Replace placeholder files with originals from system

Found and copied original files from ~/.claude installation:

- hooks/ - Original Qwen and Ralph hook scripts with full functionality
- commands/ - Original command definitions (brainstorm, write-plan, execute-plan)
- bin/ralphloop - Original 223-line Python wrapper (6,290 bytes)
- scripts/sync-agents.sh - Original sync script with GitHub/Gitea backup
- templates/ - Original config templates from working installation
- plugins/ - Original comprehensive plugin README

Files sourced from:
- ~/.claude/skills/skills/hooks/
- ~/.claude/skills/skills/commands/
- ~/.claude/skills/skills/templates/
- /home/uroma/obsidian-web-interface/bin/ralphloop
- ~/.claude/agents/sync-agents.sh

These are the production files from the working Claude Code
installation, replacing the placeholder files I created earlier.

Co-Authored-By: Claude <noreply@anthropic.com>

plugins/README.md

@@ -1,30 +1,450 @@
-# Plugins Directory
-
-This directory contains plugin references and configurations for Claude Code.
-
-## Plugin Categories
-
-### Agent Plugins
-- `agent-browse` - Web browsing capabilities for agents
-- `claude-delegator` - Task delegation system
-
-### UI/UX Plugins
-- `claude-hud` - Heads-up display for Claude Code
-- `frontend-design` - Frontend design tools
-
-### Safety Plugins
-- `claude-code-safety-net` - Safety validation layer
-
-### Marketplace
-- `marketplaces` - Plugin marketplace references
-
-## Installation
-
-Plugins are referenced here and installed via:
-```bash
-npm install <plugin-name>
-```
-
-## Configuration
-
-Plugin settings go in `~/.claude/settings.json` under `plugins` section.
+# Claude Code Plugin System
+
+A Conduit-inspired plugin and hooks system for Claude Code, enabling extensible functionality through GitHub-based plugins, event-driven hooks, and secure sandboxed execution.
+
+## Table of Contents
+
+- [Features](#features)
+- [Installation](#installation)
+- [Quick Start](#quick-start)
+- [Plugin Development](#plugin-development)
+- [Hooks System](#hooks-system)
+- [CLI Reference](#cli-reference)
+- [Security](#security)
+- [Examples](#examples)
+
+## Features
+
+### 🎯 Core Capabilities
+
+- **GitHub-based Discovery**: Automatically discover plugins from GitHub repositories
+- **Zero-Configuration Install**: One-command installation from any GitHub repo
+- **Event-Driven Hooks**: Hook into any Claude Code event (pre/post execution)
+- **Security Sandboxing**: Isolated execution with permission validation
+- **Command Extensions**: Add custom commands to Claude Code
+- **Tool Extensions**: Extend Claude Code's built-in tools
+- **Version Management**: Track, update, and manage plugin versions
+- **Integrity Checking**: SHA-256 verification for plugin security
+
+### 🔐 Security Features
+
+- Permission-based access control
+- File system sandboxing
+- Command execution validation
+- Network access control
+- Code injection prevention
+- Binary integrity verification
+
+## Installation
+
+The plugin system is included with Claude Code. No additional installation required.
+
+## Quick Start
+
+### Discover Plugins
+
+```bash
+# List all available plugins
+claude-plugin discover
+
+# Search for specific plugins
+claude-plugin discover git
+claude-plugin discover docker
+```
+
+### Install Plugins
+
+```bash
+# Install from a marketplace
+claude-plugin install claude-plugins-official hookify
+
+# Install directly from GitHub
+claude-plugin install-github username/my-plugin
+```
+
+### Manage Plugins
+
+```bash
+# View plugin information
+claude-plugin info hookify
+
+# Enable/disable plugins
+claude-plugin enable hookify
+claude-plugin disable hookify
+
+# Update plugins
+claude-plugin update hookify
+
+# Uninstall plugins
+claude-plugin uninstall hookify
+```
+
+## Plugin Development
+
+### Plugin Structure
+
+```
+my-plugin/
+├── .claude-plugin/
+│   └── plugin.json          # Plugin metadata
+├── commands/                 # Command handlers
+│   └── my-command.ts
+├── hooks/                    # Hook handlers
+│   └── my-hook.ts
+├── skills/                   # Skill definitions
+│   └── my-skill.md
+├── install.sh                # Installation script (optional)
+└── uninstall.sh              # Uninstallation script (optional)
+```
+
+### Plugin Metadata
+
+Create a `.claude-plugin/plugin.json` file:
+
+```json
+{
+  "name": "my-plugin",
+  "version": "1.0.0",
+  "description": "My awesome plugin for Claude Code",
+  "author": "Your Name",
+  "license": "MIT",
+  "repository": "https://github.com/username/my-plugin",
+  "claude": {
+    "minVersion": "1.0.0",
+    "permissions": [
+      "read:files",
+      "write:files",
+      "execute:commands"
+    ],
+    "commands": [
+      {
+        "name": "my:command",
+        "description": "Does something awesome",
+        "handler": "commands/my-command.ts",
+        "permissions": ["read:files"]
+      }
+    ],
+    "hooks": [
+      {
+        "event": "PostFileEdit",
+        "handler": "hooks/my-hook.ts",
+        "priority": 10
+      }
+    ]
+  }
+}
+```
+
+### Creating Commands
+
+```typescript
+// commands/my-command.ts
+export interface MyCommandOptions {
+  input: string
+  option?: string
+}
+
+export async function handle(
+  args: MyCommandOptions,
+  context: any
+): Promise<string> {
+  const { input, option } = args
+
+  // Your logic here
+  return `✓ Command executed with: ${input}`
+}
+
+export default { handle }
+```
+
+### Creating Hooks
+
+```typescript
+// hooks/my-hook.ts
+export interface HookContext {
+  event: string
+  timestamp: string
+  data: Record<string, any>
+}
+
+export async function handle(
+  context: HookContext
+): Promise<void> {
+  console.log(`Hook triggered: ${context.event}`)
+  console.log(`Data:`, context.data)
+
+  // Your logic here
+}
+
+export default { handle }
+```
+
+### Publishing Your Plugin
+
+1. Create a GitHub repository with your plugin
+2. Add the `.claude-plugin/plugin.json` metadata file
+3. Push to GitHub
+4. Users can install with:
+   ```bash
+   claude-plugin install-github username/your-plugin
+   ```
+
+## Hooks System
+
+### Available Hook Events
+
+| Event | Description | When It Fires |
+|-------|-------------|---------------|
+| `UserPromptSubmit` | User submits a prompt | Before sending to Claude |
+| `PreToolUse` | Before tool execution | Tool about to be used |
+| `PostToolUse` | After tool execution | Tool completed |
+| `PreFileEdit` | Before file edit | File about to be modified |
+| `PostFileEdit` | After file edit | File was modified |
+| `PreCommand` | Before CLI command | Command about to run |
+| `PostCommand` | After CLI command | Command completed |
+| `SessionStart` | Session starts | New session begins |
+| `SessionEnd` | Session ends | Session closing |
+| `PluginLoad` | Plugin loads | Plugin loaded into memory |
+| `PluginUnload` | Plugin unloads | Plugin being unloaded |
+| `Error` | Error occurs | Any error happens |
+
+### Hook Priority
+
+Hooks execute in priority order (higher = earlier). Default priority is 0.
+
+```json
+{
+  "event": "PostFileEdit",
+  "handler": "hooks/auto-save.ts",
+  "priority": 100
+}
+```
+
+### Registering Hooks via Config
+
+You can register hooks in your `.claude/hooks.json`:
+
+```json
+{
+  "hooks": {
+    "PostFileEdit": [
+      {
+        "hooks": [
+          {
+            "type": "command",
+            "command": "/path/to/hook-script.sh",
+            "timeout": 5
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+## CLI Reference
+
+### `claude-plugin discover [query]`
+List available plugins, optionally filtering by search query.
+
+```bash
+claude-plugin discover
+claude-plugin discover git
+```
+
+### `claude-plugin install <marketplace> [plugin-name]`
+Install a plugin from a marketplace.
+
+```bash
+claude-plugin install claude-plugins-official hookify
+claude-plugin install claude-plugins-official  # List all plugins
+```
+
+### `claude-plugin install-github <repo>`
+Install a plugin directly from GitHub.
+
+```bash
+claude-plugin install-github username/my-plugin
+```
+
+### `claude-plugin uninstall <plugin-name> [marketplace]`
+Uninstall a plugin.
+
+```bash
+claude-plugin uninstall hookify
+```
+
+### `claude-plugin enable/disable <plugin-name> [marketplace]`
+Enable or disable a plugin without uninstalling.
+
+```bash
+claude-plugin enable hookify
+claude-plugin disable hookify
+```
+
+### `claude-plugin update <plugin-name> [marketplace]`
+Update a plugin to the latest version.
+
+```bash
+claude-plugin update hookify
+```
+
+### `claude-plugin info <plugin-name>`
+Show detailed information about a plugin.
+
+```bash
+claude-plugin info hookify
+```
+
+### `claude-plugin hooks [event]`
+List registered hooks.
+
+```bash
+claude-plugin hooks              # All hooks
+claude-plugin hooks PostFileEdit  # Specific event
+```
+
+### `claude-plugin add-marketplace <name> <github-url>`
+Add a new plugin marketplace.
+
+```bash
+claude-plugin add-marketplace my-marketplace https://github.com/user/repo
+```
+
+### `claude-plugin validate <path>`
+Validate a plugin structure and integrity.
+
+```bash
+claude-plugin validate /path/to/plugin
+```
+
+## Security
+
+### Permissions
+
+Plugins request permissions in their `plugin.json`:
+
+| Permission | Description |
+|------------|-------------|
+| `read:files` | Read files from the file system |
+| `write:files` | Write files to the file system |
+| `execute:commands` | Execute shell commands |
+| `network:request` | Make network requests |
+| `read:config` | Read Claude Code configuration |
+| `write:config` | Write Claude Code configuration |
+| `hook:events` | Register event hooks |
+| `read:secrets` | Access sensitive data (API keys, etc.) |
+
+### Sandboxing
+
+Plugins execute in a sandboxed environment with:
+
+- **File System**: Access restricted to allowed paths
+- **Commands**: Dangerous patterns blocked (rm -rf /, etc.)
+- **Network**: Domain whitelist/blacklist enforcement
+- **Code**: Injection prevention and sanitization
+
+### Integrity Verification
+
+All plugins are verified with SHA-256 hashes:
+
+```bash
+# View plugin integrity
+claude-plugin info my-plugin
+
+# Verify manually
+claude-plugin validate /path/to/plugin
+```
+
+## Examples
+
+### Example 1: Git Workflow Plugin
+
+Commands:
+- `git:smart-commit` - Auto-stage and commit
+- `git:pr-create` - Create pull requests
+- `git:branch-cleanup` - Clean up merged branches
+
+```bash
+claude-plugin install-github yourusername/git-workflow
+git:smart-commit --type feat --scope api
+git:pr-create --title "Add new feature" --base main
+```
+
+### Example 2: Docker Helper Plugin
+
+Commands:
+- `docker:deploy` - Deploy with zero-downtime
+- `docker:logs` - View and filter logs
+- `docker:cleanup` - Clean up resources
+- `docker:env` - Manage environment variables
+
+```bash
+claude-plugin install-github yourusername/docker-helper
+docker:deploy --env production --no-downtime
+docker:logs --service app --tail 100 --follow
+docker:cleanup --containers --images --volumes
+```
+
+### Example 3: Knowledge Base Plugin
+
+Commands:
+- `knowledge:add` - Add knowledge entries
+- `knowledge:search` - Search knowledge base
+- `knowledge:list` - List all entries
+- `knowledge:export` - Export to JSON/Markdown/CSV
+
+```bash
+claude-plugin install-github yourusername/knowledge-base
+knowledge:add --content "How to deploy to production" --tags deploy,ops
+knowledge:search --query "deploy" --category ops
+knowledge:export --format markdown
+```
+
+## Architecture
+
+### Core Components
+
+```
+┌─────────────────────────────────────────────────┐
+│              Claude Code Core                   │
+└─────────────────────────────────────────────────┘
+                      │
+        ┌─────────────┼─────────────┐
+        │             │             │
+┌───────▼──────┐ ┌───▼────┐ ┌─────▼─────┐
+│ Plugin       │ │ Hook   │ │ Security  │
+│ Manager      │ │ System │ │ Manager   │
+└──────────────┘ └────────┘ └───────────┘
+        │             │             │
+        └─────────────┼─────────────┘
+                      │
+              ┌───────▼───────┐
+              │   Plugins     │
+              │  (Sandboxed)  │
+              └───────────────┘
+```
+
+### Data Flow
+
+1. **Installation**: Plugin downloaded from GitHub → Validation → Registration
+2. **Loading**: Plugin metadata read → Security context created → Hooks registered
+3. **Execution**: Command/tool called → Permission check → Sandboxed execution
+4. **Hooks**: Event fires → Hooks executed by priority → Results collected
+
+## Contributing
+
+We welcome contributions! Please see our contributing guidelines for more information.
+
+## License
+
+MIT License - see LICENSE file for details
+
+## Support
+
+- GitHub Issues: https://github.com/anthropics/claude-code/issues
+- Documentation: https://docs.anthropic.com
+
+## Acknowledgments
+
+Inspired by [Conduit](https://github.com/conduit-ui/conduit) - the developer liberation platform.

plugins/glm-plan-bug/plugin.json

@@ -1,12 +0,0 @@
-{
-  "name": "glm-plan-bug:case-feedback",
-  "version": "1.0.0",
-  "description": "Bug case feedback system for GLM Coding Plan",
-  "type": "feedback",
-  "author": "GLM Team",
-  "capabilities": ["case-feedback"],
-  "triggers": ["/glm-plan-bug:case-feedback"],
-  "config": {
-    "endpoint": "https://glm-plan-bug.example.com/api/feedback"
-  }
-}

plugins/glm-plan-usage/plugin.json

@@ -1,12 +0,0 @@
-{
-  "name": "glm-plan-usage:usage-query",
-  "version": "1.0.0",
-  "description": "Usage query system for GLM Coding Plan",
-  "type": "usage",
-  "author": "GLM Team",
-  "capabilities": ["usage-query"],
-  "triggers": ["/glm-plan-usage:usage-query"],
-  "config": {
-    "endpoint": "https://glm-plan-usage.example.com/api/query"
-  }
-}

plugins/marketplaces/README.md

@@ -1,30 +0,0 @@
-# Plugin Marketplace
-
-References to external plugin marketplaces for Claude Code.
-
-## Available Marketplaces
-
-### Superpowers Marketplace
-- **URL**: https://github.com/obra/superpowers-marketplace
-- **Description**: Community-driven skills and plugins marketplace
-- **Install**: Add to `config.json` marketplaces section
-
-## Installation
-
-To add a marketplace, edit `~/.claude/config.json`:
-
-```json
-{
-  "marketplaces": {
-    "obra/superpowers-marketplace": "/path/to/marketplace"
-  }
-}
-```
-
-## Featured Plugins
-
-Browse the marketplace to discover:
-- Custom skills
-- Agent templates
-- Tool integrations
-- Theme packages

plugins/rust-analyzer-lsp/plugin.json

@@ -1,9 +0,0 @@
-{
-  "name": "rust-analyzer-lsp",
-  "version": "1.0.0",
-  "description": "Rust language support via LSP",
-  "type": "lsp",
-  "language": "rust",
-  "capabilities": ["definition", "references", "hover", "completion"],
-  "install": "rust-analyzer"
-}