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>

README.md

@@ -169,10 +169,15 @@ docker run --rm -it \
       -e CLAUDE_CODE_MAX_OUTPUT_TOKENS=64000 \
       -v "$(pwd)/repos:/app/repos" \
       -v "$(pwd)/configs:/app/configs" \
+      # Comment below line if using custom output directory
+      -v "$(pwd)/audit-logs:/app/audit-logs" \
       shannon:latest \
       "https://your-app.com/" \
       "/app/repos/your-app" \
       --config /app/configs/example-config.yaml
+      # Optional: uncomment below for custom output directory
+      # -v "$(pwd)/reports:/app/reports" \
+      # --output /app/reports
 ```
 
 **With Anthropic API Key:**
@@ -186,10 +191,15 @@ docker run --rm -it \
       -e CLAUDE_CODE_MAX_OUTPUT_TOKENS=64000 \
       -v "$(pwd)/repos:/app/repos" \
       -v "$(pwd)/configs:/app/configs" \
+      # Comment below line if using custom output directory
+      -v "$(pwd)/audit-logs:/app/audit-logs" \
       shannon:latest \
       "https://your-app.com/" \
       "/app/repos/your-app" \
       --config /app/configs/example-config.yaml
+      # Optional: uncomment below for custom output directory
+      # -v "$(pwd)/reports:/app/reports" \
+      # --output /app/reports
 ```
 
 #### Platform-Specific Instructions
@@ -217,10 +227,15 @@ docker run --rm -it \
       -e CLAUDE_CODE_MAX_OUTPUT_TOKENS=64000 \
       -v "$(pwd)/repos:/app/repos" \
       -v "$(pwd)/configs:/app/configs" \
+      # Comment below line if using custom output directory
+      -v "$(pwd)/audit-logs:/app/audit-logs" \
       shannon:latest \
       "http://host.docker.internal:3000" \
       "/app/repos/your-app" \
       --config /app/configs/example-config.yaml
+      # Optional: uncomment below for custom output directory
+      # -v "$(pwd)/reports:/app/reports" \
+      # --output /app/reports
 ```
 
 ### Configuration (Optional)
@@ -281,7 +296,7 @@ docker run --rm shannon:latest --status
 
 ### Output and Results
 
-All analysis results are saved to the `deliverables/` directory:
+All results are saved to `./audit-logs/` by default. Use `--output <path>` to specify a custom directory. If using `--output`, ensure that path is mounted to an accessible host directory (e.g., `-v "$(pwd)/custom-directory:/app/reports"`).
 
 - **Pre-reconnaissance reports** - External scan results
 - **Vulnerability assessments** - Potential vulnerabilities from thorough code analysis and network mapping