chore: remove ~500 lines of dead code identified by knip

Remove unused files and exports to improve codebase maintainability:

Phase 1 - Deleted files (5):
- login_resources/generate-totp-standalone.mjs (replaced by MCP tool)
- mcp-server/src/tools/index.js (unused barrel export)
- mcp-server/src/utils/index.js (unused barrel export)
- mcp-server/src/validation/index.js (unused barrel export)
- src/agent-status.js (deprecated 309-line status manager)

Phase 2 - Removed unused exports (3):
- mcp-server/src/index.js: shannonHelperServer constant
- mcp-server/src/utils/error-formatter.js: createFileSystemError function
- src/utils/git-manager.js: cleanWorkspace (now internal-only)

Phase 3 - Unexported internal functions (4):
- src/checkpoint-manager.js: runSingleAgent, runAgentRange,
  runParallelVuln, runParallelExploit (internal use only)

All Shannon CLI commands tested and verified working.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

mcp-server/src/utils/error-formatter.js

@@ -31,24 +31,6 @@ export function createValidationError(message, retryable = true, context) {
   };
 }
 
-/**
- * Create a file system error response
- *
- * @param {string} message
- * @param {boolean} [retryable=false]
- * @param {Record<string, unknown>} [context]
- * @returns {ErrorResponse}
- */
-export function createFileSystemError(message, retryable = false, context) {
-  return {
-    status: 'error',
-    message,
-    errorType: 'FileSystemError',
-    retryable,
-    context,
-  };
-}
-
 /**
  * Create a crypto error response
  *

mcp-server/src/utils/index.js

@@ -1,6 +0,0 @@
-/**
- * Utilities barrel export
- */
-
-export * from './file-operations.js';
-export * from './error-formatter.js';