Commit Graph

47 Commits

Author SHA1 Message Date
ajmallesh 8e4fafba99 refactor: remove ~275 lines of dead code and enable stricter tsconfig
- Delete unused src/cli/ui.ts, remove zod dependency, drop 4 dead functions (logError, handleToolError, getRetryDelay, displayTimingSummary)
- Remove 8 unused types/interfaces and 3 duplicate formatting utils from audit/utils.ts
- Narrow export surface: make 7 message-handler functions private, remove unused audit re-exports, unexport AgentDefinition and path constants
- Remove unused runClaudePrompt params (sessionMetadata, attemptNumber) and update caller
- Enable tsconfig noUnusedLocals, noUnusedParameters, noImplicitReturns, noImplicitOverride, noFallthroughCasesInSwitch
2026-02-16 11:55:59 -08:00
ajmallesh 13731f5ebf 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
2026-02-16 11:30:00 -08:00
ezl-keygraph 45e9f305ea refactor: remove ./shannon query CLI command
Query functionality is redundant with the Temporal Web UI
at http://localhost:8233. Removes query.ts, CLI handler,
npm script, and all documentation references.
2026-02-16 10:51:08 -08:00
ajmallesh 539bd873cc fix: improve resume edge cases and shell quoting
- Early exit when all agents already completed instead of running empty workflow
- Descriptive error when deliverables missing from disk despite session.json success
- Quote $WORKSPACE in shannon CLI to prevent word splitting
2026-02-16 10:50:52 -08:00
ezl-keygraph 1b696cac1b fix: store checkpoint as success commit hash and show cumulative metrics
- Swap commitGitSuccess/getGitCommitHash order so checkpoint in
  session.json points to the success commit (which contains deliverables)
  instead of the pre-agent marker commit
- Simplify restoreGitCheckpoint: git reset --hard now naturally preserves
  completed agent deliverables, removing the in-memory backup/restore
- Show cumulative cost/duration in workflow.log from session.json
- Fill in per-agent metrics for skipped agents in workflow.log breakdown
- Display cumulative cost in client output for resume runs
2026-02-14 02:52:11 +05:30
ezl-keygraph 7f9c5cc496 fix: copy deliverables to audit-logs once at workflow end instead of per-agent
Moves the copyDeliverablesToAudit call from runAgentActivity (called after
every agent) to logWorkflowComplete (called once at workflow end). This
prevents intermediate agent runs from copying incomplete or rogue deliverables
into the audit trail.
2026-02-14 01:21:02 +05:30
ezl-keygraph dbcb4587ee fix: update session.json status on workflow completion
logWorkflowComplete wrote to workflow.log but never called
updateSessionStatus, leaving all workspaces stuck as "in-progress"
in session.json. Also derive audit path for model injection instead
of requiring explicit outputPath.
2026-02-13 22:41:07 +05:30
ezl-keygraph f017a41436 fix: set originalWorkflowId in logPhaseTransition and remove path import from agents.ts
logPhaseTransition was the first activity to create session.json but
didn't pass workflowId, so originalWorkflowId was never set. This
caused terminateExistingWorkflows to look up the workspace name instead
of the actual workflow ID during resume.

Also remove path import from types/agents.ts to fix Temporal workflow
bundle determinism error.
2026-02-13 22:09:07 +05:30
ezl-keygraph ee5d7b80a0 feat: add named workspaces and workspace listing
Support WORKSPACE=<name> flag for friendly workspace names that
auto-resume if they exist or create a new named workspace otherwise.
Add ./shannon workspaces command to list all workspaces with status,
duration, and cost.
2026-02-13 20:53:18 +05:30
ezl-keygraph f932fad2ed feat: add workflow resume from workspace via --workspace flag
When a workflow is interrupted (VM crash, Ctrl+C, Docker restart), it can
now be resumed by passing the workspace name. The system reads session.json
to determine which agents completed, validates deliverables exist on disk,
restores the git checkpoint, and skips already-completed agents.

- Add --workspace CLI flag and auto-terminate conflicting workflows
- Add loadResumeState, restoreGitCheckpoint, recordResumeAttempt activities
- Add skip logic for all 5 pipeline phases including parallel execution
- Separate sessionId (persistent directory) from workflowId (execution ID)
- Track resume attempts in session.json for audit trail
- Derive AgentName type from ALL_AGENTS array to eliminate duplication
- Add getDeliverablePath mapping for deliverable validation
2026-02-13 20:26:16 +05:30
ezl-keygraph c169b0d0a6 fix: restore CLAUDE_CODE_MAX_OUTPUT_TOKENS env var support
Re-add the env var that was removed during SDK upgrade. Needed for
controlling output token limits in SDK subprocesses.
2026-02-12 08:51:39 -08:00
ajmallesh 80bc8e3a44 feat: copy deliverables to audit-logs for self-contained audit trail 2026-02-12 08:51:39 -08:00
Arjun Malleswaran 2f4fa89e7b fix: add file_path parameter to save_deliverable for large reports (#123)
* fix: add file_path parameter to save_deliverable for large reports

Large deliverable reports can exceed output token limits when passed as
inline content. This change allows agents to write reports to disk first
and pass a file_path instead.

Changes:
- Add file_path parameter to save_deliverable MCP tool with path
  traversal protection
- Pass CLAUDE_CODE_MAX_OUTPUT_TOKENS env var to SDK subprocesses
- Fix false positive error detection by extracting only text content
  (not tool_use JSON) when checking for API errors
- Update all prompts to instruct agents to use file_path for large
  reports and stop immediately after completion

* docs: simplify and condense CLAUDE.md

Reduce verbosity while preserving all essential information for AI
assistance. Makes the documentation more scannable and focused.

* feat: add issue number detection to pr command

The /pr command now automatically detects issue numbers from:
1. Explicit arguments (e.g., /pr 123 or /pr 123,456)
2. Branch name patterns (e.g., fix/123-bug, issue-456-feature)

Adds "Closes #X" lines to PR body to auto-close issues on merge.

* chore: remove CLAUDE_CODE_MAX_OUTPUT_TOKENS env var handling

No longer needed with the new Claude Agent SDK version.

* fix: restore max_output_tokens error handling
2026-02-11 13:40:49 -08:00
ezl-keygraph 3c13a9a7e6 feat: upgrade claude-agent-sdk to 0.2.38 and adapt to new SDK types (#113)
* feat: upgrade claude-agent-sdk to 0.2.38 and adapt to new SDK types

- Bump @anthropic-ai/claude-agent-sdk from 0.1.x to 0.2.38 (both root and mcp-server)
- Bump zod from 3.x to 4.x (SDK peer dependency)
- Add allowDangerouslySkipPermissions to query options (required for bypassPermissions)
- Suppress new SDK message types (tool_progress, tool_use_summary, auth_status)
- Use structured error field on assistant messages instead of text-sniffing
- Add stop_reason to result message handling for diagnostics
- Add SDKAssistantMessageError type matching SDK's string literal union

* chore: remove CLAUDE_CODE_MAX_OUTPUT_TOKENS from all config and docs
2026-02-11 00:19:59 +05:30
Arjun Malleswaran 9809c769e3 fix: extend heartbeat timeout to prevent stalls during sub-agent execution (#108)
* fix: extend heartbeat timeout to prevent stalls during sub-agent execution

* feat: add /pr command for creating pull requests with conventional commits
2026-02-09 10:58:03 -08:00
ajmallesh 63741d780e revert: remove '402' billing pattern causing false positives
Reverts 5428422 - the pattern matched tool call IDs containing "402"
2026-01-16 17:29:54 -08:00
ajmallesh 9606ffcf70 fix: add universal billing error detection for router mode
- Add HTTP 402 and 'insufficient credits' patterns to error classification
- Detect provider billing errors in both exception and message content paths
2026-01-16 11:18:27 -08:00
ajmallesh cd04c7a6d2 feat: add model tracking and reporting across pipeline
- Track actual model name from router through audit logs, session.json, and query output
- Add router-utils.ts to resolve model names from ROUTER_DEFAULT env var
- Inject model info into final report's Executive Summary section
- Update documentation with supported providers, pricing, and config examples
- Update router-config.json with latest model versions (GPT-5.2, Gemini 2.5, etc.)
2026-01-15 18:30:19 -08:00
Arjun Malleswaran 20b5939e35 Feat/temporal (#52)
* refactor: modularize claude-executor and extract shared utilities

- Extract message handling into src/ai/message-handlers.ts with pure functions
- Extract output formatting into src/ai/output-formatters.ts
- Extract progress management into src/ai/progress-manager.ts
- Add audit-logger.ts with Null Object pattern for optional logging
- Add shared utilities: formatting.ts, file-io.ts, functional.ts
- Consolidate getPromptNameForAgent into src/types/agents.ts

* feat: add Claude Code custom commands for debug and review

* feat: add Temporal integration foundation (phase 1-2)

- Add Temporal SDK dependencies (@temporalio/client, worker, workflow, activity)
- Add shared types for pipeline state, metrics, and progress queries
- Add classifyErrorForTemporal() for retry behavior classification
- Add docker-compose for Temporal server with SQLite persistence

* feat: add Temporal activities for agent execution (phase 3)

- Add activities.ts with heartbeat loop, git checkpoint/rollback, and error classification
- Export runClaudePrompt, validateAgentOutput, ClaudePromptResult for Temporal use
- Track attempt number via Temporal Context for accurate audit logging
- Rollback git workspace before retry to ensure clean state

* feat: add Temporal workflow for 5-phase pipeline orchestration (phase 4)

* feat: add Temporal worker, client, and query tools (phase 5)

- Add worker.ts with workflow bundling and graceful shutdown
- Add client.ts CLI to start pipelines with progress polling
- Add query.ts CLI to inspect running workflow state
- Fix buffer overflow by truncating error messages and stack traces
- Skip git operations gracefully on non-git repositories
- Add kill.sh/start.sh dev scripts and Dockerfile.worker

* feat: fix Docker worker container setup

- Install uv instead of deprecated uvx package
- Add mcp-server and configs directories to container
- Mount target repo dynamically via TARGET_REPO env variable

* fix: add report assembly step to Temporal workflow

- Add assembleReportActivity to concatenate exploitation evidence files before report agent runs
- Call assembleFinalReport in workflow Phase 5 before runReportAgent
- Ensure deliverables directory exists before writing final report
- Simplify pipeline-testing report prompt to just prepend header

* refactor: consolidate Docker setup to root docker-compose.yml

* feat: improve Temporal client UX and env handling

- Change default to fire-and-forget (--wait flag to opt-in)
- Add splash screen and improve console output formatting
- Add .env to gitignore, remove from dockerignore for container access
- Add Taskfile for common development commands

* refactor: simplify session ID handling and improve Taskfile options

- Include hostname in workflow ID for better audit log organization
- Extract sanitizeHostname utility to audit/utils.ts for reuse
- Remove unused generateSessionLogPath and buildLogFilePath functions
- Simplify Taskfile with CONFIG/OUTPUT/CLEAN named parameters

* chore: add .env.example and simplify .gitignore

* docs: update README and CLAUDE.md for Temporal workflow usage

- Replace Docker CLI instructions with Task-based commands
- Add monitoring/stopping sections and workflow examples
- Document Temporal orchestration layer and troubleshooting
- Simplify file structure to key files overview

* refactor: replace Taskfile with bash CLI script

- Add shannon bash script with start/logs/query/stop/help commands
- Remove Taskfile.yml dependency (no longer requires Task installation)
- Update README.md and CLAUDE.md to use ./shannon commands
- Update client.ts output to show ./shannon commands

* docs: fix deliverable filename in README

* refactor: remove direct CLI and .shannon-store.json in favor of Temporal

- Delete src/shannon.ts direct CLI entry point (Temporal is now the only mode)
- Remove .shannon-store.json session lock (Temporal handles workflow deduplication)
- Remove broken scripts/export-metrics.js (imported non-existent function)
- Update package.json to remove main, start script, and bin entry
- Clean up CLAUDE.md and debug.md to remove obsolete references

* chore: remove licensing comments from prompt files to prevent leaking into actual prompts

* fix: resolve parallel workflow race conditions and retry logic bugs

- Fix save_deliverable race condition using closure pattern instead of global variable
- Fix error classification order so OutputValidationError matches before generic validation
- Fix ApplicationFailure re-classification bug by checking instanceof before re-throwing
- Add per-error-type retry limits (3 for output validation, 50 for billing)
- Add fast retry intervals for pipeline testing mode (10s vs 5min)
- Increase worker concurrent activities to 25 for parallel workflows

* refactor: pipeline vuln→exploit workflow for parallel execution

- Replace sync barrier between vuln/exploit phases with independent pipelines
- Each vuln type runs: vuln agent → queue check → conditional exploit
- Add checkExploitationQueue activity to skip exploits when no vulns found
- Use Promise.allSettled for graceful failure handling across pipelines
- Add PipelineSummary type for aggregated cost/duration/turns metrics

* fix: re-throw retryable errors in checkExploitationQueue

* fix: detect and retry on Claude Code spending cap errors

- Add spending cap pattern detection in detectApiError() with retryable error
- Add matching patterns to classifyErrorForTemporal() for proper Temporal retry
- Add defense-in-depth safeguard in runClaudePrompt() for $0 cost / low turn detection
- Add final sanity check in activities before declaring success

* fix: increase heartbeat timeout to prevent false worker-dead detection

Original 30s timeout was from POC spec assuming <5min activities. With
hour-long activities and multiple concurrent workflows sharing one worker,
resource contention causes event loop stalls exceeding 30s, triggering
false heartbeat timeouts. Increased to 10min (prod) and 5min (testing).

* fix: temporal db init

* fix: persist home dir

* feat: add per-workflow unified logging with ./shannon logs ID=<workflow-id>

- Add WorkflowLogger class for human-readable, per-workflow log files
- Create workflow.log in audit-logs/{workflowId}/ with phase, agent, tool, and LLM events
- Update ./shannon logs to require ID param and tail specific workflow log
- Add phase transition logging at workflow boundaries
- Include workflow completion summary with agent breakdown (duration, cost)
- Mount audit-logs volume in docker-compose for host access

* feat: configurable OUTPUT directory with auto-discovery

- Add OUTPUT=<path> option to write reports to custom directory
- Mount custom output dir as volume for container-to-host persistence
- Auto-discover workflow logs regardless of output path used
- Display host output path in workflow start message
- Add ASCII splash screen to ./shannon help

---------

Co-authored-by: ezl-keygraph <ezhil@keygraph.io>
2026-01-15 11:30:46 -08:00
Arjun Malleswaran 51e621d0d5 Feat/temporal (#46)
* refactor: modularize claude-executor and extract shared utilities

- Extract message handling into src/ai/message-handlers.ts with pure functions
- Extract output formatting into src/ai/output-formatters.ts
- Extract progress management into src/ai/progress-manager.ts
- Add audit-logger.ts with Null Object pattern for optional logging
- Add shared utilities: formatting.ts, file-io.ts, functional.ts
- Consolidate getPromptNameForAgent into src/types/agents.ts

* feat: add Claude Code custom commands for debug and review

* feat: add Temporal integration foundation (phase 1-2)

- Add Temporal SDK dependencies (@temporalio/client, worker, workflow, activity)
- Add shared types for pipeline state, metrics, and progress queries
- Add classifyErrorForTemporal() for retry behavior classification
- Add docker-compose for Temporal server with SQLite persistence

* feat: add Temporal activities for agent execution (phase 3)

- Add activities.ts with heartbeat loop, git checkpoint/rollback, and error classification
- Export runClaudePrompt, validateAgentOutput, ClaudePromptResult for Temporal use
- Track attempt number via Temporal Context for accurate audit logging
- Rollback git workspace before retry to ensure clean state

* feat: add Temporal workflow for 5-phase pipeline orchestration (phase 4)

* feat: add Temporal worker, client, and query tools (phase 5)

- Add worker.ts with workflow bundling and graceful shutdown
- Add client.ts CLI to start pipelines with progress polling
- Add query.ts CLI to inspect running workflow state
- Fix buffer overflow by truncating error messages and stack traces
- Skip git operations gracefully on non-git repositories
- Add kill.sh/start.sh dev scripts and Dockerfile.worker

* feat: fix Docker worker container setup

- Install uv instead of deprecated uvx package
- Add mcp-server and configs directories to container
- Mount target repo dynamically via TARGET_REPO env variable

* fix: add report assembly step to Temporal workflow

- Add assembleReportActivity to concatenate exploitation evidence files before report agent runs
- Call assembleFinalReport in workflow Phase 5 before runReportAgent
- Ensure deliverables directory exists before writing final report
- Simplify pipeline-testing report prompt to just prepend header

* refactor: consolidate Docker setup to root docker-compose.yml

* feat: improve Temporal client UX and env handling

- Change default to fire-and-forget (--wait flag to opt-in)
- Add splash screen and improve console output formatting
- Add .env to gitignore, remove from dockerignore for container access
- Add Taskfile for common development commands

* refactor: simplify session ID handling and improve Taskfile options

- Include hostname in workflow ID for better audit log organization
- Extract sanitizeHostname utility to audit/utils.ts for reuse
- Remove unused generateSessionLogPath and buildLogFilePath functions
- Simplify Taskfile with CONFIG/OUTPUT/CLEAN named parameters

* chore: add .env.example and simplify .gitignore

* docs: update README and CLAUDE.md for Temporal workflow usage

- Replace Docker CLI instructions with Task-based commands
- Add monitoring/stopping sections and workflow examples
- Document Temporal orchestration layer and troubleshooting
- Simplify file structure to key files overview

* refactor: replace Taskfile with bash CLI script

- Add shannon bash script with start/logs/query/stop/help commands
- Remove Taskfile.yml dependency (no longer requires Task installation)
- Update README.md and CLAUDE.md to use ./shannon commands
- Update client.ts output to show ./shannon commands

* docs: fix deliverable filename in README

* refactor: remove direct CLI and .shannon-store.json in favor of Temporal

- Delete src/shannon.ts direct CLI entry point (Temporal is now the only mode)
- Remove .shannon-store.json session lock (Temporal handles workflow deduplication)
- Remove broken scripts/export-metrics.js (imported non-existent function)
- Update package.json to remove main, start script, and bin entry
- Clean up CLAUDE.md and debug.md to remove obsolete references

* chore: remove licensing comments from prompt files to prevent leaking into actual prompts

* fix: resolve parallel workflow race conditions and retry logic bugs

- Fix save_deliverable race condition using closure pattern instead of global variable
- Fix error classification order so OutputValidationError matches before generic validation
- Fix ApplicationFailure re-classification bug by checking instanceof before re-throwing
- Add per-error-type retry limits (3 for output validation, 50 for billing)
- Add fast retry intervals for pipeline testing mode (10s vs 5min)
- Increase worker concurrent activities to 25 for parallel workflows

* refactor: pipeline vuln→exploit workflow for parallel execution

- Replace sync barrier between vuln/exploit phases with independent pipelines
- Each vuln type runs: vuln agent → queue check → conditional exploit
- Add checkExploitationQueue activity to skip exploits when no vulns found
- Use Promise.allSettled for graceful failure handling across pipelines
- Add PipelineSummary type for aggregated cost/duration/turns metrics

* fix: re-throw retryable errors in checkExploitationQueue

* fix: detect and retry on Claude Code spending cap errors

- Add spending cap pattern detection in detectApiError() with retryable error
- Add matching patterns to classifyErrorForTemporal() for proper Temporal retry
- Add defense-in-depth safeguard in runClaudePrompt() for $0 cost / low turn detection
- Add final sanity check in activities before declaring success

* fix: increase heartbeat timeout to prevent false worker-dead detection

Original 30s timeout was from POC spec assuming <5min activities. With
hour-long activities and multiple concurrent workflows sharing one worker,
resource contention causes event loop stalls exceeding 30s, triggering
false heartbeat timeouts. Increased to 10min (prod) and 5min (testing).

* fix: temporal db init

* fix: persist home dir

* feat: add per-workflow unified logging with ./shannon logs ID=<workflow-id>

- Add WorkflowLogger class for human-readable, per-workflow log files
- Create workflow.log in audit-logs/{workflowId}/ with phase, agent, tool, and LLM events
- Update ./shannon logs to require ID param and tail specific workflow log
- Add phase transition logging at workflow boundaries
- Include workflow completion summary with agent breakdown (duration, cost)
- Mount audit-logs volume in docker-compose for host access

---------

Co-authored-by: ezl-keygraph <ezhil@keygraph.io>
2026-01-15 10:36:11 -08:00
ezl-keygraph 45acb16711 refactor: remove orchestration layer (#45)
* refactor: remove orchestration layer and simplify CLI

Remove the complex orchestration layer including checkpoint management,
rollback/recovery commands, and session management commands. This
consolidates the execution logic directly in shannon.ts for a simpler
fire-and-forget execution model.

Changes:
- Remove checkpoint-manager.ts and rollback functionality
- Remove command-handler.ts and cli/prompts.ts
- Simplify session-manager.ts to just agent definitions
- Consolidate orchestration logic in shannon.ts
- Update CLAUDE.md documentation

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

* refactor: move session lock logic to shannon.ts, simplify session-manager

- Reduce session-manager.ts to only AGENTS, AGENT_ORDER, getParallelGroups()
- Move Session interface and lock file functions to shannon.ts
- Simplify Session to only: id, webUrl, repoPath, status, startedAt
- Remove unused types/session.ts

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

* refactor: use crypto.randomUUID() for session ID generation

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

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-12 22:58:17 +05:30
ezl-keygraph 8381198c41 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>
2026-01-08 23:50:42 +05:30
ezl-keygraph 3ac07a4718 feat: typescript migration (#40)
* chore: initialize TypeScript configuration and build setup

- Add tsconfig.json for root and mcp-server with strict type checking
- Install typescript and @types/node as devDependencies
- Add npm build script for TypeScript compilation
- Update main entrypoint to compiled dist/shannon.js
- Update Dockerfile to build TypeScript before running
- Configure output directory and module resolution for Node.js

* refactor: migrate codebase from JavaScript to TypeScript

- Convert all 37 JavaScript files to TypeScript (.js -> .ts)
- Add type definitions in src/types/ for agents, config, errors, session
- Update mcp-server with proper TypeScript types
- Move entry point from shannon.mjs to src/shannon.ts
- Update tsconfig.json with rootDir: "./src" for cleaner dist output
- Update Dockerfile to build TypeScript before runtime
- Update package.json paths to use compiled dist/shannon.js

No runtime behavior changes - pure type safety migration.

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

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

* docs: update CLI references from ./shannon.mjs to shannon

- Update help text in src/cli/ui.ts
- Update usage examples in src/cli/command-handler.ts
- Update setup message in src/shannon.ts
- Update CLAUDE.md documentation with TypeScript file structure
- Replace all ./shannon.mjs references with shannon command

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

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

* chore: remove unnecessary eslint-disable comments

ESLint is not configured in this project, making these comments redundant.

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

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

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-08 00:18:25 +05:30
ajmallesh 39766d0afc fix: support absolute config paths in checkpoint manager
Co-Authored-By: Khaushik-keygraph <khaushik.contractor@keygraph.io>
2025-12-15 10:34:25 -08:00
Khaushik-keygraph ad0d1a04e9 chore: added flag additions for minimizing logs 2025-12-09 23:59:12 +05:30
ajmallesh 7c2edeb4c0 chore: change license to AGPL-3.0 2025-11-26 18:45:36 -08:00
ajmallesh e4eb59870a chore: add MPL license comments 2025-11-13 16:55:13 +05:30
ajmallesh 34850477a2 refactor: update injection display name and add max tokens docs
- Change agent prefix from [SQLi/Cmd] to [Injection] to reflect expanded scope
- Add README documentation for CLAUDE_CODE_MAX_OUTPUT_TOKENS environment variable

This update aligns the display naming with the expanded injection analysis scope
that now covers SQLi, Command Injection, LFI/RFI, SSTI, Path Traversal, and
Insecure Deserialization vulnerabilities.

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

Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-03 10:21:17 -08:00
ajmallesh cc36fe933d fix: err handling for claude code session limit 2025-10-30 10:28:35 -07:00
ajmallesh a099500d9b Revert "feat: improve audit log naming with timestamp and app context"
This reverts the timestamp-based naming scheme that was causing audit log
fragmentation. Each agent execution was creating a new folder because the
timestamp kept changing.

Reverting back to simple, stable naming: {hostname}_{sessionId}

This ensures ONE folder per session, preventing the bug where multiple
folders were created for the same session.

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

Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-27 13:30:25 -07:00
ajmallesh f0b8c3aa6e fix: use session's original createdAt instead of current time
Fixed bug where audit system would create duplicate folders for the same
session because it was using current time instead of the session's original
createdAt timestamp.

Bug behavior:
- Session created at T1 → folder: {T1}_app_host_id/
- Audit re-initialized at T2 → NEW folder: {T2}_app_host_id/
- Result: 2 folders per session with same ID but different timestamps

Root cause:
- metrics-tracker.js:65 was calling formatTimestamp() (current time)
- Should use sessionMetadata.createdAt (original creation time)

Impact: Each running benchmark was creating 2 audit log folders instead of 1

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

Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-27 10:55:53 -07:00
ajmallesh 258830b030 feat: improve audit log naming with timestamp and app context
Enhances audit log directory naming from `{hostname}_{uuid}` to
`{timestamp}_{appName}_{hostname}_{shortId}` for better discoverability
and benchmarking analysis.

Changes:
- Add extractAppName() helper to extract app name from config files
- Add smart fallback: use port number for localhost without config
- Update generateSessionIdentifier() to include timestamp prefix
- Shorten session ID to first 8 characters for readability

Examples:
- With config: 20251025T193847Z_myapp_localhost_efc60ee0/
- Without config: 20251025T193913Z_8080_localhost_d47e3bfd/
- Remote: 20251024T004401Z_noconfig_example-com_d47e3bfd/

Benefits:
- Chronologically sortable audit logs
- Instant app identification in directory listings
- Efficient filtering for benchmarking queries
- Non-breaking: existing logs keep their names

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-27 10:14:19 -07:00
ajmallesh f40f52f118 fix: enable Playwright MCP browser automation in Docker containers
Resolves Playwright browser installation failures in Docker by using Wolfi's
system Chromium instead of downloading Playwright's bundled browsers at runtime.

## Problem
When running in Docker, agents attempted to install browsers via `browser_install`
tool, which failed due to:
- Permission issues (non-root user couldn't install system dependencies)
- npx @playwright/mcp spawns with its own Playwright dependency separate from
  global installations
- Playwright's bundled browsers require runtime download (~280MB) and glibc deps
- Environment variables alone (PLAYWRIGHT_BROWSERS_PATH) weren't sufficient

## Solution
**Dockerfile changes:**
- Use Wolfi's native `chromium` package (guaranteed compatible, already installed)
- Remove Playwright browser installation step (saves ~280MB and build time)
- Add explicit `SHANNON_DOCKER=true` environment variable for reliable detection
- Set PLAYWRIGHT_CHROMIUM_EXECUTABLE_PATH to point to system Chromium

**Code changes (claude-executor.js):**
- Detect Docker via `process.env.SHANNON_DOCKER` (more reliable than /.dockerenv)
- Conditionally add `--executable-path /usr/bin/chromium-browser` CLI arg for Docker
- Local: Use Playwright's bundled browsers (downloaded to ~/Library/Caches/)
- Docker: Use system Chromium with no runtime downloads

## Research Findings
- @playwright/mcp has separate playwright-core dependency (v1.56.0-alpha)
- MCP server spawned via npx doesn't inherit browser binaries from global install
- --executable-path CLI argument is required (env vars insufficient)
- /.dockerenv file is unreliable (missing in BuildKit, K8s, can be spoofed)

## Testing
 Docker: All 5 parallel agents successfully navigate, screenshot, create deliverables
 Local: All 5 parallel agents successfully navigate, screenshot, create deliverables
 No browser_install calls, no permission errors
 Image size reduced by ~280MB

Fixes #docker-playwright-browser-issues

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-23 17:56:19 -07:00
ajmallesh f13c7421f4 refactor: remove ~500 lines of dead code and consolidate duplicates
Comprehensive codebase cleanup based on parallel agent analysis and automated
dead code detection (knip, depcheck). Reduces codebase by ~10% with zero
functional changes.

## Phase 1: Obsolete MCP Setup Removal (~82 lines)
- Delete setupMCP() and cleanupMCP() functions from environment.js
- Remove all calls to cleanupMCP() (8 instances across 3 files)
- Migrate from claude CLI to SDK's mcpServers option
- Remove --log flag (obsolete logging system)

## Phase 2: Dead Code Removal (~317 lines)
- Delete src/utils/logger.js entirely (127 lines, superseded by audit system)
- Remove handleConfigError() and handleError() from error-handling.js
- Remove isToolAvailable() from tool-checker.js
- Remove 5 dead methods from audit-session.js (logSessionFailure, logMessage,
  markRolledBack, updateValidation, getValidation)
- Remove 6 wrapper methods from audit/logger.js (all callers use logEvent directly)
- Remove formatCost(), updateMessage(), compose() utilities (unused)

## Phase 3: Consolidation (~195 lines)
- Extract SessionMutex to src/utils/concurrency.js (was duplicated in 2 files)
- Consolidate formatDuration to src/audit/utils.js (was in 3 files)
- Extract readline prompts to src/cli/prompts.js (was duplicated in 2 files)
- Create validator factories in constants.js (reduce 72 lines to 30)

## Impact
- Total reduction: 488 lines (20 files modified, 2 created, 1 deleted)
- Codebase: ~4,900 → ~4,400 LOC (10% reduction)
- Zero functional changes, all tests pass
- Improved maintainability and DRY compliance

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-23 17:01:17 -07:00
ajmallesh 9be2e71ff2 refactor: deduplicate prompt templates with shared content system
Implemented @include() directive system to eliminate ~800 lines of duplicated content across 10 specialist prompt files. All prompt-related content now consolidated under prompts/ directory for better maintainability.

Changes:
- Added processIncludes() to prompt-manager.js for generic @include() support
- Created prompts/shared/ with 5 reusable template files
- Refactored all 10 specialist prompts to use @include() for common sections
- Moved login_instructions.txt to prompts/shared/ (deleted login_resources/)
- Updated CLAUDE.md to reflect new structure

Impact: -137 net lines, zero breaking changes, infinitely scalable for future shared content.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-23 16:19:25 -07:00
ajmallesh 2966157596 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.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-23 12:46:51 -07:00
ajmallesh eae0b8d654 feat: migrate to use MCP tools instead of helper scripts 2025-10-23 11:56:47 -07:00
ajmallesh cfe8dc8bc8 fix: critical bug - exploitation phase was always skipped
ROOT CAUSE:
- Exploitation phase checked session.validationResults to determine eligibility
- validationResults field was removed during audit system refactor
- Field never existed in session schema, so all exploits were skipped

THE FIX:
- Exploitation phase now validates queue files directly when checking eligibility
- Reads exploitation_queue.json and checks if vulnerabilities array is non-empty
- No need to store validation results - just re-validate on demand

CHANGES:
1. runParallelExploit() now calls safeValidateQueueAndDeliverable() directly
2. Removed validationResults parameter from markAgentCompleted()
3. Simplified calculateVulnerabilityAnalysisSummary() - no longer needs validation data
4. Simplified calculateExploitationSummary() - no longer needs validation data

IMPACT:
- Exploitation agents will now run when vulnerabilities are found
- Queue files are the single source of truth for eligibility
- Simpler architecture - no duplicate state storage

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-22 17:41:41 -07:00
ajmallesh 255956d113 chore: remove run-metadata.json functionality
Reasoning:
- Pollutes target repo with run-metadata.json
- Redundant with audit system (session.json has all metadata)
- Less useful than comprehensive audit logs
- Target repos should stay clean - only deliverables belong there

All debugging info now lives in audit-logs/{hostname}_{sessionId}/session.json

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-22 16:19:40 -07:00
ajmallesh 27334a4dd6 feat: implement unified audit system v3.0 with crash-safety and self-healing
## Unified Audit System (v3.0)
- Implemented crash-safe, append-only logging to audit-logs/{hostname}_{sessionId}/
- Added session.json with comprehensive metrics (timing, cost, attempts)
- Agent execution logs with turn-by-turn detail
- Prompt snapshots saved to audit-logs/.../prompts/{agent}.md
- SessionMutex prevents race conditions during parallel execution
- Self-healing reconciliation before every CLI command

## Session Metadata Standardization
- Fixed critical bug: standardized on 'id' field (not 'sessionId') throughout codebase
- Updated: shannon.mjs (recon, report), src/phases/pre-recon.js
- Added validation in AuditSession to fail fast on incorrect field usage
- JavaScript shorthand syntax was causing wrong field names

## Schema Improvements
- session.json: Added cost_usd per phase, removed redundant final_cost_usd
- Renamed 'percentage' -> 'duration_percentage' for clarity
- Simplified agent metrics to single total_cost_usd field
- Removed unused validation object from schema

## Legacy System Removal
- Removed savePromptSnapshot() - prompts now only saved by audit system
- Removed target repo pollution (prompt-snapshots/ no longer created)
- Single source of truth: audit-logs/{hostname}_{sessionId}/prompts/

## Export Script Simplification
- Removed JSON export mode (session.json already exists)
- CSV-only export with clean columns: agent, phase, status, attempts, duration_ms, cost_usd
- Tested on real session data

## Documentation
- Updated CLAUDE.md with audit system architecture
- Added .gitignore entry for audit-logs/

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-22 16:09:08 -07:00
ajmallesh a9e00ca19f chore: remove screenshot saving from Playwright MCP instances
Remove unnecessary screenshot storage to reduce file I/O and disk usage:
- Removed screenshot directory creation
- Removed --output-dir flag from Playwright MCP setup
- Agents can still take screenshots, but they won't persist to disk

Screenshots were not being used by any part of Shannon for analysis
or reporting, making their storage unnecessary overhead.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-22 12:15:47 -07:00
ajmallesh e1237416f5 chore: remove permanent deliverables copying to Documents folder
Simplified deliverable management by removing automatic copying to ~/Documents/pentest-deliverables/. All deliverables now remain only in <target-repo>/deliverables/, eliminating file duplication and improving UX.

Changes:
- Removed savePermanentDeliverables() function from src/setup/deliverables.js
- Removed function call and related console output from shannon.mjs
- Removed unused 'os' import from deliverables.js

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-10-22 12:11:48 -07:00
ajmallesh ac682b0172 chore: save deliverable script decoupling deliverable creation from the actual content 2025-10-22 11:31:58 -07:00
ajmallesh 66c549f3b7 chore: upgrade model from Sonnet 4 -> Sonnet 4.5 2025-10-21 16:34:56 -07:00
Khaushik-keygraph e0ff1453a5 chore: optimized logging 2025-10-17 13:59:34 +05:30
Khaushik-keygraph 46a30fd8c9 chore: added logging 2025-10-17 13:52:13 +05:30
ajmallesh 8f52722d56 Initial commit
Co-Authored-By: Nellie Mullane <nellie@keygraph.io>
2025-10-03 19:35:08 -07:00