Add --diagnose flag, remove obsolete helper scripts, fix docs

- Add --diagnose option that shows all PCI paths, storage controllers,
  block devices, and validates current mappings. Replaces the separate
  diagnose-drives.sh script.
- Remove diagnose-drives.sh (incorporated into --diagnose).
- Remove get-serials.sh (redundant with SMART data in main table).
- Remove test-paths.sh (referenced non-existent 0c:00.0 controller).
- Remove todo.md (massively outdated).
- Fix storage controller text overflowing box borders in large1 and
  micro layouts by adding truncation (%-69.69s, %-57.57s).
- Fix chassis name to CX4712 in README.
- Update server mapping statuses from "Requires mapping" to actual
  partially-mapped states.
- Add ⚠ health indicator to README output column docs.
- Update Claude.md metrics to match current state.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Claude.md

@@ -159,9 +159,9 @@ The project began with:
 
 ## Metrics
 
-- **Lines of Code:** ~330 (main script)
+- **Lines of Code:** ~1178 (main script)
-- **Supported Chassis Types:** 4 (10-bay, large1, micro, spare)
+- **Supported Chassis Types:** 3 (10bay, large1, micro)
-- **Mapped Servers:** 1 fully (compute-storage-01), 3 pending
+- **Mapped Servers:** 1 fully (compute-storage-01), 3 partially (storage-01, large1, compute-storage-gpu-01), 2 stubs (micro1, monitor-02)
 - **Features Added:** 10+
 - **Bugs Fixed:** 6 major, multiple minor
 - **Documentation:** Comprehensive README + this file
@@ -206,4 +206,4 @@ The result is a robust infrastructure management tool that provides instant visi
 - **Human Developer:** LotusGuild
 - **AI Assistant:** Claude Sonnet 4.5 (Anthropic)
 - **Development Date:** January 6, 2026
-- **Project:** Drive Atlas v1.0
+- **Project:** Drive Atlas v1.1.0

README.md

@@ -41,14 +41,14 @@ bash <(wget -qO- http://10.10.10.63:3000/LotusGuild/driveAtlas/raw/branch/main/d
 
 | Chassis Type | Description | Servers Using It |
 |-------------|-------------|------------------|
-| **10-Bay Hot-swap** | Sliger CX471225 4U 10x 3.5" NAS (with unused 2x 5.25" bays) | compute-storage-01, compute-storage-gpu-01, storage-01 |
+| **10-Bay Hot-swap** | Sliger CX4712 4U 10x 3.5" NAS (with unused 2x 5.25" bays) | compute-storage-01, compute-storage-gpu-01, storage-01 |
 | **Large1 Grid** | Unique 3x5 grid layout (1/1 configuration) | large1 |
 | **Micro** | Compact 2-drive layout | micro1, monitor-02 |
 
 ### Server Details
 
 #### compute-storage-01 (formerly medium2)
-- **Chassis:** Sliger CX471225 4U (10-Bay Hot-swap)
+- **Chassis:** Sliger CX4712 4U (10-Bay Hot-swap)
 - **Motherboard:** B650D4U3-2Q/BCM
 - **Controllers:**
   - 01:00.0 - LSI SAS3008 HBA (bays 5-10 via 2x mini-SAS HD)
@@ -57,20 +57,20 @@ bash <(wget -qO- http://10.10.10.63:3000/LotusGuild/driveAtlas/raw/branch/main/d
 - **Status:** ✅ Fully mapped and verified
 
 #### storage-01
-- **Chassis:** Sliger CX471225 4U (10-Bay Hot-swap)
+- **Chassis:** Sliger CX4712 4U (10-Bay Hot-swap)
-- **Motherboard:** Different from compute-storage-01
+- **Motherboard:** ASRock A320M-HDV R4.0
-- **Controllers:** Motherboard SATA only (no HBA currently)
+- **Controllers:** AMD SATA (bays 1-4), LSI SAS3416 HBA (bays 5+, U.2 NVMe)
-- **Status:** ⚠️ Requires PCI path mapping
+- **Status:** ⚠️ Partially mapped (5 of 10 bays)
 
 #### large1
 - **Chassis:** Unique 3x5 grid (15 bays total)
 - **Note:** 1/1 configuration, will not be replicated
-- **Status:** ⚠️ Requires PCI path mapping
+- **Status:** ⚠️ Partially mapped (14 bays + 2 M.2)
 
 #### compute-storage-gpu-01
-- **Chassis:** Sliger CX471225 4U (10-Bay Hot-swap)
+- **Chassis:** Sliger CX4712 4U (10-Bay Hot-swap)
-- **Motherboard:** Same as compute-storage-01
+- **Motherboard:** ASUS PRIME B550-PLUS
-- **Status:** ⚠️ Requires PCI path mapping
+- **Status:** ⚠️ Partially mapped (5 SATA + 1 M.2)
 
 ## Output Example
 
@@ -130,15 +130,15 @@ declare -A SERVER_MAPPINGS=(
 
 ## Setting Up a New Server
 
-### Step 1: Run Diagnostic Script
+### Step 1: Run Diagnostic Mode
 
 First, gather PCI path information:
 
 ```bash
-bash diagnose-drives.sh > server-diagnostic.txt
+bash driveAtlas.sh --diagnose
 ```
 
-This will show all available PCI paths and their associated drives.
+This will show all available PCI paths, storage controllers, and their associated drives.
 
 ### Step 2: Physical Bay Identification
 
@@ -192,7 +192,7 @@ DEBUG=1 bash driveAtlas.sh
 | **SIZE** | Drive capacity |
 | **TYPE** | SSD or HDD (detected via SMART) |
 | **TEMP** | Current temperature from SMART |
-| **HEALTH** | SMART health status (✓ = passed, ✗ = failed) |
+| **HEALTH** | SMART health status (✓ = passed, ⚠ = passed with warnings, ✗ = failed) |
 | **MODEL** | Drive model number |
 | **SERIAL** | Drive serial number (for physical verification) |
 | **CEPH OSD** | Ceph OSD ID if drive hosts an OSD |
@@ -235,17 +235,15 @@ DEBUG=1 bash driveAtlas.sh
 
 ## Files
 
-- [driveAtlas.sh](driveAtlas.sh) - Main script
+- [driveAtlas.sh](driveAtlas.sh) - Main script (includes `--diagnose` mode for PCI path discovery)
-- [diagnose-drives.sh](diagnose-drives.sh) - PCI path diagnostic tool
 - [README.md](README.md) - This file
 - [CLAUDE.md](CLAUDE.md) - AI-assisted development notes
-- [todo.txt](todo.txt) - Development notes and task tracking
 
 ## Contributing
 
 When adding support for a new server:
 
-1. Run `diagnose-drives.sh` and save output
+1. Run `driveAtlas.sh --diagnose` and save output
 2. Physically label or identify drives by serial number
 3. Create mapping in `SERVER_MAPPINGS`
 4. Test thoroughly

diagnose-drives.sh

@@ -1,59 +0,0 @@
-#!/bin/bash
-
-# Drive Atlas Diagnostic Script
-# Run this on each server to gather PCI path information
-
-echo "=== Server Information ==="
-echo "Hostname: $(hostname)"
-echo "Date: $(date)"
-echo ""
-
-echo "=== All /dev/disk/by-path/ entries ==="
-ls -la /dev/disk/by-path/ | grep -v "part" | sort
-echo ""
-
-echo "=== Organized by PCI Address ==="
-for path in /dev/disk/by-path/*; do
-    if [ -L "$path" ]; then
-        # Skip partitions
-        if [[ "$path" =~ -part[0-9]+$ ]]; then
-            continue
-        fi
-
-        basename_path=$(basename "$path")
-        target=$(readlink -f "$path")
-        device=$(basename "$target")
-
-        echo "Path: $basename_path"
-        echo "  -> Device: $device"
-
-        # Try to get size
-        if [ -b "$target" ]; then
-            size=$(lsblk -d -n -o SIZE "$target" 2>/dev/null)
-            echo "  -> Size: $size"
-        fi
-
-        # Try to get SMART info for model
-        if command -v smartctl >/dev/null 2>&1; then
-            model=$(sudo smartctl -i "$target" 2>/dev/null | grep "Device Model\|Model Number" | cut -d: -f2 | xargs)
-            if [ -n "$model" ]; then
-                echo "  -> Model: $model"
-            fi
-        fi
-        echo ""
-    fi
-done
-
-echo "=== PCI Devices with Storage Controllers ==="
-lspci | grep -i "storage\|raid\|sata\|sas\|nvme"
-echo ""
-
-echo "=== Current Block Devices ==="
-lsblk -d -o NAME,SIZE,TYPE,TRAN | grep -v "rbd\|loop"
-echo ""
-
-echo "=== Recommendations ==="
-echo "1. Note the PCI addresses (e.g., 0c:00.0) of your storage controllers"
-echo "2. For each bay, physically identify which drive is in it"
-echo "3. Match the PCI path pattern to the bay number"
-echo "4. Example: pci-0000:0c:00.0-ata-1 might be bay 1 on controller 0c:00.0"

get-serials.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-echo "=== Drive Serial Numbers ==="
-for dev in sd{a..j}; do
-    if [ -b "/dev/$dev" ]; then
-        serial=$(sudo smartctl -i /dev/$dev 2>/dev/null | grep "Serial Number" | awk '{print $3}')
-        model=$(sudo smartctl -i /dev/$dev 2>/dev/null | grep "Device Model\|Model Number" | cut -d: -f2 | xargs)
-        size=$(lsblk -d -n -o SIZE /dev/$dev 2>/dev/null)
-        echo "/dev/$dev: $serial ($size - $model)"
-    fi
-done

test-paths.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-echo "=== Checking /dev/disk/by-path/ ==="
-ls -la /dev/disk/by-path/ | grep -v "part" | grep "pci-0000:0c:00.0" | head -20
-echo ""
-echo "=== Checking if paths exist from mapping ==="
-echo "pci-0000:0c:00.0-ata-3:"
-ls -la /dev/disk/by-path/pci-0000:0c:00.0-ata-3 2>&1
-
-echo "pci-0000:0c:00.0-ata-1:"
-ls -la /dev/disk/by-path/pci-0000:0c:00.0-ata-1 2>&1