feat: Add skipped tests for task-manager and utils modules, and address potential issues

This commit introduces a comprehensive set of skipped tests to both  and . These skipped tests serve as a blueprint for future test implementation, outlining the necessary test cases for currently untested functionalities.

- Ensures sync with bin/ folder by adding -r/--research to the  command
- Fixes an issue that improperly parsed command line args
- Ensures confirmation card on dependency add/remove
- Properly formats some sub-task dependencies

**Potentially addressed issues:**

While primarily focused on adding test coverage, this commit also implicitly addresses potential issues by:

- **Improving error handling coverage:** The addition of skipped tests for error scenarios in functions like , , , and  highlights areas where error handling needs to be robustly tested and potentially improved in the codebase.
- **Enhancing dependency validation:** Skipped tests for  include validation of dependencies, prompting a review of the dependency validation logic and ensuring its correctness.
- **Standardizing test coverage:** By creating a clear roadmap for testing all functions, this commit contributes to a more standardized and complete test suite, reducing the likelihood of undiscovered bugs in the future.

**task-manager.test.js:**

- Added skipped test blocks for the following functions:
    - : Includes tests for handling valid JSON responses, malformed JSON, missing tasks in responses, Perplexity AI research integration, Claude fallback, and parallel task processing.
    - : Covers tests for updating tasks based on context, handling Claude streaming, Perplexity AI integration, scenarios with no tasks to update, and error handling during updates.
    - : Includes tests for generating task files from , formatting dependencies with status indicators, handling tasks without subtasks, empty task arrays, and dependency validation before file generation.
    - : Covers tests for updating task status, subtask status using dot notation, updating multiple tasks, automatic subtask status updates, parent task update suggestions, and handling non-existent task IDs.
    - : Includes tests for updating regular and subtask statuses, handling parent tasks without subtasks, and non-existent subtask IDs.
    - : Covers tests for displaying all tasks, filtering by status, displaying subtasks, showing completion statistics, identifying the next task, and handling empty task arrays.
    - : Includes tests for generating subtasks, using complexity reports for subtask counts, Perplexity AI integration, appending subtasks, skipping completed tasks, and error handling during subtask generation.
    - : Covers tests for expanding all pending tasks, sorting by complexity, skipping tasks with existing subtasks (unless forced), using task-specific parameters from complexity reports, handling empty task arrays, and error handling for individual tasks.
    - : Includes tests for clearing subtasks from specific and multiple tasks, handling tasks without subtasks, non-existent task IDs, and regenerating task files after clearing subtasks.
    - : Covers tests for adding new tasks using AI, handling Claude streaming, validating dependencies, handling malformed AI responses, and using existing task context for generation.

**utils.test.js:**

- Added skipped test blocks for the following functions:
    - : Tests for logging messages according to log levels and filtering messages below configured levels.
    - : Tests for reading and parsing valid JSON files, handling file not found errors, and invalid JSON formats.
    - : Tests for writing JSON data to files and handling file write errors.
    - : Tests for escaping double quotes in prompts and handling prompts without special characters.
    - : Tests for reading and parsing complexity reports, handling missing report files, and custom report paths.
    - : Tests for finding tasks in reports by ID, handling non-existent task IDs, and invalid report structures.
    - : Tests for verifying existing task and subtask IDs, handling non-existent IDs, and invalid inputs.
    - : Tests for formatting numeric and string task IDs and preserving dot notation for subtasks.
    - : Tests for detecting simple and complex cycles in dependency graphs, handling acyclic graphs, and empty dependency maps.

These skipped tests provide a clear roadmap for future test development, ensuring comprehensive coverage for core functionalities in both modules. They document the intended behavior of each function and outline various scenarios, including happy paths, edge cases, and error conditions, thereby improving the overall test strategy and maintainability of the Task Master CLI.

tasks/task_016.txt

@@ -1,7 +1,7 @@
 # Task ID: 16
 # Title: Create Configuration Management System
 # Status: done
-# Dependencies: ✅ 1 (done), ✅ 2 (done)
+# Dependencies: 1, 2
 # Priority: high
 # Description: Implement robust configuration handling with environment variables and .env files.
 # Details:
@@ -25,31 +25,31 @@ Test configuration loading from various sources (environment variables, .env fil
 
 
 ## 2. Implement .env File Support [done]
-### Dependencies: 1 (done)
+### Dependencies: 16.1
 ### Description: Add support for loading configuration from .env files using dotenv or a similar library. Implement file detection, parsing, and merging with existing environment variables. Handle multiple environments (.env.development, .env.production, etc.) and implement proper error handling for file reading issues.
 ### Details:
 
 
 ## 3. Implement Configuration Validation [done]
-### Dependencies: 1 (done), 2 (done)
+### Dependencies: 16.1, 16.2
 ### Description: Create a validation system for configuration values using a schema validation library like Joi, Zod, or Ajv. Define schemas for all configuration categories (API keys, file paths, feature flags, etc.). Implement validation that runs at startup and provides clear error messages for invalid configurations.
 ### Details:
 
 
 ## 4. Create Configuration Defaults and Override System [done]
-### Dependencies: 1 (done), 2 (done), 3 (done)
+### Dependencies: 16.1, 16.2, 16.3
 ### Description: Implement a system of sensible defaults for all configuration values with the ability to override them via environment variables or .env files. Create a unified configuration object that combines defaults, .env values, and environment variables with proper precedence. Implement a caching mechanism to avoid repeated environment lookups.
 ### Details:
 
 
 ## 5. Create .env.example Template [done]
-### Dependencies: 1 (done), 2 (done), 3 (done), 4 (done)
+### Dependencies: 16.1, 16.2, 16.3, 16.4
 ### Description: Generate a comprehensive .env.example file that documents all supported environment variables, their purpose, format, and default values. Include comments explaining the purpose of each variable and provide examples. Ensure sensitive values are not included but have clear placeholders.
 ### Details:
 
 
 ## 6. Implement Secure API Key Handling [done]
-### Dependencies: 1 (done), 2 (done), 3 (done), 4 (done)
+### Dependencies: 16.1, 16.2, 16.3, 16.4
 ### Description: Create a secure mechanism for handling sensitive configuration values like API keys. Implement masking of sensitive values in logs and error messages. Add validation for API key formats and implement a mechanism to detect and warn about insecure storage of API keys (e.g., committed to git). Add support for key rotation and refresh.
 ### Details: