refactor: Standardize configuration and environment variable access

This commit centralizes configuration and environment variable access across various modules by consistently utilizing getters from scripts/modules/config-manager.js. This replaces direct access to process.env and the global CONFIG object, leading to improved consistency, maintainability, testability, and better handling of session-specific configurations within the MCP context.

Key changes include:

- Centralized Getters: Replaced numerous instances of process.env.* and CONFIG.* with corresponding getter functions (e.g., getLogLevel, getMainModelId, getResearchMaxTokens, getMainTemperature, isApiKeySet, getDebugFlag, getDefaultSubtasks).

- Session Awareness: Ensured that the session object is passed to config getters where necessary, particularly within AI service calls (ai-services.js, add-task.js) and error handling (ai-services.js), allowing for session-specific environment overrides.

- API Key Checks: Standardized API key availability checks using isApiKeySet() instead of directly checking process.env.* (e.g., for Perplexity in commands.js and ai-services.js).

- Client Instantiation Cleanup: Removed now-redundant/obsolete local client instantiation functions (getAnthropicClient, getPerplexityClient) from ai-services.js and the global Anthropic client initialization from dependency-manager.js. Client creation should now rely on the config manager and factory patterns.

- Consistent Debug Flag Usage: Standardized calls to getDebugFlag() in commands.js, removing potentially unnecessary null arguments.

- Accurate Progress Calculation: Updated AI stream progress reporting (ai-services.js, add-task.js) to use getMainMaxTokens(session) for more accurate calculations.

- Minor Cleanup: Removed unused  import from scripts/modules/commands.js.

Specific module updates:

- :

  - Uses getLogLevel() instead of process.env.LOG_LEVEL.

- :

  - Replaced direct env/config access for model IDs, tokens, temperature, API keys, and default subtasks with appropriate getters.

  - Passed session to handleClaudeError.

  - Removed local getPerplexityClient and getAnthropicClient functions.

  - Updated progress calculations to use getMainMaxTokens(session).

- :

  - Uses isApiKeySet('perplexity') for API key checks.

  - Uses getDebugFlag() consistently for debug checks.

  - Removed unused  import.

- :

  - Removed global Anthropic client initialization.

- :

  - Uses config getters (getResearch..., getMain...) for Perplexity and Claude API call parameters, preserving customEnv override logic.

This refactoring also resolves a potential SyntaxError: Identifier 'getPerplexityClient' has already been declared by removing the duplicated/obsolete function definition previously present in ai-services.js.

mcp-server/src/logger.js

@@ -1,5 +1,6 @@
 import chalk from 'chalk';
 import { isSilentMode } from '../../scripts/modules/utils.js';
+import { getLogLevel } from '../../scripts/modules/config-manager.js';
 
 // Define log levels
 const LOG_LEVELS = {
@@ -10,10 +11,8 @@ const LOG_LEVELS = {
 	success: 4
 };
 
-// Get log level from environment or default to info
-const LOG_LEVEL = process.env.LOG_LEVEL
-	? (LOG_LEVELS[process.env.LOG_LEVEL.toLowerCase()] ?? LOG_LEVELS.info)
-	: LOG_LEVELS.info;
+// Get log level from config manager or default to info
+const LOG_LEVEL = LOG_LEVELS[getLogLevel().toLowerCase()] ?? LOG_LEVELS.info;
 
 /**
  * Logs a message with the specified level