diff --git a/.claude/skills/command-guide/SKILL.md b/.claude/skills/command-guide/SKILL.md
index 7ff2d3a3..f6e1a42a 100644
--- a/.claude/skills/command-guide/SKILL.md
+++ b/.claude/skills/command-guide/SKILL.md
@@ -123,15 +123,16 @@ Comprehensive command guide for Claude DMS3 workflow system covering 69 commands
 1. Detect complexity indicators (多个命令对比、工作流程分析、最佳实践)
 2. Construct analysis prompt for gemini/qwen:
    ```bash
-   cd reference && gemini -p "
+   gemini -p "
    PURPOSE: Analyze command documentation to answer user query
    TASK: [extracted user question with context]
    MODE: analysis
-   CONTEXT: @agents/**/* @commands/**/*
+   CONTEXT: @**/*
    EXPECTED: Comprehensive answer with examples and recommendations
    RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-patterns.txt) | Focus on practical usage | analysis=READ-ONLY
-   " -m gemini-3-pro-preview-11-2025
+   " -m gemini-3-pro-preview-11-2025 --include-directories ~/.claude/skills/command-guide/reference
    ```
+   Note: Use absolute path `~/.claude/skills/command-guide/reference` for reference documentation access
 3. Return CLI analysis results to user
 
 **Query Classification**:
@@ -192,7 +193,11 @@ Complete backup of all command and agent documentation for deep analysis:
   - `task/` - Task management commands (4 files)
   - `workflow/` - Workflow commands (46 files)
 
-**Usage**: Mode 6 queries these files directly for detailed command/agent analysis, or uses CLI tools (gemini/qwen) for complex cross-command analysis.
+**Installation Path**: `~/.claude/skills/command-guide/` (skill designed for global installation)
+
+**Absolute Reference Path**: `~/.claude/skills/command-guide/reference/`
+
+**Usage**: Mode 6 queries these files directly for detailed command/agent analysis, or uses CLI tools (gemini/qwen) with absolute paths for complex cross-command analysis.
 
 ---
 
@@ -264,10 +269,15 @@ Team members get latest indexes via `git pull`.
 
 ---
 
-**Version**: 1.3.0 (Deep command analysis with reference documentation backup)
+**Version**: 1.3.1 (Path configuration for global installation)
 **Last Updated**: 2025-11-06
 **Maintainer**: Claude DMS3 Team
 
+**Changelog v1.3.1**:
+- ✅ Updated all paths to use absolute paths (`~/.claude/skills/command-guide/`)
+- ✅ CLI commands now use `--include-directories` with absolute reference path
+- ✅ Ensures skill works correctly when installed in `~/.claude/skills/`
+
 **Changelog v1.3.0**:
 - ✅ Added Mode 6: Deep Command Analysis with CLI-assisted queries
 - ✅ Created reference documentation backup (80 files: 11 agents + 69 commands)
diff --git a/.claude/skills/command-guide/guides/implementation-details.md b/.claude/skills/command-guide/guides/implementation-details.md
index a5744398..b96fcda3 100644
--- a/.claude/skills/command-guide/guides/implementation-details.md
+++ b/.claude/skills/command-guide/guides/implementation-details.md
@@ -518,6 +518,9 @@ async function reportIssue(issueType) {
 
 ## Mode 6: Deep Command Analysis 🔬
 
+**Path Configuration Note**:
+This mode uses absolute paths (`~/.claude/skills/command-guide/reference`) to ensure the skill works correctly regardless of where it's installed. The skill is designed to be installed in `~/.claude/skills/` (user's global Claude configuration directory).
+
 ### Trigger Analysis
 
 **Keywords**: 详细说明, 命令原理, agent 如何工作, 实现细节, 对比命令, 最佳实践
@@ -591,15 +594,18 @@ async function handleSimpleQuery(query) {
   const isAgent = entityName.includes('-agent') || entityName.includes('agent');
   const isCommand = entityName.includes(':') || entityName.startsWith('/');
 
+  // Base path for reference documentation
+  const basePath = '~/.claude/skills/command-guide/reference';
+
   let filePath;
   if (isAgent) {
-    // Agent query
+    // Agent query - use absolute path
     const agentFileName = entityName.replace(/^\//, '').replace(/-agent$/, '-agent');
-    filePath = `reference/agents/${agentFileName}.md`;
+    filePath = `${basePath}/agents/${agentFileName}.md`;
   } else if (isCommand) {
     // Command query - need to find in command hierarchy
     const cmdName = entityName.replace(/^\//, '');
-    filePath = await locateCommandFile(cmdName);
+    filePath = await locateCommandFile(cmdName, basePath);
   }
 
   // Read documentation
@@ -618,16 +624,16 @@ async function handleSimpleQuery(query) {
   };
 }
 
-async function locateCommandFile(commandName) {
+async function locateCommandFile(commandName, basePath) {
   // Parse command category from name
-  // e.g., "workflow:plan" → "reference/commands/workflow/plan.md"
+  // e.g., "workflow:plan" → "~/.claude/skills/command-guide/reference/commands/workflow/plan.md"
   const [category, name] = commandName.split(':');
 
-  // Search in reference/commands hierarchy
+  // Search in reference/commands hierarchy using absolute paths
   const possiblePaths = [
-    `reference/commands/${category}/${name}.md`,
-    `reference/commands/${category}/${name}/*.md`,
-    `reference/commands/${name}.md`
+    `${basePath}/commands/${category}/${name}.md`,
+    `${basePath}/commands/${category}/${name}/*.md`,
+    `${basePath}/commands/${name}.md`
   ];
 
   for (const path of possiblePaths) {
@@ -737,11 +743,12 @@ function buildCLIPrompt(userQuery, classification, contextPaths) {
   }
 
   // Construct full prompt using Standard Template
+  // Note: CONTEXT uses @**/* because we'll use --include-directories to specify the reference path
   return `PURPOSE: Analyze command/agent documentation to provide comprehensive answer to user query
 TASK:
 ${taskDescription}
 MODE: analysis
-CONTEXT: ${contextRef}
+CONTEXT: @**/*
 EXPECTED: Comprehensive answer with examples, comparisons, and recommendations in markdown format
 RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-patterns.txt) | Focus on practical usage and real-world scenarios | analysis=READ-ONLY
 
@@ -749,11 +756,13 @@ User Question: ${question}`;
 }
 
 async function executeCLIAnalysis(prompt) {
-  // Change to reference directory for correct file context
-  const cwd = 'reference';
+  // Use absolute path for reference directory
+  // This ensures the command works regardless of where the skill is installed
+  const referencePath = '~/.claude/skills/command-guide/reference';
 
-  // Execute gemini with analysis prompt
-  const command = `cd ${cwd} && gemini -p "${escapePrompt(prompt)}" -m gemini-3-pro-preview-11-2025`;
+  // Execute gemini with analysis prompt using --include-directories
+  // This allows gemini to access reference docs while maintaining correct file context
+  const command = `gemini -p "${escapePrompt(prompt)}" -m gemini-3-pro-preview-11-2025 --include-directories ${referencePath}`;
 
   try {
     const result = await execBash(command, { timeout: 120000 }); // 2 min timeout
@@ -761,7 +770,7 @@ async function executeCLIAnalysis(prompt) {
   } catch (error) {
     // Fallback to qwen if gemini fails
     console.warn('Gemini failed, falling back to qwen');
-    const fallbackCmd = `cd ${cwd} && qwen -p "${escapePrompt(prompt)}" -m coder-model`;
+    const fallbackCmd = `qwen -p "${escapePrompt(prompt)}" -m coder-model --include-directories ${referencePath}`;
     const result = await execBash(fallbackCmd, { timeout: 120000 });
     return parseAnalysisResult(result.stdout);
   }
@@ -816,17 +825,21 @@ function extractAllEntities(query) {
 }
 
 async function resolveEntityPath(entityName) {
+  // Base path for reference documentation
+  const basePath = '~/.claude/skills/command-guide/reference';
   const isAgent = entityName.includes('-agent');
 
   if (isAgent) {
+    // Return relative path within reference directory (used for @context in CLI)
     return `agents/${entityName}.md`;
   } else {
     // Command - need to find in hierarchy
     const [category] = entityName.split(':');
-    // Use glob to find the file
-    const matches = await glob(`commands/${category}/**/${entityName.split(':')[1]}.md`);
+    // Use glob to find the file (glob pattern uses absolute path)
+    const matches = await glob(`${basePath}/commands/${category}/**/${entityName.split(':')[1]}.md`);
     if (matches.length > 0) {
-      return matches[0];
+      // Return relative path within reference directory
+      return matches[0].replace(`${basePath}/`, '');
     }
     throw new Error(`Entity file not found: ${entityName}`);
   }
@@ -870,7 +883,7 @@ function escapePrompt(prompt) {
     workflow: "## Workflow\n1. Analyze requirements\n2. Break down into tasks...",
     examples: "## Examples\n```bash\n/workflow:plan --agent \"feature\"\n```"
   },
-  full_path: "reference/agents/action-planning-agent.md",
+  full_path: "~/.claude/skills/command-guide/reference/agents/action-planning-agent.md",
   related: ["workflow:plan", "task:create", "conceptual-planning-agent"]
 }
 ```
@@ -921,8 +934,8 @@ function escapePrompt(prompt) {
     format: "markdown"
   },
   source_files: [
-    "commands/workflow/plan.md",
-    "commands/workflow/tdd-plan.md"
+    "~/.claude/skills/command-guide/reference/commands/workflow/plan.md",
+    "~/.claude/skills/command-guide/reference/commands/workflow/tdd-plan.md"
   ]
 }
 ```