feat: add explicit skills folder handling to create-rule.js

Update create-rule script to properly handle the new skills folder
structure for claude-code and claude-code-4.5.

**Changes:**
- Exclude 'skills' from main directory copy
- Copy skills folder explicitly with progress indication
- Apply template substitutions to skills files
- Show clear progress: "Copying skills folder"

**Behavior:**
Skills are now excluded from the main recursive copy and copied
separately with proper template substitutions and progress feedback.
This ensures:
- Skills copied only once (no duplication)
- Template variables properly substituted
- Clear user feedback during installation
- Consistent with output-styles handling

**Impact:**
When users run `node create-rule.js --tool=claude-code` or
`--tool=claude-code-4.5`, the skills folder will be properly
copied to `~/.claude/skills/` with all agent prompts, workflows,
scripts, and documentation intact.

Author: stevengonsalvez

create-rule.js

@@ -36,7 +36,7 @@ const TOOL_CONFIG = {
         ruleDir: 'claude-code',
         targetSubdir: '.claude',
         copyEntireFolder: true,
-        excludeFiles: ['settings.local.json'],
+        excludeFiles: ['settings.local.json', 'skills'],
         templateSubstitutions: {
             'CLAUDE.md': {
                 'TOOL_DIR': '.claude',
@@ -52,7 +52,7 @@ const TOOL_CONFIG = {
         ruleDir: 'claude-code-4.5',
         targetSubdir: '.claude',
         copyEntireFolder: true,
-        excludeFiles: ['settings.local.json'],
+        excludeFiles: ['settings.local.json', 'skills'],
         templateSubstitutions: {
             'CLAUDE.md': {
                 'TOOL_DIR': '.claude',
@@ -393,13 +393,25 @@ async function handleFullDirectoryCopy(tool, config, overrideHomeDir = null, tar
         showProgress('Copying output-styles folder');
         const outputStylesSource = path.join(__dirname, 'claude-code', 'output-styles');
         const outputStylesDest = path.join(destDir, 'output-styles');
-        
+
         if (fs.existsSync(outputStylesSource)) {
             const outputStylesFiles = copyDirectoryRecursive(outputStylesSource, outputStylesDest, [], {});
             completeProgress(`Copied ${outputStylesFiles} output-styles files`);
         }
     }
 
+    // Copy skills folder for claude-code and claude-code-4.5
+    if (tool === 'claude-code' || tool === 'claude-code-4.5') {
+        showProgress('Copying skills folder');
+        const skillsSource = path.join(__dirname, config.ruleDir, 'skills');
+        const skillsDest = path.join(destDir, 'skills');
+
+        if (fs.existsSync(skillsSource)) {
+            const skillsFiles = copyDirectoryRecursive(skillsSource, skillsDest, [], config.templateSubstitutions || {});
+            completeProgress(`Copied ${skillsFiles} skill files`);
+        }
+    }
+
     // Copy tool-specific files if they exist
     if (config.toolSpecificFiles) {
         showProgress('Copying tool-specific files');