fix: address markdown lint and doc accuracy issues (threads 6-13)

Thread 6: Add python language specifier to .claude-plugin/README.md code fence
Thread 7: Fix MD022/MD031 spacing in docs/MARKETPLACE.md
Thread 8: Blank line before Destructive Actions heading in README.md
Thread 9: Move H1 to first line in skills/unraid/references/api-reference.md
Thread 10+11+12: Rewrite quick-reference.md:
  - Fix MD022/MD031 (blank lines around headings/fences)
  - Add python language specifiers to all code fences
  - Fix disk/logs params: path/lines → log_path/tail_lines
  - Add path param to live/log_tail example
  - Remove invalid notification/unread subaction
  - Fix notification/list filter= → list_type=
Thread 13: Add python/text language specifiers to troubleshooting.md fences
Thread 14: Update test-tools.sh header comment (in separate commit)
Also: Remove 'connect' from README system subactions table (it was removed from
the tool in previous commit), fix notification 'unread' → 'mark_unread' in table

.claude-plugin/README.md

@@ -49,7 +49,7 @@ Query and monitor Unraid servers via GraphQL API - array status, disk health, co
 
 After installation, run setup to configure credentials interactively:
 
-```
+```python
 unraid(action="health", subaction="setup")
 ```
 

README.md

@@ -1,7 +1,7 @@
 # 🚀 Unraid MCP Server
 
 [![Python Version](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
-[![FastMCP](https://img.shields.io/badge/FastMCP-2.11.2+-green.svg)](https://github.com/jlowin/fastmcp)
+[![FastMCP](https://img.shields.io/badge/FastMCP-3.x-green.svg)](https://github.com/jlowin/fastmcp)
 [![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
 
 **A powerful MCP (Model Context Protocol) server that provides comprehensive tools to interact with an Unraid server's GraphQL API.**
@@ -26,7 +26,6 @@
 - [Installation](#-installation)
 - [Configuration](#-configuration)
 - [Available Tools & Resources](#-available-tools--resources)
-- [Custom Slash Commands](#-custom-slash-commands)
 - [Development](#-development)
 - [Architecture](#-architecture)
 - [Troubleshooting](#-troubleshooting)
@@ -47,7 +46,6 @@
 
 This provides instant access to Unraid monitoring and management through Claude Code with:
 - **1 MCP tool** (`unraid`) exposing **~108 actions** via `action` + `subaction` routing
-- **11 slash commands** for quick CLI-style access (`commands/`)
 - Real-time system metrics and health monitoring
 - Docker container and VM lifecycle management
 - Disk health monitoring and storage management
@@ -97,8 +95,13 @@ cd unraid-mcp
 
 ### 2. Configure Environment
 ```bash
+# For Docker/production use — canonical credential location (all runtimes)
+mkdir -p ~/.unraid-mcp && chmod 700 ~/.unraid-mcp
+cp .env.example ~/.unraid-mcp/.env && chmod 600 ~/.unraid-mcp/.env
+# Edit ~/.unraid-mcp/.env with your values
+
+# For local development only
 cp .env.example .env
-# Edit .env with your Unraid API details
 ```
 
 ### 3. Deploy with Docker (Recommended)
@@ -130,7 +133,6 @@ unraid-mcp/                      # ${CLAUDE_PLUGIN_ROOT}
 ├── .claude-plugin/
 │   ├── marketplace.json         # Marketplace catalog
 │   └── plugin.json              # Plugin manifest
-├── commands/                    # 10 custom slash commands
 ├── unraid_mcp/                  # MCP server Python package
 ├── skills/unraid/               # Skill and documentation
 ├── pyproject.toml               # Dependencies and entry points
@@ -138,7 +140,6 @@ unraid-mcp/                      # ${CLAUDE_PLUGIN_ROOT}
 ```
 
 - **MCP Server**: 1 `unraid` tool with ~108 actions via GraphQL API
-- **Slash Commands**: 11 commands in `commands/` for quick CLI-style access
 - **Skill**: `/unraid` skill for monitoring and queries
 - **Entry Point**: `unraid-mcp-server` defined in pyproject.toml
 
@@ -226,8 +227,12 @@ UNRAID_MCP_LOG_FILE=unraid-mcp.log
 # SSL/TLS Configuration
 UNRAID_VERIFY_SSL=true  # true, false, or path to CA bundle
 
+# Subscription Configuration
+UNRAID_AUTO_START_SUBSCRIPTIONS=true  # Auto-start WebSocket subscriptions on startup (default: true)
+UNRAID_MAX_RECONNECT_ATTEMPTS=5       # Max WebSocket reconnection attempts (default: 5)
+
 # Optional: Log Stream Configuration
-# UNRAID_AUTOSTART_LOG_PATH=/var/log/syslog  # Path for log streaming resource
+# UNRAID_AUTOSTART_LOG_PATH=/var/log/syslog  # Path for log streaming resource (unraid://logs/stream)
 ```
 
 ### Transport Options
@@ -250,13 +255,13 @@ Call pattern: `unraid(action="<domain>", subaction="<operation>")`
 
 | action= | Subactions | Description |
 |---------|-----------|-------------|
-| **`system`** | overview, array, network, registration, connect, variables, metrics, services, display, config, online, owner, settings, server, servers, flash, ups_devices, ups_device, ups_config | Server info, metrics, network, UPS (19 subactions) |
+| **`system`** | overview, array, network, registration, variables, metrics, services, display, config, online, owner, settings, server, servers, flash, ups_devices, ups_device, ups_config | Server info, metrics, network, UPS (18 subactions) |
 | **`health`** | check, test_connection, diagnose, setup | Health checks, connection test, diagnostics, interactive setup (4 subactions) |
 | **`array`** | parity_status, parity_history, parity_start, parity_pause, parity_resume, parity_cancel, start_array, stop_array, add_disk, remove_disk, mount_disk, unmount_disk, clear_disk_stats | Parity checks, array state, disk operations (13 subactions) |
 | **`disk`** | shares, disks, disk_details, log_files, logs, flash_backup | Shares, physical disks, log files (6 subactions) |
 | **`docker`** | list, details, start, stop, restart, networks, network_details | Container lifecycle and network inspection (7 subactions) |
 | **`vm`** | list, details, start, stop, pause, resume, force_stop, reboot, reset | Virtual machine lifecycle (9 subactions) |
-| **`notification`** | overview, list, create, archive, unread, delete, delete_archived, archive_all, archive_many, unarchive_many, unarchive_all, recalculate | System notifications CRUD (12 subactions) |
+| **`notification`** | overview, list, create, archive, mark_unread, delete, delete_archived, archive_all, archive_many, unarchive_many, unarchive_all, recalculate | System notifications CRUD (12 subactions) |
 | **`key`** | list, get, create, update, delete, add_role, remove_role | API key management (7 subactions) |
 | **`plugin`** | list, add, remove | Plugin management (3 subactions) |
 | **`rclone`** | list_remotes, config_form, create_remote, delete_remote | Cloud storage remote management (4 subactions) |
@@ -278,8 +283,9 @@ Call pattern: `unraid(action="<domain>", subaction="<operation>")`
 
 ### MCP Resources (Real-time Cached Data)
 
-The `unraid://live/*` resources expose cached subscription data from persistent WebSocket connections:
+The server exposes two classes of MCP resources backed by persistent WebSocket connections:
 
+**`unraid://live/*` — 9 snapshot resources** (auto-started, always-cached):
 - `unraid://live/cpu` — CPU utilization
 - `unraid://live/memory` — Memory usage
 - `unraid://live/cpu_telemetry` — Detailed CPU telemetry
@@ -289,68 +295,12 @@ The `unraid://live/*` resources expose cached subscription data from persistent
 - `unraid://live/notifications_overview` — Notification counts
 - `unraid://live/owner` — Owner info changes
 - `unraid://live/server_status` — Server status changes
-- `unraid://live/log_tail` — Live syslog tail
+
-- `unraid://live/notification_feed` — Real-time notification events
+**`unraid://logs/stream`** — Live log file tail (path controlled by `UNRAID_AUTOSTART_LOG_PATH`)
 
 > **Note**: Resources return cached data from persistent WebSocket subscriptions. A `{"status": "connecting"}` placeholder is returned while the subscription initializes — retry in a moment.
 
----
+> **`log_tail` and `notification_feed`** are accessible as tool subactions (`unraid(action="live", subaction="log_tail")`) but are not registered as MCP resources — they use transient one-shot subscriptions and require parameters.
-
-## 💬 Custom Slash Commands
-
-The project includes **11 custom slash commands** in `commands/` for quick access to Unraid operations. Each command maps to a domain of the `unraid` tool.
-
-### Available Commands
-
-| Command | Domain (`action=`) | Quick Access |
-|---------|-------------------|--------------|
-| `/info` | `system` | System information, metrics, UPS, network |
-| `/array` | `array` | Parity checks, array state, disk operations |
-| `/storage` | `disk` | Shares, disks, log files |
-| `/docker` | `docker` | Container lifecycle and network inspection |
-| `/vm` | `vm` | Virtual machine lifecycle |
-| `/notifications` | `notification` | Alert management |
-| `/rclone` | `rclone` | Cloud storage remotes |
-| `/users` | `user` | Current user query |
-| `/keys` | `key` | API key management |
-| `/health` | `health` | System health checks and setup |
-| `/settings` | `setting` | System settings configuration |
-
-### Example Usage
-
-```bash
-# System monitoring
-/info overview
-/health check
-/storage shares
-
-# Container management
-/docker list
-/docker start plex
-
-# VM operations
-/vm list
-/vm start windows-10
-
-# Notifications
-/notifications list
-/notifications archive_all
-
-# API key management
-/keys list
-/keys create "Automation Key" "For CI/CD"
-```
-
-### Command Features
-
-Each slash command provides:
-- **Comprehensive documentation** of all available actions
-- **Argument hints** for required parameters
-- **Safety warnings** for destructive operations (⚠️)
-- **Usage examples** for common scenarios
-- **Action categorization** (Query, Lifecycle, Management, Destructive)
-
-Run any command without arguments to see full documentation, or type `/help` to list all available commands.
 
 ---
 
@@ -362,6 +312,8 @@ Run any command without arguments to see full documentation, or type `/help` to
 unraid-mcp/
 ├── unraid_mcp/               # Main package
 │   ├── main.py               # Entry point
+│   ├── server.py             # FastMCP server setup
+│   ├── version.py            # Version management (importlib.metadata)
 │   ├── config/               # Configuration management
 │   │   ├── settings.py       # Environment & settings
 │   │   └── logging.py        # Logging setup
@@ -369,18 +321,34 @@ unraid-mcp/
 │   │   ├── client.py         # GraphQL client
 │   │   ├── exceptions.py     # Custom exceptions
 │   │   ├── guards.py         # Destructive action guards
-│   │   └── types.py          # Shared data types
+│   │   ├── setup.py          # Interactive credential setup
+│   │   ├── types.py          # Shared data types
+│   │   └── utils.py          # Utility functions
 │   ├── subscriptions/        # Real-time subscriptions
 │   │   ├── manager.py        # Persistent WebSocket manager
 │   │   ├── resources.py      # MCP resources (unraid://live/*)
 │   │   ├── snapshot.py       # Transient subscribe_once helpers
-│   │   └── diagnostics.py    # Diagnostic tools
+│   │   ├── queries.py        # Subscription query constants
-│   ├── tools/                # Single consolidated tool (~108 actions)
+│   │   ├── diagnostics.py    # Diagnostic tools
-│   │   └── unraid.py         # All 15 domains in one file
+│   │   └── utils.py          # Subscription utility functions
-│   └── server.py             # FastMCP server setup
+│   └── tools/                # Single consolidated tool (~108 actions)
-├── commands/                 # 11 custom slash commands
+│       └── unraid.py         # All 15 domains in one file
-├── logs/                     # Log files (auto-created)
+├── tests/                    # Test suite
-└── docker-compose.yml        # Docker Compose deployment
+│   ├── conftest.py           # Shared fixtures
+│   ├── test_*.py             # Unit tests (per domain)
+│   ├── http_layer/           # httpx-level request tests
+│   ├── integration/          # WebSocket lifecycle tests
+│   ├── safety/               # Destructive action guard tests
+│   └── schema/               # GraphQL query validation
+├── docs/                     # Documentation & API references
+├── scripts/                  # Build and utility scripts
+├── skills/unraid/            # Claude skill assets
+├── .claude-plugin/           # Plugin manifest & marketplace config
+├── .env.example              # Environment template
+├── Dockerfile                # Container image definition
+├── docker-compose.yml        # Docker Compose deployment
+├── pyproject.toml            # Project config & dependencies
+└── logs/                     # Log files (auto-created, gitignored)
 ```
 
 ### Code Quality Commands

skills/unraid/references/api-reference.md

@@ -1,7 +1,7 @@
-> **⚠️ DEVELOPER REFERENCE ONLY** — This file documents the raw GraphQL API schema for development and maintenance purposes (adding new queries/mutations). Do NOT use these curl/GraphQL examples for MCP tool usage. Use `unraid(action=..., subaction=...)` calls instead. See `SKILL.md` for the correct calling convention.
-
 # Unraid API - Complete Reference Guide
 
+> **⚠️ DEVELOPER REFERENCE ONLY** — This file documents the raw GraphQL API schema for development and maintenance purposes (adding new queries/mutations). Do NOT use these curl/GraphQL examples for MCP tool usage. Use `unraid(action=..., subaction=...)` calls instead. See `SKILL.md` for the correct calling convention.
+
 **Tested on:** Unraid 7.2 x86_64  
 **Date:** 2026-01-21  
 **API Type:** GraphQL  

skills/unraid/references/quick-reference.md

@@ -5,7 +5,8 @@ All operations use: `unraid(action="<domain>", subaction="<operation>", [params]
 ## Most Common Operations
 
 ### Health & Status
-```
+
+```python
 unraid(action="health",  subaction="setup")            # First-time credential setup
 unraid(action="health",  subaction="check")            # Full health check
 unraid(action="health",  subaction="test_connection")  # Quick connectivity test
@@ -15,7 +16,8 @@ unraid(action="system",  subaction="online")           # Online status
 ```
 
 ### Array & Disks
-```
+
+```python
 unraid(action="system",  subaction="array")             # Array status overview
 unraid(action="disk",    subaction="disks")             # All disks with temps & health
 unraid(action="array",   subaction="parity_status")     # Current parity check
@@ -25,14 +27,17 @@ unraid(action="array",   subaction="stop_array",  confirm=True)   # ⚠️ Stop
 ```
 
 ### Logs
-```
+
+```python
 unraid(action="disk", subaction="log_files")                                          # List available logs
-unraid(action="disk", subaction="logs", path="syslog", lines=50)      # Read syslog
+unraid(action="disk", subaction="logs", log_path="syslog", tail_lines=50)             # Read syslog
-unraid(action="disk", subaction="logs", path="/var/log/syslog")       # Full path also works
+unraid(action="disk", subaction="logs", log_path="/var/log/syslog")                   # Full path also works
+unraid(action="live", subaction="log_tail", log_path="/var/log/syslog")               # Live tail
 ```
 
 ### Docker Containers
-```
+
+```python
 unraid(action="docker", subaction="list")
 unraid(action="docker", subaction="details",  container_id="plex")
 unraid(action="docker", subaction="start",    container_id="nginx")
@@ -42,7 +47,8 @@ unraid(action="docker", subaction="networks")
 ```
 
 ### Virtual Machines
-```
+
+```python
 unraid(action="vm", subaction="list")
 unraid(action="vm", subaction="details",    vm_id="<id>")
 unraid(action="vm", subaction="start",      vm_id="<id>")
@@ -52,37 +58,41 @@ unraid(action="vm", subaction="force_stop", vm_id="<id>", confirm=True)   # ⚠
 ```
 
 ### Notifications
-```
+
+```python
 unraid(action="notification", subaction="overview")
-unraid(action="notification", subaction="unread")
+unraid(action="notification", subaction="list",    list_type="UNREAD", limit=10)
-unraid(action="notification", subaction="list",    filter="UNREAD", limit=10)
 unraid(action="notification", subaction="archive", notification_id="<id>")
 unraid(action="notification", subaction="create",  title="Test", subject="Subject",
                                                    description="Body", importance="normal")
 ```
 
 ### API Keys
-```
+
+```python
 unraid(action="key", subaction="list")
 unraid(action="key", subaction="create", name="my-key", roles=["viewer"])
 unraid(action="key", subaction="delete", key_id="<id>", confirm=True)   # ⚠️
 ```
 
 ### Plugins
-```
+
+```python
 unraid(action="plugin", subaction="list")
 unraid(action="plugin", subaction="add",    names=["community.applications"])
 unraid(action="plugin", subaction="remove", names=["old.plugin"], confirm=True)   # ⚠️
 ```
 
 ### rclone
-```
+
+```python
 unraid(action="rclone", subaction="list_remotes")
 unraid(action="rclone", subaction="delete_remote", name="<remote>", confirm=True)   # ⚠️
 ```
 
 ### Live Subscriptions (real-time)
-```
+
+```python
 unraid(action="live", subaction="cpu")
 unraid(action="live", subaction="memory")
 unraid(action="live", subaction="parity_progress")
@@ -90,6 +100,7 @@ unraid(action="live", subaction="log_tail")
 unraid(action="live", subaction="notification_feed")
 unraid(action="live", subaction="ups_status")
 ```
+
 > Returns `{"status": "connecting"}` on first call — retry momentarily.
 
 ---

skills/unraid/references/troubleshooting.md

@@ -5,7 +5,8 @@
 **Error:** `CredentialsNotConfiguredError` or message containing `~/.unraid-mcp/.env`
 
 **Fix:** Run setup to configure credentials interactively:
-```
+
+```python
 unraid(action="health", subaction="setup")
 ```
 
@@ -20,12 +21,14 @@ This writes `UNRAID_API_URL` and `UNRAID_API_KEY` to `~/.unraid-mcp/.env`. Re-ru
 **Diagnostic steps:**
 
 1. Test basic connectivity:
-```
+
+```python
 unraid(action="health", subaction="test_connection")
 ```
 
 2. Full diagnostic report:
-```
+
+```python
 unraid(action="health", subaction="diagnose")
 ```
 
@@ -57,7 +60,8 @@ unraid(action="health", subaction="diagnose")
 **Error:** `Action 'X' was not confirmed. Re-run with confirm=True to bypass elicitation.`
 
 **Fix:** Add `confirm=True` to the call:
-```
+
+```python
 unraid(action="array", subaction="stop_array", confirm=True)
 unraid(action="vm",    subaction="force_stop", vm_id="<id>", confirm=True)
 ```

tests/mcporter/test-tools.sh

@@ -2,7 +2,7 @@
 # =============================================================================
 # test-tools.sh — Integration smoke-test for unraid-mcp MCP server tools
 #
-# Exercises every non-destructive action using the consolidated `unraid` tool
+# Exercises broad non-destructive smoke coverage of the consolidated `unraid` tool
 # (action + subaction pattern). The server is launched ad-hoc via mcporter's
 # --stdio flag so no persistent process or registered server entry is required.
 #
@@ -298,6 +298,24 @@ skip_test() {
   SKIP_COUNT=$(( SKIP_COUNT + 1 ))
 }
 
+# ---------------------------------------------------------------------------
+# Safe JSON payload builder
+#   Usage: _json_payload '<jq-template-with-$vars>' key1=value1 key2=value2 ...
+#   Uses jq --arg to safely encode shell values into JSON, preventing injection
+#   via special characters in variable values (e.g., quotes, backslashes).
+# ---------------------------------------------------------------------------
+_json_payload() {
+  local template="${1:?template required}"; shift
+  local jq_args=()
+  local pair k v
+  for pair in "$@"; do
+    k="${pair%%=*}"
+    v="${pair#*=}"
+    jq_args+=(--arg "$k" "$v")
+  done
+  jq -n "${jq_args[@]}" "$template"
+}
+
 # ---------------------------------------------------------------------------
 # ID extractors
 # ---------------------------------------------------------------------------
@@ -441,9 +459,9 @@ suite_system() {
   ups_id="$(get_ups_id)" || ups_id=''
   if [[ -n "${ups_id}" ]]; then
     run_test "system: ups_device" \
-      "$(printf '{"action":"system","subaction":"ups_device","device_id":"%s"}' "${ups_id}")"
+      "$(_json_payload '{"action":"system","subaction":"ups_device","device_id":$v}' v="${ups_id}")"
     run_test "system: ups_config" \
-      "$(printf '{"action":"system","subaction":"ups_config","device_id":"%s"}' "${ups_id}")"
+      "$(_json_payload '{"action":"system","subaction":"ups_config","device_id":$v}' v="${ups_id}")"
   else
     skip_test "system: ups_device" "no UPS devices found"
     skip_test "system: ups_config" "no UPS devices found"
@@ -469,7 +487,7 @@ suite_disk() {
   disk_id="$(get_disk_id)" || disk_id=''
   if [[ -n "${disk_id}" ]]; then
     run_test "disk: disk_details" \
-      "$(printf '{"action":"disk","subaction":"disk_details","disk_id":"%s"}' "${disk_id}")"
+      "$(_json_payload '{"action":"disk","subaction":"disk_details","disk_id":$v}' v="${disk_id}")"
   else
     skip_test "disk: disk_details" "no disks found"
   fi
@@ -478,7 +496,7 @@ suite_disk() {
   log_path="$(get_log_path)" || log_path=''
   if [[ -n "${log_path}" ]]; then
     run_test "disk: logs" \
-      "$(printf '{"action":"disk","subaction":"logs","log_path":"%s","tail_lines":20}' "${log_path}")"
+      "$(_json_payload '{"action":"disk","subaction":"logs","log_path":$v,"tail_lines":20}' v="${log_path}")"
   else
     skip_test "disk: logs" "no log files found"
   fi
@@ -495,7 +513,7 @@ suite_docker() {
   container_id="$(get_docker_id)" || container_id=''
   if [[ -n "${container_id}" ]]; then
     run_test "docker: details" \
-      "$(printf '{"action":"docker","subaction":"details","container_id":"%s"}' "${container_id}")"
+      "$(_json_payload '{"action":"docker","subaction":"details","container_id":$v}' v="${container_id}")"
   else
     skip_test "docker: details" "no containers found"
   fi
@@ -504,7 +522,7 @@ suite_docker() {
   network_id="$(get_network_id)" || network_id=''
   if [[ -n "${network_id}" ]]; then
     run_test "docker: network_details" \
-      "$(printf '{"action":"docker","subaction":"network_details","network_id":"%s"}' "${network_id}")"
+      "$(_json_payload '{"action":"docker","subaction":"network_details","network_id":$v}' v="${network_id}")"
   else
     skip_test "docker: network_details" "no networks found"
   fi
@@ -520,7 +538,7 @@ suite_vm() {
   vm_id="$(get_vm_id)" || vm_id=''
   if [[ -n "${vm_id}" ]]; then
     run_test "vm: details" \
-      "$(printf '{"action":"vm","subaction":"details","vm_id":"%s"}' "${vm_id}")"
+      "$(_json_payload '{"action":"vm","subaction":"details","vm_id":$v}' v="${vm_id}")"
   else
     skip_test "vm: details" "no VMs found (or VM service unavailable)"
   fi
@@ -558,7 +576,7 @@ suite_key() {
   key_id="$(get_key_id)" || key_id=''
   if [[ -n "${key_id}" ]]; then
     run_test "key: get" \
-      "$(printf '{"action":"key","subaction":"get","key_id":"%s"}' "${key_id}")"
+      "$(_json_payload '{"action":"key","subaction":"get","key_id":$v}' v="${key_id}")"
   else
     skip_test "key: get" "no API keys found"
   fi