fix: install skills in flat structure for auto-discovery

CLAUDE.md

@@ -414,18 +414,20 @@ src/
 └── claude/                   # Claude Code assets
     ├── agents/devflow/         # Sub-agent definitions
     ├── commands/devflow/       # Slash command definitions
-    ├── skills/devflow/         # Auto-activate skill definitions
+    ├── skills/devflow/         # Skill source (installed flat)
     ├── scripts/                # Supporting scripts
     └── settings.json           # Claude Code settings
 ```
 
 ### Installation Paths
 - Commands: `~/.claude/commands/devflow/`
 - Agents: `~/.claude/agents/devflow/`
-- Skills: `~/.claude/skills/devflow/`
+- Skills: `~/.claude/skills/` (flat structure - no devflow/ subdirectory)
 - Scripts: `~/.devflow/scripts/`
 - Settings: `~/.claude/settings.json`
 
+**Note:** Skills are installed flat (directly under `skills/`) for Claude Code auto-discovery. Commands and agents use the `devflow/` subdirectory for namespacing.
+
 ## Testing Guidelines
 
 ### Command Testing

README.md

@@ -202,7 +202,7 @@ Covers patterns for all major languages and operating systems.
 **User Scope** (default):
 - Installs commands to `~/.claude/commands/devflow/`
 - Installs sub-agents to `~/.claude/agents/devflow/`
-- Installs skills to `~/.claude/skills/devflow/`
+- Installs skills to `~/.claude/skills/`
 - Installs scripts to `~/.devflow/scripts/`
 - Updates `~/.claude/settings.json` (statusline and model)
 - Creates `.claudeignore` at git repository root
@@ -211,7 +211,7 @@ Covers patterns for all major languages and operating systems.
 **Local Scope** (`--scope local`):
 - Installs commands to `<git-root>/.claude/commands/devflow/`
 - Installs sub-agents to `<git-root>/.claude/agents/devflow/`
-- Installs skills to `<git-root>/.claude/skills/devflow/`
+- Installs skills to `<git-root>/.claude/skills/`
 - Installs scripts to `<git-root>/.devflow/scripts/`
 - Creates `<git-root>/.claude/settings.json` (statusline and model)
 - Creates `.claudeignore` at git repository root
@@ -287,7 +287,7 @@ src/
 └── claude/                # Claude Code configuration
     ├── agents/devflow/     # Sub-agent definitions (.md)
     ├── commands/devflow/   # Slash command definitions (.md)
-    ├── skills/devflow/     # Auto-activate skill definitions (.md)
+    ├── skills/devflow/     # Skill source (installed flat to ~/.claude/skills/)
     ├── scripts/            # statusline.sh
     └── settings.json       # Claude Code settings
 ```

src/cli/commands/init.ts

@@ -164,7 +164,7 @@ export const initCommand = new Command('init')
           name: 'agents'
         },
         {
-          target: path.join(claudeDir, 'skills', 'devflow'),
+          target: path.join(claudeDir, 'skills'),
           source: path.join(claudeSourceDir, 'skills', 'devflow'),
           name: 'skills'
         },
@@ -177,10 +177,39 @@ export const initCommand = new Command('init')
 
       // Clean old DevFlow files before installing
       for (const dir of devflowDirectories) {
-        try {
-          await fs.rm(dir.target, { recursive: true, force: true });
-        } catch (e) {
-          // Directory might not exist on first install
+        if (dir.name === 'skills') {
+          // Special handling for skills: clean old nested structure and individual skills
+          // Remove old devflow/ subdirectory if it exists (migration from old structure)
+          const oldSkillsDir = path.join(claudeDir, 'skills', 'devflow');
+          try {
+            await fs.rm(oldSkillsDir, { recursive: true, force: true });
+          } catch (e) {
+            // Directory might not exist
+          }
+
+          // Remove individual skill directories that we're about to reinstall
+          try {
+            const skillEntries = await fs.readdir(dir.source, { withFileTypes: true });
+            for (const entry of skillEntries) {
+              if (entry.isDirectory()) {
+                const skillTarget = path.join(dir.target, entry.name);
+                try {
+                  await fs.rm(skillTarget, { recursive: true, force: true });
+                } catch (e) {
+                  // Skill might not exist
+                }
+              }
+            }
+          } catch (e) {
+            // Source directory might not exist
+          }
+        } else {
+          // For other components (commands, agents, scripts), clean the entire directory
+          try {
+            await fs.rm(dir.target, { recursive: true, force: true });
+          } catch (e) {
+            // Directory might not exist on first install
+          }
         }
       }
 

src/cli/commands/uninstall.ts

@@ -85,7 +85,6 @@ export const uninstallCommand = new Command('uninstall')
       const devflowDirectories = [
         { path: path.join(claudeDir, 'commands', 'devflow'), name: 'commands' },
         { path: path.join(claudeDir, 'agents', 'devflow'), name: 'agents' },
-        { path: path.join(claudeDir, 'skills', 'devflow'), name: 'skills' },
         { path: devflowScriptsDir, name: 'scripts' }
       ];
 
@@ -100,6 +99,40 @@ export const uninstallCommand = new Command('uninstall')
         }
       }
 
+      // Remove individual DevFlow skills (flat structure)
+      const skillsDir = path.join(claudeDir, 'skills');
+      const devflowSkills = [
+        'pattern-check',
+        'test-design',
+        'code-smell',
+        'research',
+        'debug',
+        'input-validation',
+        'error-handling'
+      ];
+
+      let skillsRemoved = 0;
+      for (const skillName of devflowSkills) {
+        try {
+          const skillPath = path.join(skillsDir, skillName);
+          await fs.rm(skillPath, { recursive: true, force: true });
+          skillsRemoved++;
+        } catch (error) {
+          // Skill might not exist, continue
+        }
+      }
+
+      if (skillsRemoved > 0) {
+        console.log(`  ✅ Removed ${skillsRemoved} DevFlow skills`);
+      }
+
+      // Also remove old nested skills structure if it exists (migration cleanup)
+      try {
+        await fs.rm(path.join(claudeDir, 'skills', 'devflow'), { recursive: true, force: true });
+      } catch {
+        // Old structure doesn't exist, ignore
+      }
+
       console.log();
     }