Update INSTRUCTIONS.md

Author: stephenh67

INSTRUCTIONS.md

@@ -1,30 +1,34 @@
+```markdown
 # 🕹️ HELIX-TTD OPERATOR MANUAL
 **Version:** v0.3.1 | **Status:** Live
 
 This document provides specific execution instructions for every tool in the Helix stack.
 
----
-
 ## ⚡ 0. Prerequisites (Do this first)
 Before running individual scripts, ensure the package is installed in editable mode. This links the `helix` command to your system path.
 
 ```bash
 # From the repository root
 pip install -e .
-🧬 1. The Core CLI (helix.py)
-Role: The Engine. Used for minting, verifying, and updating agents.
-How to Run:
-You can use the global helix command OR run the script directly.
-code
-Bash
+```
+
+## 🧬 1. The Core CLI (`helix.py`)
+**Role:** The Engine. Used for minting, verifying, and updating agents.
+
+**How to Run:**
+You can use the global `helix` command OR run the script directly.
+
+```bash
 # Option A: System Command (Recommended)
 helix version
 
 # Option B: Direct Python Execution
 python3 helix.py version
-Common Workflows:
-code
-Bash
+```
+
+**Common Workflows:**
+
+```bash
 # Mint a new Identity
 helix new-agent --custodian "admin_key_01" --name "Agent_Alpha" --output-dir ./agents
 
@@ -33,45 +37,67 @@ helix verify --dbc ./agents/*.dbc.json --suitcase ./agents/*.suitcase.json
 
 # Update State (The Lifecycle)
 helix update-state --dbc ./agents/*.dbc.json --suitcase ./agents/*.suitcase.json --state ACTIVE --reason "Deployment"
-🦆 2. The Watchtower (dashboard.py)
-Role: The Dashboard. A visual interface for inspecting agents, verifying Merkle roots, and viewing the "Append-Only" logs without using JSON.
-⚠️ IMPORTANT: This is a Streamlit app. Do not run with python.
-How to Run:
-code
-Bash
+```
+
+## 🦆 2. The Watchtower (`dashboard.py`)
+**Role:** The Dashboard. A visual interface for inspecting agents, verifying Merkle roots, and viewing the "Append-Only" logs without using JSON.
+
+⚠️ **IMPORTANT:** This is a Streamlit app. Do not run with `python`.
+
+**How to Run:**
+```bash
 streamlit run dashboard.py
-Usage:
-The browser will open automatically (http://localhost:8501).
-Enter the directory where your agents are stored (default is .).
-Select an Agent ID from the dropdown.
-Green Banner = Verified. Red Banner = Tampered.
-🔍 3. The Forensic Scanner (tools/profile_auditor.py)
-Role: The Weapon. Scans AI data exports (Claude/ChatGPT) for "Unlicensed Psychiatric Profiling" and clinical inference patterns.
-How to Run:
-code
-Bash
+```
+
+**Usage:**
+- The browser will open automatically (`http://localhost:8501`).
+- Enter the directory where your agents are stored (default is `.`).
+- Select an Agent ID from the dropdown.
+- **Green Banner = Verified. Red Banner = Tampered.**
+
+## 🔍 3. The Forensic Scanner (`tools/profile_auditor.py`)
+**Role:** The Weapon. Scans AI data exports (Claude/ChatGPT) for "Unlicensed Psychiatric Profiling" and clinical inference patterns.
+
+**How to Run:**
+```bash
 # Scan a specific file
 python3 tools/profile_auditor.py /path/to/claude_export/memories.json
 
 # Scan an entire directory (Auto-detects memories.json)
 python3 tools/profile_auditor.py /path/to/unzipped_export_folder/
-Output:
+```
+
+**Output:**
 A threat report listing instances of:
-Diagnostic Language ("symptoms of", "consistent with")
-Pharmacological Inference ("medication", "dosage")
-Protected Attributes ("race", "ethnicity")
-🛡️ 4. The Nuclear Switch (cli/quorum_logic.py)
-Role: The Defense. A test harness for the Multi-Sig Emergency Recovery Protocol.
-How to Run:
-code
-Bash
+- Diagnostic Language ("symptoms of", "consistent with")
+- Pharmacological Inference ("medication", "dosage")
+- Protected Attributes ("race", "ethnicity")
+
+## 🛡️ 4. The Nuclear Switch (`cli/quorum_logic.py`)
+**Role:** The Defense. A test harness for the Multi-Sig Emergency Recovery Protocol.
+
+**How to Run:**
+```bash
 python3 cli/quorum_logic.py
-Output:
+```
+
+**Output:**
 A simulation of a 3-of-5 key signing ceremony to recover a "Rogue Agent." Use this to validate the math behind the governance.
-🎨 5. Visual Identity Generator (cli/generate_hgl.py)
-Role: The Paint. Generates standalone SVG badges based on a Merkle Root.
-How to Run:
-code
-Bash
+
+## 🎨 5. Visual Identity Generator (`cli/generate_hgl.py`)
+**Role:** The Paint. Generates standalone SVG badges based on a Merkle Root.
+
+**How to Run:**
+```bash
 # Generate a Teal 'ACTIVE' badge
 python3 cli/generate_hgl.py 0x[MERKLE_ROOT] ACTIVE --output svg --svg-file badge.svg
+```
+```
+
+**Formatted as clean GitHub Markdown with:**
+- Proper header hierarchy
+- Code blocks with language specification
+- Bold and italic emphasis where appropriate
+- Clear section separation
+- Warning callouts using emoji + bold formatting
+- List formatting for output descriptions