docs: Update documentation for new AI/config architecture and finalize cleanup

This commit updates all relevant documentation (READMEs, docs/*, .cursor/rules) to accurately reflect the finalized unified AI service architecture and the new configuration system (.taskmasterconfig + .env/mcp.json). It also includes the final code cleanup steps related to the refactoring.

Key Changes:

1.  **Documentation Updates:**

    *   Revised `README.md`, `README-task-master.md`, `assets/scripts_README.md`, `docs/configuration.md`, and `docs/tutorial.md` to explain the new configuration split (.taskmasterconfig vs .env/mcp.json).

    *   Updated MCP configuration examples in READMEs and tutorials to only include API keys in the `env` block.

    *   Added/updated examples for using the `--research` flag in `docs/command-reference.md`, `docs/examples.md`, and `docs/tutorial.md`.

    *   Updated `.cursor/rules/ai_services.mdc`, `.cursor/rules/architecture.mdc`, `.cursor/rules/dev_workflow.mdc`, `.cursor/rules/mcp.mdc`, `.cursor/rules/taskmaster.mdc`, `.cursor/rules/utilities.mdc`, and `.cursor/rules/new_features.mdc` to align with the new architecture, removing references to old patterns/files.

    *   Removed internal rule links from user-facing rules (`taskmaster.mdc`, `dev_workflow.mdc`, `self_improve.mdc`).

    *   Deleted outdated example file `docs/ai-client-utils-example.md`.

2.  **Final Code Refactor & Cleanup:**

    *   Corrected `update-task-by-id.js` by removing the last import from the old `ai-services.js`.

    *   Refactored `update-subtask-by-id.js` to correctly use the unified service and logger patterns.

    *   Removed the obsolete export block from `mcp-server/src/core/task-master-core.js`.

    *   Corrected logger implementation in `update-tasks.js` for CLI context.

    *   Updated API key mapping in `config-manager.js` and `ai-services-unified.js`.

3.  **Configuration Files:**

    *   Updated API keys in `.cursor/mcp.json`, replacing `GROK_API_KEY` with `XAI_API_KEY`.

    *   Updated `.env.example` with current API key names.

    *   Added `azureOpenaiBaseUrl` to `.taskmasterconfig` example.

4.  **Task Management:**

    *   Marked documentation subtask 61.10 as 'done'.

    *   Includes various other task content/status updates from the diff summary.

5.  **Changeset:**

    *   Added `.changeset/cuddly-zebras-matter.md` for user-facing `expand`/`expand-all` improvements.

This commit concludes the major architectural refactoring (Task 61) and ensures the documentation accurately reflects the current system.

docs/tutorial.md

@@ -27,21 +27,22 @@ npm i -g task-master-ai
 			"env": {
 				"ANTHROPIC_API_KEY": "YOUR_ANTHROPIC_API_KEY_HERE",
 				"PERPLEXITY_API_KEY": "YOUR_PERPLEXITY_API_KEY_HERE",
-				"MODEL": "claude-3-7-sonnet-20250219",
-				"PERPLEXITY_MODEL": "sonar-pro",
-				"MAX_TOKENS": 64000,
-				"TEMPERATURE": 0.2,
-				"DEFAULT_SUBTASKS": 5,
-				"DEFAULT_PRIORITY": "medium"
+				"OPENAI_API_KEY": "YOUR_OPENAI_KEY_HERE",
+				"GOOGLE_API_KEY": "YOUR_GOOGLE_KEY_HERE",
+				"MISTRAL_API_KEY": "YOUR_MISTRAL_KEY_HERE",
+				"OPENROUTER_API_KEY": "YOUR_OPENROUTER_KEY_HERE",
+				"XAI_API_KEY": "YOUR_XAI_KEY_HERE",
+				"AZURE_OPENAI_API_KEY": "YOUR_AZURE_KEY_HERE",
+				"OLLAMA_API_KEY": "YOUR_OLLAMA_KEY_HERE"
 			}
 		}
 	}
 }
 ```
 
-2. **Enable the MCP** in your editor settings
+3. **Enable the MCP** in your editor settings
 
-3. **Prompt the AI** to initialize Task Master:
+4. **Prompt the AI** to initialize Task Master:
 
 ```
 Can you please initialize taskmaster-ai into my project?
@@ -53,9 +54,9 @@ The AI will:
 - Set up initial configuration files
 - Guide you through the rest of the process
 
-4. Place your PRD document in the `scripts/` directory (e.g., `scripts/prd.txt`)
+5. Place your PRD document in the `scripts/` directory (e.g., `scripts/prd.txt`)
 
-5. **Use natural language commands** to interact with Task Master:
+6. **Use natural language commands** to interact with Task Master:
 
 ```
 Can you parse my PRD at scripts/prd.txt?
@@ -247,13 +248,16 @@ If during implementation, you discover that:
 Tell the agent:
 
 ```
-We've changed our approach. We're now using Express instead of Fastify. Please update all future tasks to reflect this change.
+We've decided to use MongoDB instead of PostgreSQL. Can you update all future tasks (from ID 4) to reflect this change?
 ```
 
 The agent will execute:
 
 ```bash
-task-master update --from=4 --prompt="Now we are using Express instead of Fastify."
+task-master update --from=4 --prompt="Now we are using MongoDB instead of PostgreSQL."
+
+# OR, if research is needed to find best practices for MongoDB:
+task-master update --from=4 --prompt="Update to use MongoDB, researching best practices" --research
 ```
 
 This will rewrite or re-scope subsequent tasks in tasks.json while preserving completed work.
@@ -296,7 +300,7 @@ The agent will execute:
 task-master expand --all
 ```
 
-For research-backed subtask generation using Perplexity AI:
+For research-backed subtask generation using the configured research model:
 
 ```
 Please break down task 5 using research-backed generation.