@sudosandwich/limps 3.2.0 → 3.3.1

package/README.md

@@ -50,7 +50,7 @@ cd ~/Documents/my-planning-docs
 limps init
 
 # Start the HTTP daemon
-limps start
+limps server start
 # → Daemon starts on http://127.0.0.1:4269/mcp
 # → PID file written to OS-standard location
 # → Ready for MCP client connections
@@ -62,7 +62,7 @@ limps config print --client claude-code
 
 That's it. Your AI assistant now has access to your documents via HTTP transport. The folder can be anywhere—local, synced, or in a repo; limps does not require a git repository or a `plans/` directory.
 
-**Tip:** `limps status-server` shows the status of the current project if a config is found in the working directory (or passed via `--config`). Run it from a directory where no limps config can be resolved to list all running limps daemons on your system.
+**Tip:** `limps server status` always includes system-wide daemon discovery. If a project config is found (or passed via `--config`), it also reconciles the configured project target against that global list.
 
 ## Features
 
@@ -81,7 +81,7 @@ That's it. Your AI assistant now has access to your documents via HTTP transport
 
 - **Local only** — Your data stays on disk (SQLite index + your files). No cloud, no subscription.
 - **Restart after changes** — If you change the indexed folder or config, restart the MCP server (or rely on the file watcher) so the index and tools reflect the current state.
-- **Daemon management** — The HTTP server runs as a background process. Use `limps start`, `limps stop`, and `limps status-server` to manage the daemon lifecycle. PID files are stored in OS-standard directories for system-wide awareness.
+- **Daemon management** — The HTTP server runs as a background process. Use `limps server start`, `limps server stop`, and `limps server status` to manage the daemon lifecycle. PID files are stored in OS-standard directories for system-wide awareness.
 - **Sandboxed user code** — `process_doc` and `process_docs` run your JavaScript in a QuickJS sandbox with time and memory limits; no network or Node APIs.
 - **One optional network call** — `limps version --check` fetches from the npm registry to compare versions. All other commands (serve, init, list, search, create/update/delete docs, process_doc, etc.) do **not** contact the internet. Omit `version --check` if you want zero external calls.
 
@@ -145,7 +145,7 @@ v3 uses **HTTP transport exclusively**. stdio transport has been removed.
 
 1. **Start the HTTP daemon** for each project:
    ```bash
-   limps start --config /path/to/.limps/config.json
+   limps server start --config /path/to/.limps/config.json
    ```
 
 2. **Update MCP client configs** — Replace stdio configs with HTTP transport:
@@ -173,7 +173,7 @@ v3 removes the centralized project registry. If you previously used `limps confi
 
 **Removed commands:** `config list`, `config use`, `config add`, `config remove`, `config set`, `config discover`, `config migrate`, `config sync-mcp`, `serve`.
 
-**Replaced by:** `limps init` + `limps start` + `limps config print`.
+**Replaced by:** `limps init` + `limps server start` + `limps config print`.
 
 ## Project Setup
 
@@ -199,7 +199,7 @@ If the directory contains a `plans/` subdirectory, limps uses it. Otherwise, it
 Each project has its own `.limps/config.json`. Use `--config` to target a specific project:
 
 ```bash
-limps list-plans --config ~/docs/project-b/.limps/config.json
+limps plan list --config ~/docs/project-b/.limps/config.json
 ```
 
 ## Client Setup
@@ -216,7 +216,7 @@ The output tells you exactly what JSON (or TOML) to add and where the config fil
 
 ### Per-Client Examples
 
-All clients connect to the HTTP daemon. Start the daemon first with `limps start`, then configure your client.
+All clients connect to the HTTP daemon. Start the daemon first with `limps server start`, then configure your client.
 
 <details>
 <summary><b>Cursor</b></summary>
@@ -317,13 +317,13 @@ limps v3 uses **HTTP transport exclusively** via a persistent daemon. This allow
 
 ```bash
 # Start the daemon
-limps start
+limps server start
 
 # Check status (shows uptime, sessions, PID)
-limps status-server
+limps server status
 
 # Stop the daemon
-limps stop
+limps server stop
 ```
 
 The daemon runs at `http://127.0.0.1:4269/mcp` by default. Use `limps config print` to generate the correct MCP client configuration:
@@ -381,7 +381,7 @@ Example custom server config:
 - **Linux**: `$XDG_DATA_HOME/limps/pids/` or `~/.local/share/limps/pids/`
 - **Windows**: `%APPDATA%/limps/pids/`
 
-This enables `limps status-server` to perform system-wide daemon discovery when no project configuration can be resolved; when a limps config is found for the current directory, the CLI runs in project mode and reports status for that project instead.
+This enables `limps server status` to perform system-wide daemon discovery from any directory. When a limps config is found for the current directory (or passed via `--config`), the CLI also reports and reconciles that project's configured target.
 
 - **Remote clients**: Use an MCP-compatible HTTPS proxy for remote clients (e.g., ChatGPT).
 
@@ -418,27 +418,51 @@ Each PID file is named by port number (`limps-{port}.pid`) to enable system-wide
   "port": 4269,
   "host": "127.0.0.1",
   "startedAt": "2026-02-08T12:00:00.000Z",
-  "configPath": "/path/to/project/.limps/config.json"
+  "configPath": "/path/to/project/.limps/config.json",
+  "logPath": "/Users/you/Library/Application Support/limps/logs/limps-4269.log"
 }
 ```
 
-This port-based naming allows `limps status-server` to find all running daemons across different projects without needing a config file.
+This port-based naming allows `limps server status` to find all running daemons across different projects without needing a config file.
+
+Daemon logs are written to OS-standard application log directories:
+
+**macOS:**
+```
+~/Library/Application Support/limps/logs/
+```
+
+**Linux:**
+```
+$XDG_DATA_HOME/limps/logs/
+# or if XDG_DATA_HOME is not set:
+~/.local/share/limps/logs/
+```
+
+**Windows:**
+```
+%APPDATA%/limps/logs/
+```
+
+Daemon logs are intentionally operational-only: limps redacts uncaught exception/rejection payloads and does not persist raw AI prompt/response content.
+Daemon log files are append-only and are not auto-rotated; if you run long-lived daemons, rotate or truncate these files with your system tooling.
 
 ### Starting the Daemon
 
 **Background mode (default):**
 
 ```bash
-limps start
+limps server start
 # → Daemon starts on http://127.0.0.1:4269/mcp
 # → PID file written to OS-standard location
+# → Logs written to OS-standard log file (append mode)
 # → Process detaches and runs in background
 ```
 
 **Foreground mode (debugging):**
 
 ```bash
-limps start --foreground
+limps server start --foreground
 # → Runs in foreground (blocks terminal)
 # → Logs appear in stderr
 # → Useful for debugging startup issues
@@ -461,54 +485,63 @@ Configure `server.port` and `server.host` in your `.limps/config.json`:
 Then start normally:
 
 ```bash
-limps start
+limps server start
 # → Starts using server.port/server.host from config
 # → PID file: limps-8080.pid
 ```
 
 The `start` command performs health verification by polling the `/health` endpoint for up to 5 seconds, issuing repeated HTTP requests. Each individual health-check request has its own shorter timeout (for example, ~1000ms). If any request fails during this window, you'll see one of these error codes:
 
-- **TIMEOUT** — A single health-check HTTP request exceeded its per-request timeout (e.g., ~1000ms). The daemon may be slow to start or system resources may be constrained. Try `limps start --foreground` to see logs.
+- **TIMEOUT** — A single health-check HTTP request exceeded its per-request timeout (e.g., ~1000ms). The daemon may be slow to start or system resources may be constrained. Try `limps server start --foreground` to see logs.
 - **NETWORK_ERROR** — Cannot connect to daemon. Port may be blocked or already in use by another process.
 - **NON_200_STATUS** — Health endpoint returned a non-200 status code. Check daemon logs with foreground mode.
 - **INVALID_RESPONSE** — Health endpoint responded, but the response was invalid or could not be parsed as expected (for example, malformed or missing required fields).
 
 ### Checking Daemon Status
 
-**Project mode (when config is found):**
+**With project config (reconciled with global discovery):**
 
 ```bash
 # From within a project directory with .limps/config.json
-limps status-server
+limps server status
+# Project target:
 # limps server is running
 # PID: 12345 | 127.0.0.1:4269
 # Uptime: 2h 15m
 # Sessions: 3
+# Log: /Users/you/Library/Application Support/limps/logs/limps-4269.log
+# Project target is present in system-wide daemon discovery.
+# System-wide daemons:
+# 127.0.0.1:4269 (PID 12345) [project target]
+#   Uptime: 2h 15m | Sessions: 3
+#   Log: /Users/you/Library/Application Support/limps/logs/limps-4269.log
 
 # Or specify config explicitly
-limps status-server --config /path/to/.limps/config.json
+limps server status --config /path/to/.limps/config.json
 ```
 
-**System-wide discovery (when no config is found):**
+**Without project config (global discovery only):**
 
 ```bash
 # From a directory without a limps config
 cd /tmp
-limps status-server
+limps server status
 # Found 2 running daemons:
 # 127.0.0.1:4269 (PID 12345)
 #   Uptime: 2h 15m | Sessions: 3
+#   Log: /Users/you/Library/Application Support/limps/logs/limps-4269.log
 # 127.0.0.1:8080 (PID 67890)
 #   Uptime: 45m 30s | Sessions: 1
+#   Log: /Users/you/Library/Application Support/limps/logs/limps-8080.log
 ```
 
-When `limps status-server` cannot resolve a config file in the current directory (and no `--config` is provided), it scans the system PID directory and reports all running limps daemons. When a config is found, it shows only that project's daemon status.
+When `limps server status` cannot resolve a config file in the current directory (and no `--config` is provided), it reports global daemon discovery only. When a config is found, it reports both the configured project target and the global daemon list.
 
 ### Stopping the Daemon
 
 ```bash
 # From the project directory (where your .limps config lives):
-limps stop
+limps server stop
 # → Gracefully shuts down daemon
 # → Closes all MCP sessions
 # → Stops file watchers
@@ -516,7 +549,7 @@ limps stop
 # → Process exits
 
 # Or from any directory, by specifying the config explicitly:
-limps stop --config /path/to/.limps/config.json
+limps server stop --config /path/to/.limps/config.json
 ```
 
 The `stop` command is project-specific and resolves the config to determine which daemon to stop. The daemon performs a graceful shutdown by:
@@ -530,13 +563,13 @@ The `stop` command is project-specific and resolves the config to determine whic
 If you try to start a daemon on a port that's already in use, limps will detect the conflict and provide resolution guidance:
 
 ```bash
-limps start
+limps server start
 # Error: Port 4269 is already in use.
 # Process using port: node (PID 12345)
-# Command: /usr/local/bin/node /usr/local/bin/limps start
+# Command: /usr/local/bin/node /usr/local/bin/limps server start
 #
 # To stop the process: kill 12345
-# Or use a different port: limps start --port <port>
+# Or use a different port: limps server start --port <port>
 ```
 
 On systems with `lsof` available (macOS, Linux), limps can identify which process is using the port and show its command line. If `lsof` is not available, you'll see a simpler error message suggesting a different port.
@@ -546,7 +579,7 @@ On systems with `lsof` available (macOS, Linux), limps can identify which proces
 Use foreground mode for debugging, Docker deployments, or CI/CD pipelines:
 
 ```bash
-limps start --foreground
+limps server start --foreground
 ```
 
 **Use cases:**
@@ -597,13 +630,13 @@ You can run multiple limps daemons on different ports for different projects by
 # Project A with default port (4269)
 cd ~/projects/project-a
 # .limps/config.json has server.port: 4269 (or uses default)
-limps start
+limps server start
 # → Running on http://127.0.0.1:4269/mcp
 
 # Project B with custom port (8080)
 cd ~/projects/project-b
 # .limps/config.json has server.port: 8080
-limps start
+limps server start
 # → Running on http://127.0.0.1:8080/mcp
 ```
 
@@ -615,7 +648,7 @@ Discover all running daemons (run from a directory without a limps config):
 
 ```bash
 cd /tmp
-limps status-server
+limps server status
 # Found 2 running daemons:
 # 127.0.0.1:4269 (PID 12345)
 #   Uptime: 2h 15m | Sessions: 3
@@ -627,25 +660,30 @@ Each MCP client can connect to different daemons by configuring different URLs i
 
 ## CLI Commands
 
-### Viewing Plans
+### Recommended Grouped Commands
 
 ```bash
-limps list-plans              # List all plans with status
-limps list-agents <plan>      # List agents in a plan
-limps status <plan>           # Show plan progress summary
-limps next-task <plan>        # Get highest-priority available task
+limps plan list                              # List all plans with status
+limps plan agents <plan>                     # List agents in a plan
+limps plan status <plan>                     # Show plan progress summary
+limps plan next <plan>                       # Get highest-priority available task
+limps plan score --plan <plan> --agent <n>  # Score a single task
+limps plan scores --plan <plan>              # Score all available tasks in a plan
+limps docs list [path]                       # List files/directories
+limps docs search <query>                    # Search indexed docs
+limps docs process [path] --code "<js>"      # Process docs with JavaScript
+limps server start                           # Start HTTP daemon
+limps server status                          # Show daemon status
+limps server stop                            # Stop HTTP daemon
 ```
 
 ### Project Management
 
 ```bash
 limps init [path]             # Initialize new project
-limps start                   # Start HTTP daemon (background by default)
-limps start --foreground      # Start in foreground (debugging mode)
-limps stop                    # Stop HTTP daemon
-limps status-server           # Show daemon status (current project or all daemons)
 limps config show             # Display current config
 limps config print            # Print MCP client config snippets
+limps completion zsh          # Generate Zsh tab-completion script
 ```
 
 ### Health & Automation
@@ -653,9 +691,8 @@ limps config print            # Print MCP client config snippets
 ```bash
 limps health check              # Aggregate all health signals
 limps health staleness [plan]   # Find stale plans/agents
-limps health drift [plan]       # Detect file reference drift
 limps health inference [plan]   # Suggest status updates
-limps proposals list             # List auto-fix proposals
+limps proposals [plan]           # List auto-fix proposals
 limps proposals apply <id>       # Apply a proposal
 limps proposals apply-safe       # Apply all safe proposals
 ```
@@ -677,9 +714,9 @@ limps graph watch                # Watch and update incrementally
 ### Scoring & Repair
 
 ```bash
-limps score-all <plan>           # Score all agents in a plan
-limps score-task <task-id>       # Score a single task
-limps repair-plans [--fix]       # Check/fix agent frontmatter
+limps plan scores --plan <plan>                # Score all agents in a plan
+limps plan score --plan <plan> --agent <n>   # Score a single task
+limps plan repair [--fix]                   # Check/fix agent frontmatter
 ```
 
 ## Configuration
@@ -722,7 +759,7 @@ Config lives at `.limps/config.json` in your project directory, created by `limp
 
 | Variable               | Description                                                | Example                                           |
 | ---------------------- | ---------------------------------------------------------- | ------------------------------------------------- |
-| `MCP_PLANNING_CONFIG`  | Path to config file (overrides default discovery)          | `MCP_PLANNING_CONFIG=./my-config.json limps serve`|
+| `MCP_PLANNING_CONFIG`  | Path to config file (overrides default discovery)          | `MCP_PLANNING_CONFIG=./my-config.json limps server bridge`|
 | `LIMPS_ALLOWED_TOOLS`  | Comma-separated allowlist; only these tools are registered | `LIMPS_ALLOWED_TOOLS="list_docs,search_docs"`     |
 | `LIMPS_DISABLED_TOOLS` | Comma-separated denylist; tools to hide                    | `LIMPS_DISABLED_TOOLS="process_doc,process_docs"` |
 
@@ -737,30 +774,30 @@ Config lives at `.limps/config.json` in your project directory, created by `limp
 If you see this error, another process is using the port:
 
 ```bash
-limps start
+limps server start
 # Error: Port 4269 is already in use.
 # Process using port: node (PID 12345)
 ```
 
 **Resolution:**
 1. **Kill the existing process**: `kill 12345`
-2. **Or use a different port**: `limps start --port 8080`
-3. **Check if it's another limps daemon**: `limps status-server` (if so, use `limps stop` first)
+2. **Or use a different port**: `limps server start --port 8080`
+3. **Check if it's another limps daemon**: `limps server status` (if so, use `limps server stop` first)
 
 **"Daemon may have failed to start" error:**
 
 If the daemon starts but doesn't respond to health checks:
 
 ```bash
-limps start
-# Error: Daemon may have failed to start. Check logs or try: limps start --foreground
+limps server start
+# Error: Daemon may have failed to start. Check logs or try: limps server start --foreground
 ```
 
 **Resolution:**
-1. **Run in foreground to see logs**: `limps start --foreground`
+1. **Check daemon log path**: `limps server status` (or run foreground mode: `limps server start --foreground`)
 2. **Check for permission issues**: Ensure you have write access to the PID directory
 3. **Verify port is accessible**: Try `curl http://127.0.0.1:4269/health`
-4. **Enable debug logging**: `DEBUG=1 limps start --foreground`
+4. **Enable debug logging**: `DEBUG=1 limps server start --foreground`
 
 **Permission issues with PID directory:**
 
@@ -794,7 +831,7 @@ mkdir %APPDATA%\limps\pids
 
 **TIMEOUT error:**
 
-The daemon did not respond within the configured timeout. Each health-check request has its own timeout (for example, 1000ms during the final `limps start` check and 3000ms for `status-server`), and during startup limps will poll for up to about 5 seconds before reporting "Daemon may have failed to start".
+The daemon did not respond within the configured timeout. Each health-check request has its own timeout (for example, 1000ms during the final `limps server start` check and 3000ms for `limps server status`), and during startup limps will poll for up to about 5 seconds before reporting "Daemon may have failed to start".
 
 **Common causes:**
 - System resource constraints (high CPU/memory usage)
@@ -803,8 +840,8 @@ The daemon did not respond within the configured timeout. Each health-check requ
 
 **Resolution:**
 1. Check system resources: `top` or Activity Monitor
-2. Wait a bit longer and retry: `limps status-server`
-3. Run in foreground to see progress: `limps start --foreground`
+2. Wait a bit longer and retry: `limps server status`
+3. Run in foreground to see progress: `limps server start --foreground`
 
 **NETWORK_ERROR:**
 
@@ -816,17 +853,17 @@ Cannot establish connection to the daemon.
 - Incorrect host/port configuration
 
 **Resolution:**
-1. Verify daemon is running: `limps status-server`
+1. Verify daemon is running: `limps server status`
 2. Check firewall settings for port 4269
 3. Try `curl http://127.0.0.1:4269/health` manually
-4. Check daemon logs: `limps start --foreground`
+4. Check daemon logs: see `Log:` path in `limps server status` output
 
 ### Stale PID Files
 
 limps automatically cleans up stale PID files when:
-- Running `limps status-server` (discovers and removes stale files)
-- Running `limps start` (removes stale file for the target port)
-- The daemon shuts down gracefully with `limps stop`
+- Running `limps server status` (discovers and removes stale files)
+- Running `limps server start` (removes stale file for the target port)
+- The daemon shuts down gracefully with `limps server stop`
 
 If you need to manually clean up PID files:
 
@@ -843,7 +880,7 @@ del %APPDATA%\limps\pids\limps-*.pid
 
 **When to manually clean up:**
 - After a system crash or forced shutdown
-- If `limps start` reports a daemon is running but it's not
+- If `limps server start` reports a daemon is running but it's not
 - Before uninstalling limps
 
 ### Multiple Daemons Conflict
@@ -851,16 +888,16 @@ del %APPDATA%\limps\pids\limps-*.pid
 If you accidentally try to start a second daemon on the same port:
 
 ```bash
-limps start
-# Error: limps daemon already running (PID 12345 on 127.0.0.1:4269). Run 'limps stop' first.
+limps server start
+# Error: limps daemon already running (PID 12345 on 127.0.0.1:4269). Run 'limps server stop' first.
 ```
 
 This is expected behavior — limps prevents multiple daemons on the same port using PID-based locking.
 
 **Resolution:**
-1. **Check all running daemons**: `limps status-server`
-2. **Stop the existing daemon**: `limps stop`
-3. **Or start on a different port**: `limps start --port 8080`
+1. **Check all running daemons**: `limps server status`
+2. **Stop the existing daemon**: `limps server stop`
+3. **Or start on a different port**: `limps server start --port 8080`
 
 ### Debugging Connection Issues
 
@@ -869,7 +906,7 @@ If MCP clients can't connect to the daemon, verify connectivity step by step:
 **1. Check daemon status:**
 
 ```bash
-limps status-server
+limps server status
 # Should show daemon running with healthy status
 ```
 
@@ -892,7 +929,7 @@ curl -X POST http://127.0.0.1:4269/mcp \
 **4. Enable debug logging:**
 
 ```bash
-DEBUG=1 limps start --foreground
+DEBUG=1 limps server start --foreground
 # Watch for connection attempts and errors
 ```
 
@@ -913,6 +950,64 @@ Ensure the URL in your client config matches the daemon:
 }
 ```
 
+### Config Resolution Issues
+
+**Problem: limps is using the wrong config file**
+
+If `limps config path` shows a different config than expected, use the diagnostic command to understand why:
+
+```bash
+limps config show-resolution
+```
+
+This shows all three priority levels for config resolution:
+
+1. **CLI `--config` argument** (highest priority)
+2. **`MCP_PLANNING_CONFIG` environment variable** (second priority)
+3. **Local `.limps/config.json`** (searches up from cwd)
+
+**Common causes:**
+
+- **Environment variable set**: Check if `MCP_PLANNING_CONFIG` is set in your shell or IDE. This takes priority over local config files.
+  ```bash
+  # Check if set
+  echo $MCP_PLANNING_CONFIG
+  
+  # Unset if needed
+  unset MCP_PLANNING_CONFIG
+  ```
+
+- **Wrong working directory**: Config search starts from your current working directory. Make sure you're in the right directory when running limps commands.
+  ```bash
+  # Check current directory
+  pwd
+  
+  # Navigate to your project
+  cd /path/to/your/project
+  ```
+
+- **Missing `.limps/config.json`**: The config file must be in a `.limps` subdirectory, not at the project root.
+  ```bash
+  # Correct location
+  /path/to/project/.limps/config.json
+  
+  # Wrong - won't be found
+  /path/to/project/config.json
+  ```
+
+**Quick fixes:**
+
+```bash
+# Override with explicit path
+limps plan list --config /path/to/project/.limps/config.json
+
+# Or set environment variable
+export MCP_PLANNING_CONFIG=/path/to/project/.limps/config.json
+
+# Or initialize a new config in current directory
+limps init
+```
+
 ## MCP Tools
 
 limps exposes MCP tools for AI assistants:

package/dist/agent-parser.d.ts

@@ -69,7 +69,7 @@ export declare function extractAgentNumber(filename: string): string | null;
  * Extract plan folder from agent file path.
  *
  * @example
- * extractPlanFolder("/path/to/plans/0022-datagrid-stories/agents/000_agent.agent.md")
+ * extractPlanFolder("/path/to/0022-datagrid-stories/agents/000_agent.agent.md")
  * // "0022-datagrid-stories"
  *
  * @param path - Full path to agent file

package/dist/agent-parser.d.ts.map

@@ -1 +1 @@
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package/dist/agent-parser.js

@@ -63,16 +63,20 @@ export function extractAgentNumber(filename) {
  * Extract plan folder from agent file path.
  *
  * @example
- * extractPlanFolder("/path/to/plans/0022-datagrid-stories/agents/000_agent.agent.md")
+ * extractPlanFolder("/path/to/0022-datagrid-stories/agents/000_agent.agent.md")
  * // "0022-datagrid-stories"
  *
  * @param path - Full path to agent file
  * @returns Plan folder name or null if not found
  */
 export function extractPlanFolder(path) {
-    // Match plans/<folder>/agents/
-    const match = path.match(/plans[/\\]([^/\\]+)[/\\]agents[/\\]/);
-    return match ? match[1] : null;
+    // Plan folder is the path segment directly before "agents"
+    const segments = path.split(/[/\\]+/).filter(Boolean);
+    const agentsIndex = segments.lastIndexOf('agents');
+    if (agentsIndex <= 0) {
+        return null;
+    }
+    return segments[agentsIndex - 1] || null;
 }
 /**
  * Build task ID from plan folder and agent number.

package/dist/agent-parser.js.map

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package/dist/cli/config-cmd.js

@@ -406,7 +406,7 @@ export function generateChatGptInstructions(configPath) {
     lines.push(`  Server Name: ${serverName}`);
     lines.push('  Server URL: https://your-tunnel-domain.example/mcp');
     lines.push('  Authentication: (required by your proxy/deployment)');
-    lines.push(`  Local command: limps start --config ${configPath}`);
+    lines.push(`  Local command: limps server start --config ${configPath}`);
     lines.push('');
     lines.push('Tip: create one connector per project config.');
     return lines.join('\n');