refactor: remove ~750 lines of dead code across 12 files

- Delete 4 dead files: pre-recon.ts, tool-checker.ts, input-validator.ts, environment.ts
- Remove runClaudePromptWithRetry() and its now-unused imports from claude-executor.ts
- De-export unused symbols: AGENT_ORDER, getParallelGroups, logError, isRouterMode, showHelp, displayTimingSummary
- De-export unused types: ProcessingState, ProcessingResult, SdkMessage, MessageDispatchResult, MessageDispatchContext
- Remove dead import (path from zx) in session-manager.ts and deprecated comment in config.ts

src/ai/claude-executor.ts

@@ -10,10 +10,9 @@ import { fs, path } from 'zx';
 import chalk, { type ChalkInstance } from 'chalk';
 import { query } from '@anthropic-ai/claude-agent-sdk';
 
-import { isRetryableError, getRetryDelay, PentestError } from '../error-handling.js';
+import { isRetryableError, PentestError } from '../error-handling.js';
 import { timingResults, Timer } from '../utils/metrics.js';
 import { formatTimestamp } from '../utils/formatting.js';
-import { createGitCheckpoint, commitGitSuccess, rollbackGitWorkspace, getGitCommitHash } from '../utils/git-manager.js';
 import { AGENT_VALIDATORS, MCP_AGENT_MAPPING } from '../constants.js';
 import { AuditSession } from '../audit/index.js';
 import { createShannonHelperServer } from '../../mcp-server/dist/index.js';
@@ -403,153 +402,3 @@ async function processMessageStream(
 
   return { turnCount, result, apiErrorDetected, cost, model };
 }
-
-// Main entry point for agent execution. Handles retries, git checkpoints, and validation.
-export async function runClaudePromptWithRetry(
-  prompt: string,
-  sourceDir: string,
-  _allowedTools: string = 'Read',
-  context: string = '',
-  description: string = 'Claude analysis',
-  agentName: string | null = null,
-  colorFn: ChalkInstance = chalk.cyan,
-  sessionMetadata: SessionMetadata | null = null
-): Promise<ClaudePromptResult> {
-  const maxRetries = 3;
-  let lastError: Error | undefined;
-  let retryContext = context;
-
-  console.log(chalk.cyan(`Starting ${description} with ${maxRetries} max attempts`));
-
-  let auditSession: AuditSession | null = null;
-  if (sessionMetadata && agentName) {
-    auditSession = new AuditSession(sessionMetadata);
-    await auditSession.initialize();
-  }
-
-  for (let attempt = 1; attempt <= maxRetries; attempt++) {
-    await createGitCheckpoint(sourceDir, description, attempt);
-
-    if (auditSession && agentName) {
-      const fullPrompt = retryContext ? `${retryContext}\n\n${prompt}` : prompt;
-      await auditSession.startAgent(agentName, fullPrompt, attempt);
-    }
-
-    try {
-      const result = await runClaudePrompt(
-        prompt, sourceDir, retryContext,
-        description, agentName, colorFn, sessionMetadata, auditSession, attempt
-      );
-
-      if (result.success) {
-        const validationPassed = await validateAgentOutput(result, agentName, sourceDir);
-
-        if (validationPassed) {
-          if (result.apiErrorDetected) {
-            console.log(chalk.yellow(`Validation: Ready for exploitation despite API error warnings`));
-          }
-
-          if (auditSession && agentName) {
-            const commitHash = await getGitCommitHash(sourceDir);
-            const endResult: {
-              attemptNumber: number;
-              duration_ms: number;
-              cost_usd: number;
-              success: true;
-              checkpoint?: string;
-            } = {
-              attemptNumber: attempt,
-              duration_ms: result.duration,
-              cost_usd: result.cost || 0,
-              success: true,
-            };
-            if (commitHash) {
-              endResult.checkpoint = commitHash;
-            }
-            await auditSession.endAgent(agentName, endResult);
-          }
-
-          await commitGitSuccess(sourceDir, description);
-          console.log(chalk.green.bold(`${description} completed successfully on attempt ${attempt}/${maxRetries}`));
-          return result;
-        // Validation failure is retryable - agent might succeed on retry with cleaner workspace
-        } else {
-          console.log(chalk.yellow(`${description} completed but output validation failed`));
-
-          if (auditSession && agentName) {
-            await auditSession.endAgent(agentName, {
-              attemptNumber: attempt,
-              duration_ms: result.duration,
-              cost_usd: result.partialCost || result.cost || 0,
-              success: false,
-              error: 'Output validation failed',
-              isFinalAttempt: attempt === maxRetries
-            });
-          }
-
-          if (result.apiErrorDetected) {
-            console.log(chalk.yellow(`API Error detected with validation failure - treating as retryable`));
-            lastError = new Error('API Error: terminated with validation failure');
-          } else {
-            lastError = new Error('Output validation failed');
-          }
-
-          if (attempt < maxRetries) {
-            await rollbackGitWorkspace(sourceDir, 'validation failure');
-            continue;
-          } else {
-            throw new PentestError(
-              `Agent ${description} failed output validation after ${maxRetries} attempts. Required deliverable files were not created.`,
-              'validation',
-              false,
-              { description, sourceDir, attemptsExhausted: maxRetries }
-            );
-          }
-        }
-      }
-
-    } catch (error) {
-      const err = error as Error & { duration?: number; cost?: number; partialResults?: unknown };
-      lastError = err;
-
-      if (auditSession && agentName) {
-        await auditSession.endAgent(agentName, {
-          attemptNumber: attempt,
-          duration_ms: err.duration || 0,
-          cost_usd: err.cost || 0,
-          success: false,
-          error: err.message,
-          isFinalAttempt: attempt === maxRetries
-        });
-      }
-
-      if (!isRetryableError(err)) {
-        console.log(chalk.red(`${description} failed with non-retryable error: ${err.message}`));
-        await rollbackGitWorkspace(sourceDir, 'non-retryable error cleanup');
-        throw err;
-      }
-
-      if (attempt < maxRetries) {
-        await rollbackGitWorkspace(sourceDir, 'retryable error cleanup');
-
-        const delay = getRetryDelay(err, attempt);
-        const delaySeconds = (delay / 1000).toFixed(1);
-        console.log(chalk.yellow(`${description} failed (attempt ${attempt}/${maxRetries})`));
-        console.log(chalk.gray(`    Error: ${err.message}`));
-        console.log(chalk.gray(`    Workspace rolled back, retrying in ${delaySeconds}s...`));
-
-        if (err.partialResults) {
-          retryContext = `${context}\n\nPrevious partial results: ${JSON.stringify(err.partialResults)}`;
-        }
-
-        await new Promise(resolve => setTimeout(resolve, delay));
-      } else {
-        await rollbackGitWorkspace(sourceDir, 'final failure cleanup');
-        console.log(chalk.red(`${description} failed after ${maxRetries} attempts`));
-        console.log(chalk.red(`    Final error: ${err.message}`));
-      }
-    }
-  }
-
-  throw lastError;
-}