Comprehensive documentation rewrite

docs/docs/cli.md

@@ -2,38 +2,290 @@
 sidebar_position: 5
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-# CLI
+# CLI Reference
 
-## Agent
+## Agent Commands
+
+### `perry agent run`
+
+Start the agent daemon.
+
+```bash
+perry agent run
+perry agent run --port 3000
+perry agent run --config-dir ~/.my-perry
+perry agent run --no-host-access
+```
+
+| Option | Description |
+|--------|-------------|
+| `-p, --port <port>` | Port to listen on (default: 7391) |
+| `-c, --config-dir <dir>` | Configuration directory |
+| `--no-host-access` | Disable direct host machine access |
+
+### `perry agent install`
+
+Install agent as a systemd user service.
 
 ```bash
-perry agent run [--port PORT]
 perry agent install
+perry agent install --port 3000
+perry agent install --no-host-access
+```
+
+Same options as `perry agent run`.
+
+### `perry agent uninstall`
+
+Remove the systemd service.
+
+```bash
 perry agent uninstall
+```
+
+### `perry agent status`
+
+Show agent service status.
+
+```bash
 perry agent status
 ```
 
-## Workspaces
+### `perry agent logs`
+
+View agent service logs.
+
+```bash
+perry agent logs
+perry agent logs -f          # Follow logs
+perry agent logs -n 100      # Show last 100 lines
+```
+
+| Option | Description |
+|--------|-------------|
+| `-f, --follow` | Follow log output |
+| `-n, --lines <n>` | Number of lines to show (default: 50) |
+
+## Workspace Commands
+
+### `perry start <name>`
+
+Start a workspace. Creates it if it doesn't exist.
+
+```bash
+perry start myproject
+perry start myproject --clone git@github.com:user/repo.git
+perry start myproject --clone https://github.com/user/repo.git
+```
+
+| Option | Description |
+|--------|-------------|
+| `--clone <url>` | Git repository URL to clone |
+
+### `perry stop <name>`
+
+Stop a running workspace.
+
+```bash
+perry stop myproject
+```
+
+### `perry delete <name>`
+
+Delete a workspace and its data.
+
+```bash
+perry delete myproject
+perry rm myproject  # alias
+```
+
+### `perry list`
+
+List all workspaces.
 
 ```bash
-perry start <name> [--clone URL]  # Start (creates if doesn't exist)
-perry stop <name>
-perry delete <name>
 perry list
-perry logs <name>
-perry sync <name>
+perry ls  # alias
 ```
 
-## Build
+Output shows:
+- Status indicator (running/stopped)
+- Workspace name
+- SSH port
+- Repository (if cloned)
+- Creation date
+
+### `perry info [name]`
+
+Show workspace or agent info.
 
 ```bash
-perry build [--no-cache]
+perry info            # Agent info
+perry info myproject  # Workspace info
 ```
 
-## Configuration
+### `perry logs <name>`
+
+Show workspace container logs.
+
+```bash
+perry logs myproject
+perry logs myproject -n 50  # Last 50 lines
+```
+
+| Option | Description |
+|--------|-------------|
+| `-n, --tail <lines>` | Number of lines to show (default: 100) |
+
+### `perry shell <name>`
+
+Open interactive terminal to workspace.
+
+```bash
+perry shell myproject
+```
+
+Uses direct Docker exec for local agents, WebSocket for remote agents.
+
+### `perry sync <name>`
+
+Re-sync credentials and files to a running workspace.
+
+```bash
+perry sync myproject
+```
+
+Use after updating configuration to apply changes without restarting.
+
+### `perry proxy <name> [ports...]`
+
+Forward ports from workspace to local machine.
+
+```bash
+perry proxy myproject 3000           # Forward port 3000
+perry proxy myproject 8080:3000      # Local 8080 -> remote 3000
+perry proxy myproject 3000 5173      # Multiple ports
+```
+
+## Build Commands
+
+### `perry build`
+
+Build the workspace Docker image locally.
+
+```bash
+perry build
+perry build --no-cache
+```
+
+| Option | Description |
+|--------|-------------|
+| `--no-cache` | Build without Docker cache |
+
+## Configuration Commands
+
+### `perry config show`
+
+Show current configuration.
 
 ```bash
 perry config show
-perry config worker [hostname]
+```
+
+### `perry config worker [hostname]`
+
+Get or set the worker hostname.
+
+```bash
+perry config worker                    # Show current worker
+perry config worker myserver:7391      # Set worker
+perry config worker myserver.ts.net    # Tailscale hostname
+```
+
+### `perry config agent`
+
+Show agent configuration.
+
+```bash
 perry config agent
 ```
+
+## SSH Commands
+
+### `perry ssh list`
+
+List detected SSH keys on host.
+
+```bash
+perry ssh list
+```
+
+### `perry ssh show`
+
+Show current SSH configuration.
+
+```bash
+perry ssh show
+```
+
+### `perry ssh auto-authorize [on|off]`
+
+Toggle auto-authorization of host keys.
+
+```bash
+perry ssh auto-authorize        # Show current setting
+perry ssh auto-authorize on     # Enable
+perry ssh auto-authorize off    # Disable
+```
+
+### `perry ssh copy <key-path>`
+
+Add SSH key to copy list (for git operations).
+
+```bash
+perry ssh copy ~/.ssh/id_ed25519
+perry ssh copy ~/.ssh/id_ed25519 -w myproject  # Specific workspace
+```
+
+| Option | Description |
+|--------|-------------|
+| `-w, --workspace <name>` | Apply to specific workspace only |
+
+### `perry ssh authorize <key-path>`
+
+Add SSH key to authorized_keys list (for SSH access).
+
+```bash
+perry ssh authorize ~/.ssh/id_ed25519.pub
+perry ssh authorize ~/.ssh/id_ed25519.pub -w myproject
+```
+
+| Option | Description |
+|--------|-------------|
+| `-w, --workspace <name>` | Apply to specific workspace only |
+
+### `perry ssh remove <key-path>`
+
+Remove SSH key from configuration.
+
+```bash
+perry ssh remove ~/.ssh/id_ed25519
+perry ssh remove ~/.ssh/id_ed25519 --copy       # Remove from copy list only
+perry ssh remove ~/.ssh/id_ed25519 --authorize  # Remove from authorize list only
+perry ssh remove ~/.ssh/id_ed25519 -w myproject # Specific workspace
+```
+
+| Option | Description |
+|--------|-------------|
+| `-w, --workspace <name>` | Apply to specific workspace only |
+| `--copy` | Remove from copy list only |
+| `--authorize` | Remove from authorize list only |
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `PERRY_CONFIG_DIR` | Override default config directory |
+| `PERRY_PORT` | Override default agent port (7391) |
+| `PERRY_NO_HOST_ACCESS` | Disable host access when set to `true` |
+| `WS_CONFIG_DIR` | Alternative config directory override |