feat: add configurable output directory with --output flag (#41)

* feat: add configurable output directory with --output flag

Add --output CLI flag to specify custom output directory for session
folders containing audit logs, prompts, agent logs, and deliverables.

Changes:
- Add --output <path> CLI flag parsing
- Update generateAuditPath() to use custom path when provided
- Add consolidateOutputs() to copy deliverables to session folder
- Update Docker examples with volume mounts for output directories
- Default remains ./audit-logs/ when --output is not specified

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

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

* feat: add configurable output directory with --output flag

Add --output CLI flag to specify custom output directory for session
folders containing audit logs, prompts, agent logs, and deliverables.

Changes:
- Add --output <path> CLI flag parsing
- Store outputPath in Session interface for persistence
- Update generateAuditPath() to use custom path when provided
- Pass outputPath through pre-recon and checkpoint-manager
- Add consolidateOutputs() to copy deliverables to session folder
- Update Docker examples with volume mount instructions
- Default remains ./audit-logs/ when --output is not specified

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

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

* chore: add gitkeep and fix formatting

* fix: correct docker run command formatting in README

Remove invalid inline comments after backslash continuations in docker
run commands. Comments cannot appear after backslash line continuations
in shell scripts, as the backslash escapes the newline character.

Reorganized comments to appear on separate lines before or after the
command block for better clarity and proper shell syntax.

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

src/session-manager.ts

@@ -41,6 +41,7 @@ export interface Session {
   repoPath: string;
   configFile: string | null;
   targetRepo: string;
+  outputPath: string | null;
   status: 'in-progress' | 'completed' | 'failed';
   completedAgents: AgentName[];
   failedAgents: AgentName[];
@@ -265,7 +266,8 @@ export const createSession = async (
   webUrl: string,
   repoPath: string,
   configFile: string | null = null,
-  targetRepo: string | null = null
+  targetRepo: string | null = null,
+  outputPath: string | null = null
 ): Promise<Session> => {
   // Use targetRepo if provided, otherwise use repoPath
   const resolvedTargetRepo = targetRepo || repoPath;
@@ -279,9 +281,12 @@ export const createSession = async (
       console.log(chalk.blue(`📝 Reusing existing session: ${existingSession.id.substring(0, 8)}...`));
       console.log(chalk.gray(`   Progress: ${existingSession.completedAgents.length}/${Object.keys(AGENTS).length} agents completed`));
 
-      // Update last activity timestamp
-      await updateSession(existingSession.id, { lastActivity: new Date().toISOString() });
-      return existingSession;
+      // Update last activity timestamp and outputPath if provided
+      await updateSession(existingSession.id, {
+        lastActivity: new Date().toISOString(),
+        ...(outputPath && { outputPath })
+      });
+      return { ...existingSession, ...(outputPath && { outputPath }) };
     }
 
     // If completed, create a new session (allows re-running after completion)
@@ -298,6 +303,7 @@ export const createSession = async (
     repoPath,
     configFile,
     targetRepo: resolvedTargetRepo,
+    outputPath,
     status: 'in-progress',
     completedAgents: [],
     failedAgents: [],