOutput,
         parsedOutput: flattenOutputUnits(allOutputUnits, {
-          excludeTypes: ['stderr', 'progress', 'metadata', 'system']
+          excludeTypes: ['stderr', 'progress', 'metadata', 'system', 'tool_call']
         })
       };