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.
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.
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.
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
- Replace single-call "Write to deliverables/" pattern with multi-step
Write + Edit chunked writing across all 12 agent prompts
- Standardize section name to "CHUNKED WRITING (MANDATORY)" for
vuln, exploit, pre-recon, and recon agents
- Prevents agents from hitting 32K output token limit when generating
large analysis reports and exploitation evidence
* 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
Podman doesn't support the `host-gateway` special value in extra_hosts,
which causes container startup failures on macOS with Podman Desktop.
Changes:
- Add docker-compose.docker.yml with extra_hosts override for Docker
- Update shannon script to detect Podman via `command -v podman`
- Skip extra_hosts override when Podman is detected
This ensures:
- Docker users (Linux): Get host.docker.internal working automatically
- Podman users (macOS): Base config works without modification
Co-authored-by: ajmallesh <ajmallesh@gmail.com>
Deliverables saved by agents were never committed to git because
git identity was not configured in the Docker container. This left
them as untracked files, which git clean -fd destroyed whenever
another agent's retry triggered a workspace rollback. Moves git
config after ENV HOME=/tmp so the config is written to /tmp/.gitconfig
where git actually looks at runtime.
* 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
Pre-create the deliverables directory with proper permissions on the
host before starting containers, and surface permission errors instead
of silently swallowing them in save_deliverable.
* feat: use static repos/ folder mount instead of dynamic TARGET_REPO
Replace dynamic per-run TARGET_REPO bind mount with a static ./repos:/repos
mount. Users place target repositories under ./repos/ and reference them by
folder name. This fixes stale mounts when switching targets and enables
running multiple scans concurrently against different repos.
* feat: mount configs directory into worker container
* docs: add instructions for repos and configs directory setup
The container runs as non-root user 'pentest' (UID 1001), but bind-mounted
directories are owned by the host user. Added chmod 777 after mkdir to ensure
the container can write to these directories.
- Add HTTP 402 and 'insufficient credits' patterns to error classification
- Detect provider billing errors in both exception and message content paths
- 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.)
- Add DeepSeek provider config with Together.ai and official API support
- Configure deepseek and enhancetool transformers for reliable tool calling
- Add DEEPSEEK_API_KEY and DEEPSEEK_API_BASE env vars to docker-compose
- Update shannon CLI to recognize DeepSeek as valid router provider
- Add ROUTER=true flag to route requests through claude-code-router
- Add router service to docker-compose with profile-based activation
- Support OpenAI (gpt-4o) and Google Gemini (gemini-2.5-pro) as alternatives
- Add router-config.json with provider configuration template
- Update .env.example with provider API key options
- Document router mode limitations (cost tracking shows $0)
* 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>
* 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>
* 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>
* 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>
* 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>
Update GitHub Issues and Discussions links to use correct
organization name (KeygraphHQ instead of keygraph).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
