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>

src/utils/git-manager.js

@@ -72,7 +72,7 @@ export const executeGitCommandWithRetry = async (commandArgs, sourceDir, descrip
 };
 
 // Pure functions for Git workspace management
-export const cleanWorkspace = async (sourceDir, reason = 'clean start') => {
+const cleanWorkspace = async (sourceDir, reason = 'clean start') => {
   console.log(chalk.blue(`    🧹 Cleaning workspace for ${reason}`));
   try {
     // Check for uncommitted changes