Target

The raw arguments are: $ARGUMENTS

Parse the arguments as follows:

0. Default LOOP_MODE=true. If arguments contain --no-loop: strip it from the arguments and set LOOP_MODE=false. The --loop flag is accepted for backwards compatibility but is a no-op (loop is already the default).

0b. Default FIX_MODE=true. 0c. If arguments contain --scan-only: strip it from the arguments and set FIX_MODE=false. 0d. If arguments contain --fix: strip it from the arguments and set FIX_MODE=true. The remaining arguments are parsed normally below. 0e. If arguments contain --autonomous: strip it from the arguments, set AUTONOMOUS_MODE=true, and force FIX_MODE=true (canary-first + confidence-gated). 0f. If arguments contain --approve: strip it from the arguments and set APPROVE_MODE=true. When this flag is set, Fixer agents run in mode: "default" (user reviews and approves each edit). When not set, APPROVE_MODE=false and Fixers run autonomously. 0g. If arguments contain --deps: strip it and set DEP_SCAN=true. Dependency scanning runs package manager audit tools and checks if vulnerable APIs are actually called in the codebase. 0h. If arguments contain --threat-model: strip it and set THREAT_MODEL_MODE=true. Generates a STRIDE threat model at .bug-hunter/threat-model.md if one doesn't exist, then feeds it to Recon + Hunter for targeted security analysis. 0i. If arguments contain --dry-run: strip it and set DRY_RUN_MODE=true. Forces FIX_MODE=true. In dry-run mode, Phase 2 builds the fix plan and the Fixer reads code and outputs planned changes as unified diff previews, but no file edits, git commits, or lock acquisition occur. Produces fix-report.json with "dry_run": true. 0j. If arguments contain --preview: strip it, set DRY_RUN_MODE=true, and force FIX_MODE=true. Treat it as a memorable alias for --fix --dry-run. 0k. If arguments contain --plan-only: strip it and set PLAN_ONLY_MODE=true. The pipeline still scans, verifies, and builds fix-strategy.json + fix-plan.json, but it stops before the Fixer edits code. 0l. If arguments contain --plan: strip it and set PLAN_ONLY_MODE=true. Treat it as a memorable alias for --plan-only. 0m. If arguments contain --review-pr: strip it and treat it as --pr current. 0n. If arguments contain --pr with no selector after it, treat it as --pr current. 0o. If arguments contain --last-pr: strip it and treat it as --pr recent. 0p. If arguments contain --review: strip it and set FIX_MODE=false. Treat it as a memorable alias for --scan-only. 0q. If arguments contain --safe: strip it, set FIX_MODE=true, and set APPROVE_MODE=true. Treat it as a memorable alias for --fix --approve. 0r. If arguments contain --pr-security: strip it, set PR_SECURITY_MODE=true, force DEP_SCAN=true, force THREAT_MODEL_MODE=true, force FIX_MODE=false, and if no explicit --pr selector was provided treat it as --pr current. 0s. If arguments contain --security-review: strip it, set SECURITY_REVIEW_MODE=true, force DEP_SCAN=true, force THREAT_MODEL_MODE=true, and force FIX_MODE=false. 0t. If arguments contain --validate-security: strip it and set VALIDATE_SECURITY_MODE=true.

1. If arguments contain --pr <selector>: this is PR review mode.

   • Valid selectors: current, recent, or a PR number like 123.
   • If --base <base-branch> is present, pass it through for current-branch git fallback.
   • Run:

     node "$SKILL_DIR/scripts/pr-scope.cjs" resolve "<selector>" --repo-root "$PWD" [--base <base-branch>]
     

   • If it fails, report the error to the user and stop.
   • Save the JSON result to .bug-hunter/pr-scope.json for later reporting.
   • Use changedFiles from the JSON output as the scan target (scan full file contents, not just the diff).

2. If arguments contain --staged: this is staged file mode.

   • Run git diff --cached --name-only using the Bash tool to get the list of staged files.
   • If the command fails, report the error to the user and stop.
   • If no files are staged, tell the user there are no staged changes to scan and stop.
   • The scan target is the list of staged files (scan their full contents, not just the diff).

3. If arguments contain -b <branch>: this is branch diff mode.

   • Extract the branch name after -b.
   • If --base <base-branch> is also present, use that as the base branch. Otherwise default to main.
   • Run git diff --name-only <base>...<branch> using the Bash tool to get the list of changed files.
   • If the command fails (e.g. branch not found), report the error to the user and stop.
   • If no files changed, tell the user there are no changes to scan and stop.
   • The scan target is the list of changed files (scan their full contents, not just the diff).

4. If arguments do NOT contain --pr, -b, or --staged: treat the entire argument string as a path target (file or directory). If empty, scan the current working directory.

After resolving the file list (for modes 1, 2, and 3), filter out non-source files:

Remove any files matching these patterns — they are not scannable source code:

• Docs/text: *.md, *.txt, *.rst, *.adoc
• Config: *.json, *.yaml, *.yml, *.toml, *.ini, *.cfg, .env*, .gitignore, .editorconfig, .prettierrc*, .eslintrc*, tsconfig.json, jest.config.*, vitest.config.*, webpack.config.*, vite.config.*, next.config.*, tailwind.config.*
• Lockfiles: *.lock, *.sum
• Minified/maps: *.min.js, *.min.css, *.map
• Assets: *.svg, *.png, *.jpg, *.gif, *.ico, *.woff*, *.ttf, *.eot
• Project meta: LICENSE, CHANGELOG*, CONTRIBUTING*, CODE_OF_CONDUCT*, Makefile, Dockerfile, docker-compose*, Procfile
• Vendor dirs: node_modules/, vendor/, dist/, build/, .next/, __pycache__/, .venv/

If after filtering there are zero source files left, tell the user: "No scannable source files found — only config/docs/assets were changed." and stop.

Context Budget

FILE_BUDGET is computed by the triage script (Step 1), not by Recon. The triage script samples 30 files from the codebase, computes average line count, and derives:

avg_tokens_per_file = average_lines_per_file * 4
FILE_BUDGET = floor(150000 / avg_tokens_per_file)   # capped at 60, floored at 10

Triage also determines the strategy directly, so Step 3 just reads the triage output — no circular dependency.

Then determine partitioning:

| Total source files | Strategy | Hunters | Skeptics | |--------------------|----------|---------|----------| | 1 | Single-file mode | 1 general | 1 | | 2-10 | Small mode | 1 general | 1 | | 11 to FILE_BUDGET | Parallel mode (hybrid) | 1 deep Hunter (+ optional 2 read-only triage Hunters) | 1-2 by directory | | FILE_BUDGET+1 to FILE_BUDGET2 | Extended mode | Sequential chunked Hunters | 1-2 by directory | | FILE_BUDGET2+1 to FILE_BUDGET3 | Scaled mode | Sequential chunked Hunters with resume state | 1-2 by directory | | > FILE_BUDGET3 | Large-codebase mode + Loop | Domain-scoped pipelines + boundary audits | Per-domain 1-2 |

If triage was not run (e.g., Recon was called directly without the orchestrator), use the default FILE_BUDGET of 40.

File partitioning rules (Extended/Scaled modes):

• Service-aware partitioning (preferred): If Recon detected multiple service boundaries (monorepo), partition by service.
• Risk-tier partitioning (fallback): process CRITICAL then HIGH then MEDIUM then LOW.
• Keep chunk size small (recommended 20-40 files) to avoid context compaction issues.
• Persist chunk progress in .bug-hunter/state.json so restarts do not re-scan done chunks.
• Test files (CONTEXT-ONLY) are included only when needed for intent.

If the triage output shows needsLoop: true and LOOP_MODE=false (user passed --no-loop), warn the user: "This codebase has [N] source files (FILE_BUDGET: [B]). Single-pass mode will only cover a subset. Loop mode is recommended for thorough coverage (remove --no-loop to enable). Large codebases use domain-scoped auditing — see modes/large-codebase.md."

Execution Steps

Step 0: Preflight checks

Before doing anything else, verify the environment:

1. Resolve skill directory: Determine SKILL_DIR dynamically.

   • Preferred: derive it from the absolute path of the current SKILL.md (dirname of this file).
   • Fallback probe order: $HOME/.agents/skills/bug-hunter, $HOME/.claude/skills/bug-hunter, $HOME/.codex/skills/bug-hunter.
   • Use this path for ALL Read tool calls and shell commands.

2. Verify skill files exist: Run ls "$SKILL_DIR/skills/hunter/SKILL.md" via Bash. If this fails, stop and tell the user: "Bug Hunter skill files not found. Reinstall the skill and retry."

3. Node.js available: Run node --version via Bash. If it fails, stop and tell the user: "Node.js is required for doc verification. Please install Node.js to continue."

3b. Create output directory: bash mkdir -p .bug-hunter/payloads .bug-hunter/domains This directory stores all pipeline artifacts. Add .bug-hunter/ to your project's .gitignore.

4. Doc lookup availability (optional, non-blocking): Run a quick smoke test:

   node "$SKILL_DIR/scripts/doc-lookup.cjs" search "express" "middleware"
   

   • If it returns results, set DOC_LOOKUP_AVAILABLE=true.
   • If it fails, try the fallback: node "$SKILL_DIR/scripts/context7-api.cjs" search "express" "middleware"
   • If both fail, warn the user and set DOC_LOOKUP_AVAILABLE=false.
   • Missing CONTEXT7_API_KEY must NOT block execution; anonymous lookups may still work.

5. Verify helper scripts exist:

   ls "$SKILL_DIR/scripts/run-bug-hunter.cjs" "$SKILL_DIR/scripts/bug-hunter-state.cjs" "$SKILL_DIR/scripts/delta-mode.cjs" "$SKILL_DIR/scripts/payload-guard.cjs" "$SKILL_DIR/scripts/fix-lock.cjs" "$SKILL_DIR/scripts/triage.cjs" "$SKILL_DIR/scripts/doc-lookup.cjs" "$SKILL_DIR/scripts/pr-scope.cjs"
   

   If any are missing, stop and tell the user to update/reinstall the skill. Note: code-index.cjs is optional — enables cross-domain dependency analysis for boundary audits in large-codebase mode, but the pipeline works fully without it. Note: context7-api.cjs is kept as a fallback — doc-lookup.cjs is the primary doc verification script. Note: worktree-harvest.cjs is optional — enables worktree-isolated Fixer dispatch for subagent/teams backends. Without it, Fixers edit directly on the fix branch (still safe via single-writer lock + auto-revert).

5b. Check Context Hub CLI (recommended, non-blocking):

chub --help 2>/dev/null && chub update 2>/dev/null

• If chub is available, set CHUB_AVAILABLE=true. Report: ✓ Context Hub available — using curated docs for verification.
• If chub is NOT installed, set CHUB_AVAILABLE=false. Warn the user visibly:

  ⚠️ Context Hub (chub) is not installed. Doc verification will fall back to Context7 API,
     which has broader coverage but less curated results.
  
     For better doc verification accuracy, install Context Hub:
       npm install -g @aisuite/chub
  
     More info: https://github.com/andrewyng/context-hub
  

• Do NOT block the pipeline — Context7 fallback works, just with less curated results.

6. Select orchestration backend (cross-CLI portability):

   Detect which dispatch tools are available in your runtime. Use the FIRST that works:

   Option A — subagent tool (Pi agent, preferred for parallel):

   • Test: call subagent({ action: "list" }). If it returns without error, this backend works.
   • Set AGENT_BACKEND = "subagent"
   • Dispatch pattern for each phase:

     subagent({
       agent: "<role>-agent",
       task: "<filled subagent-wrapper template with prompt content + assignment>",
       output: ".bug-hunter/<phase>-output.md"
     })
     

   • Read the output file after the subagent completes.

   Option B — teams tool (Pi agent teams):

   • Test: does the teams tool exist in your available tools?
   • Set AGENT_BACKEND = "teams"
   • Dispatch pattern:

     teams({
       tasks: [{ text: "<filled subagent-wrapper template>" }],
       maxTeammates: 1
     })
     

   Option C — interactive_shell (Claude Code, Codex, other CLI agents):

   • Set AGENT_BACKEND = "interactive_shell"
   • Dispatch pattern:

     interactive_shell({
       command: 'pi "<task prompt>"',
       mode: "dispatch"
     })
     

   Option D — local-sequential (default — always works):

   • Set AGENT_BACKEND = "local-sequential"
   • Read SKILL_DIR/modes/local-sequential.md for full instructions.
   • You run all phases (Recon, Hunter, Skeptic, Referee) yourself, sequentially, within your own context window.
   • Write phase outputs to .bug-hunter/ files between phases.

   IMPORTANT: local-sequential is NOT a degraded mode. It is the expected default for most environments and the skill works fully in this mode. Subagent dispatch is an optimization for large codebases, not a requirement.

   Rules:

   • Use exactly ONE backend for the whole run.
   • If a remote backend launch fails, fall back to the next option.
   • If all remote backends fail, use local-sequential and continue.

Step 1: Parse arguments, resolve target, and run triage

Follow the rules in the Target section above. If in PR review, branch diff, or staged mode, run the appropriate resolver command now, collect the file list, and apply the filter.

Report to the user:

• Mode (full project / directory / file / PR review / branch diff / staged)
• Number of source files to scan (after filtering)
• Number of files filtered out

Then run triage (zero-token strategy decision):

Run the triage script AFTER resolving the target. This is a pure Node.js filesystem scan — no tokens consumed, runs in <2 seconds even on 2,000+ file repos.

node "$SKILL_DIR/scripts/triage.cjs" scan "<TARGET_PATH>" --output .bug-hunter/triage.json

Then read .bug-hunter/triage.json. It contains:

• strategy: which mode to use ("single-file", "small", "parallel", "extended", "scaled", "large-codebase")
• modeFile: which mode file to read
• fileBudget: computed from actual file sizes (sampled), not a guess
• totalFiles / scannableFiles: exact count
• domains: directory-level risk classification (CRITICAL/HIGH/MEDIUM/LOW/CONTEXT-ONLY)
• riskMap: file-level classification (only present when ≤200 files)
• domainFileLists: per-domain file lists (only present for large-codebase strategy)
• scanOrder: priority-ordered list for Hunters
• tokenEstimate: cost estimates for each pipeline phase
• needsLoop: whether loop mode is needed for full coverage (loop is on by default; this indicates --no-loop would cause incomplete coverage)

Set these variables from the triage output:

STRATEGY = triage.strategy
FILE_BUDGET = triage.fileBudget
TOTAL_FILES = triage.totalFiles
SCANNABLE_FILES = triage.scannableFiles
NEEDS_LOOP = triage.needsLoop

Report to the user:

Triage: [TOTAL_FILES] source files | FILE_BUDGET: [FILE_BUDGET] | Strategy: [STRATEGY]
Domains: [N] CRITICAL, [N] HIGH, [N] MEDIUM, [N] LOW
Token estimate: ~[N] tokens for full pipeline

If triage says needsLoop: true and LOOP_MODE=false (user passed --no-loop), warn:

⚠️ This codebase has [N] source files (FILE_BUDGET: [B]).
Single-pass mode will only cover a subset. Remove `--no-loop` to enable iterative coverage.
Proceeding with partial scan — highest-priority queued files only.

Triage replaces Recon's FILE_BUDGET computation. Recon still runs for tech stack identification and pattern-based analysis, but it no longer needs to count files or compute the context budget — triage already did that, for free.

Step 1b: Generate threat model (if --threat-model)

If THREAT_MODEL_MODE=true:

1. Read the bundled local skill SKILL_DIR/skills/threat-model-generation/SKILL.md before generating the threat model. This keeps the enterprise security pack end-to-end connected to the main Bug Hunter flow.

2. Use the bundled skill's Bug Hunter-native artifact conventions (.bug-hunter/threat-model.md, .bug-hunter/security-config.json).

3. Check if .bug-hunter/threat-model.md already exists.

   • If it exists and was modified within the last 90 days: use it as-is. Set THREAT_MODEL_AVAILABLE=true.
   • If it exists but is >90 days old: warn user ("Threat model is N days old — regenerating"), regenerate.
   • If it doesn't exist: generate it.

4. To generate:

   • Read $SKILL_DIR/skills/threat-model-generation/SKILL.md.
   • Dispatch the threat model generation agent (or execute locally if local-sequential).
   • Input: triage.json (if available) for file structure, or Glob-based discovery.
   • Wait for .bug-hunter/threat-model.md to be written.

5. Set THREAT_MODEL_AVAILABLE=true.

If THREAT_MODEL_MODE=false but .bug-hunter/threat-model.md exists:

• Load it anyway — free context. Set THREAT_MODEL_AVAILABLE=true.
• Report: "Existing threat model found — loading for enhanced security analysis."

Step 1c: Dependency scan (if --deps)

If DEP_SCAN=true or SECURITY_REVIEW_MODE=true or PR_SECURITY_MODE=true:

• Read the bundled local skill SKILL_DIR/skills/security-review/SKILL.md when running the broader enterprise security workflow.

If DEP_SCAN=true:

node "$SKILL_DIR/scripts/dep-scan.cjs" --target "<TARGET_PATH>" --output .bug-hunter/dep-findings.json

Report to user:

Dependencies: [N] HIGH/CRITICAL CVEs found | [R] reachable, [P] potentially reachable, [U] not reachable

If .bug-hunter/dep-findings.json exists with REACHABLE findings, include them in Hunter context as "Known Vulnerable Dependencies" — Hunter should verify if vulnerable APIs are called in scanned source files.

Step 2: Read prompt files on demand (context efficiency)

Security-pack routing:

• If PR_SECURITY_MODE=true, read SKILL_DIR/skills/commit-security-scan/SKILL.md before the normal PR-review scan.
• If SECURITY_REVIEW_MODE=true, read SKILL_DIR/skills/security-review/SKILL.md before the broader security audit flow.
• If VALIDATE_SECURITY_MODE=true, read SKILL_DIR/skills/vulnerability-validation/SKILL.md before finalizing confirmed security findings.

MANDATORY: You MUST read prompt files using the Read tool before passing them to subagents or executing them yourself. Do NOT skip this or act from memory. Use the absolute SKILL_DIR path resolved in Step 0.

Load only what you need for each phase — do NOT read all files upfront:

| Phase | Read These Files | |-------|-----------------| | PR security review | skills/commit-security-scan/SKILL.md (if PR_SECURITY_MODE=true or the user asks for PR-focused security review) | | Security review | skills/security-review/SKILL.md (if SECURITY_REVIEW_MODE=true or the user asks for an enterprise/full security audit) | | Threat Model (Step 1b) | skills/threat-model-generation/SKILL.md (only if THREAT_MODEL_MODE=true) | | Recon (Step 4) | skills/recon/SKILL.md (skip for single-file mode) | | Hunters (Step 5) | skills/hunter/SKILL.md + prompts/examples/hunter-examples.md | | Security validation | skills/vulnerability-validation/SKILL.md (if VALIDATE_SECURITY_MODE=true or confirmed security findings need exploitability validation) | | Skeptics (Step 6) | skills/skeptic/SKILL.md + prompts/examples/skeptic-examples.md | | Referee (Step 7) | skills/referee/SKILL.md | | Fixers (Phase 2) | skills/fixer/SKILL.md (only if FIX_MODE=true) |

Concrete examples for each backend:

Example A: local-sequential (most common)

# Phase B — launching Hunter yourself
# 1. Read the skill file:
read({ path: "$SKILL_DIR/skills/hunter/SKILL.md" })

# 2. You now have the Hunter's full instructions. Execute them yourself:
#    - Read each file in risk-map order using the Read tool
#    - Apply the security checklist sweep
#    - Write each finding in BUG-N format

# 3. Write your canonical findings artifact to disk:
write({ path: ".bug-hunter/findings.json", content: "<your findings json>" })

Example B: subagent dispatch

# Phase B — launching Hunter via subagent
# 1. Read the skill:
read({ path: "$SKILL_DIR/skills/hunter/SKILL.md" })
# 2. Read the wrapper template:
read({ path: "$SKILL_DIR/templates/subagent-wrapper.md" })
# 3. Fill the template with:
#    - {ROLE_NAME} = "hunter"
#    - {ROLE_DESCRIPTION} = "Bug Hunter — find behavioral bugs in source code"
#    - {PROMPT_CONTENT} = <full contents of hunter.md>
#    - {TARGET_DESCRIPTION} = "FindCoffee monorepo backend services"
#    - {FILE_LIST} = <files from Recon risk map, CRITICAL first>
#    - {RISK_MAP} = <risk map from .bug-hunter/recon.md>
#    - {TECH_STACK} = <framework, auth, DB from Recon>
#    - {PHASE_SPECIFIC_CONTEXT} = <doc-lookup instructions from doc-lookup.md>
#    - {OUTPUT_FILE_PATH} = ".bug-hunter/findings.json"
#    - {SKILL_DIR} = <absolute path>
# 4. Dispatch:
subagent({
  agent: "hunter-agent",
  task: "<the filled template>",
  output: ".bug-hunter/findings.json"
})
# 5. Read the output:
read({ path: ".bug-hunter/findings.json" })

When launching subagents, always pass SKILL_DIR explicitly in the task context so prompt commands like node "$SKILL_DIR/scripts/doc-lookup.cjs" resolve correctly. The context7-api.cjs script is kept as a fallback if doc-lookup.cjs fails.

Before every subagent launch, validate payload shape with:

node "$SKILL_DIR/scripts/payload-guard.cjs" validate "<role>" "<payload-json-path>"

If validation fails, do NOT launch the subagent. Fix the payload first.

Any mode step that says "launch subagent" means "dispatch an agent task using AGENT_BACKEND". For local-sequential, "launch" means "execute that phase's instructions yourself."

After reading each prompt, extract the key instructions and pass the content to subagents via their system prompts. You do not need to keep the full text in working memory.

Context pruning for subagents: When passing bug lists to Skeptics, Fixers, or the Referee, only include the bugs assigned to that agent — not the full merged list. For each bug, include: BUG-ID, severity, file, lines, claim, evidence, runtime trigger, cross-references. Omit: the Hunter's internal reasoning, scan coverage stats, and any "FILES SCANNED/SKIPPED" metadata. This keeps subagent prompts lean.

Step 3: Determine execution mode

Use the triage output from Step 1 — the strategy and FILE_BUDGET are already computed. Do NOT wait for Recon to determine the mode.

Read the corresponding mode file using STRATEGY from the triage JSON:

• single-file: SKILL_DIR/modes/single-file.md
• small: SKILL_DIR/modes/small.md
• parallel: SKILL_DIR/modes/parallel.md
• extended: SKILL_DIR/modes/extended.md
• scaled: SKILL_DIR/modes/scaled.md
• large-codebase: force LOOP_MODE=true and read SKILL_DIR/modes/large-codebase.md then SKILL_DIR/modes/loop.md

Backend override for local-sequential: If AGENT_BACKEND = "local-sequential", read SKILL_DIR/modes/local-sequential.md instead of the size-based mode file. The local-sequential mode handles all sizes internally with its own chunking logic.

If LOOP_MODE=true, also read (loop.md includes experiment tracking with iteration caps, stop-file safety, and auto-resume):

• SKILL_DIR/modes/fix-loop.md when FIX_MODE=true
• SKILL_DIR/modes/loop.md otherwise

CRITICAL — experiment tracking initialization: When LOOP_MODE=true, initialize experiment tracking BEFORE the first pipeline iteration by running:

node "$SKILL_DIR/scripts/experiment-loop.cjs" init \
  .bug-hunter/experiment.jsonl \
  "bug-hunt-$(date +%Y%m%d)" \
  bugs_confirmed \
  higher \
  count \
  --max-iterations "$MAX_LOOP_ITERATIONS"

Then before each iteration, call check-continue:

node "$SKILL_DIR/scripts/experiment-loop.cjs" check-continue \
  .bug-hunter/experiment.jsonl \
  --stop-file .bug-hunter/experiment.stop

If continue is false, stop the loop immediately. After each iteration, log the result with log. This is active by default — no --experiment flag needed.

CRITICAL — ralph-loop integration: When LOOP_MODE=true, you MUST call the ralph_start tool before running the first pipeline iteration. The loop mode files (loop.md / fix-loop.md) contain the exact ralph_start call to make, including the taskContent and maxIterations parameters. Without calling ralph_start, the loop will NOT iterate — it will run once and stop. After each iteration, call ralph_done to continue, or output <promise>COMPLETE</promise> when done.

Report the chosen mode to the user.

Then follow the steps in the loaded mode file. Each mode file contains the specific steps for running Recon, Hunters, Skeptics, and Referee for that mode. Each mode also references modes/_dispatch.md for backend-specific dispatch patterns. Execute them in order.

Branch-diff and staged optimization: For -b and --staged modes, if the file count ≤ FILE_BUDGET, always use small or parallel mode regardless of total codebase size. The triage script already handles this since it only scans the provided target files.

For extended and scaled modes, initialize state before chunk execution:

node "$SKILL_DIR/scripts/bug-hunter-state.cjs" init ".bug-hunter/state.json" "<mode>" "<files-json-path>" 30

Then apply hash-based skip filtering before each chunk:

node "$SKILL_DIR/scripts/bug-hunter-state.cjs" hash-filter ".bug-hunter/state.json" "<chunk-files-json-path>"

For full autonomous chunk orchestration with timeouts, retries, and journaling, extended/scaled modes can use:

node "$SKILL_DIR/scripts/run-bug-hunter.cjs" run --skill-dir "$SKILL_DIR" --files-json "<files-json-path>" --mode "<mode>"

See run-bug-hunter.cjs --help for all options (delta-mode, canary-size, expand-on-low-confidence, etc.).

Step 7: Present the Final Report

After the mode-specific steps complete, display the final report:

1. Scan metadata

• Mode (single-file / small / parallel-hybrid / extended / scaled / loop)
• Files scanned: N source files (N filtered out)
• Architecture: [summary from Recon]
• Tech stack: [framework, auth, DB from Recon]

2. Pipeline summary

Triage:    [N] source files | FILE_BUDGET: [B] | Strategy: [STRATEGY]
Recon:     mapped N files -> CRITICAL: X | HIGH: Y | MEDIUM: Z | Tests: T
Hunters:   [deep scan findings: W | optional triage findings: T | merged: U unique]
Gap-fill:  [N files re-scanned, M additional findings] (or "not needed")
Skeptics:  [challenged X | disproved: D, accepted: A]
Referee:   confirmed N real bugs -> Critical: X | Medium: Y | Low: Z

3. Confirmed bugs table

(sorted by severity — from Referee output)

4. Low-confidence items

Flagged for manual review.

• Include an Auto-fix eligibility field per bug:
  • ELIGIBLE: Referee confidence >= 75%
  • MANUAL_REVIEW: confidence < 75% or missing confidence
• If low-confidence items exist, expand scan scope from delta mode using trust-boundary overlays before finalizing report.

5. Dismissed findings

In a collapsed <details> section (for transparency).

6. Agent accuracy stats

• Deep Hunter accuracy: X/Y confirmed (Z%)
• Optional triage value: N triage-only findings promoted to deep scan
• Skeptic accuracy: X/Y correct challenges (Z%)

7. Coverage assessment

• If ALL queued scannable source files scanned: "Full queued coverage achieved."
• If any missed: list them with note about --loop mode.

7b. Coverage enforcement (mandatory)

If the coverage assessment shows ANY queued scannable source files were not scanned, the pipeline is NOT complete:

1. If LOOP_MODE=true (default): the ralph-loop will automatically continue to the next iteration covering missed files. Call ralph_done to proceed to the next iteration. Do NOT output <promise>COMPLETE</promise> until all queued scannable source files show DONE.

2. If LOOP_MODE=false (--no-loop was specified) AND missed files exist:

   • If total files ≤ FILE_BUDGET × 3: Output the report with a WARNING:

     ⚠️ PARTIAL COVERAGE: [N] queued source files were not scanned.
     Run `/bug-hunter [path]` for complete coverage (loop is on by default).
     Unscanned files: [list them]
     

   • If total files > FILE_BUDGET × 3: The report MUST include:

     🚨 LARGE CODEBASE: [N] source files (FILE_BUDGET: [B]).
     Single-pass audit covered [X]% of queued source files.
     Use `/bug-hunter [path]` for full coverage (loop is on by default).
     

3. Do NOT claim "audit complete" or "full coverage achieved" unless ALL queued scannable source files have status DONE. A partial audit is still valuable — report what you found honestly.

4. Autonomous runs must keep descending through the remaining priority queue after the current prioritized chunk is done:

   • Finish current CRITICAL/HIGH work first.
   • Immediately continue with remaining MEDIUM files.
   • Then continue with remaining LOW files.
   • Only stop when the queue is exhausted, the user interrupts, or a hard blocker prevents safe progress.

If zero bugs were confirmed, say so clearly — a clean report is a good result.

Routing after report:

• If there are confirmed security findings AND (VALIDATE_SECURITY_MODE=true OR PR_SECURITY_MODE=true OR SECURITY_REVIEW_MODE=true):
  • Read SKILL_DIR/skills/vulnerability-validation/SKILL.md.
  • Re-check reachability, exploitability, PoC quality, and CVSS details for the confirmed security findings before finalizing the security summary.
• If confirmed bugs > 0 AND PLAN_ONLY_MODE=true:
  • Build fix-strategy.json and fix-plan.json.
  • Present the strategy clusters (safe autofix vs manual review vs larger refactor vs architectural remediation).
  • Stop before the Fixer edits code.
• If confirmed bugs > 0 AND FIX_MODE=true:
  • Build and present fix-strategy.json first.
  • Auto-fix only ELIGIBLE bugs.
  • Apply canary-first rollout: fix top critical eligible subset first, verify, then continue remaining eligible fixes.
  • Keep MANUAL_REVIEW bugs in report only (do not auto-edit).
  • Run final global consistency pass over merged findings before applying fixes.
  • Read SKILL_DIR/modes/fix-pipeline.md and execute Phase 2 on eligible subset.
• If confirmed bugs > 0 AND FIX_MODE=false: stop after report (scan-only mode).
• If zero bugs confirmed: stop here. The report is the final output.

8. JSON output (always generated)

After the markdown report, write a machine-readable findings file to .bug-hunter/findings.json:

{
  "version": "3.0.0",
  "scan_id": "scan-YYYY-MM-DD-HHmmss",
  "scan_date": "<ISO 8601>",
  "mode": "<strategy>",
  "target": "<target path>",
  "files_scanned": 0,
  "threat_model_loaded": false,
  "confirmed": [
    {
      "id": "BUG-1",
      "severity": "CRITICAL",
      "category": "security",
      "stride": "Tampering",
      "cwe": "CWE-89",
      "file": "src/api/users.ts",
      "lines": "45-49",
      "claim": "SQL injection via unsanitized query parameter",
      "reachability": "EXTERNAL",
      "exploitability": "EASY",
      "cvss_vector": "CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:N",
      "cvss_score": 9.1,
      "poc": { "payload": "...", "request": "...", "expected": "...", "actual": "..." }
    }
  ],
  "dismissed": [
    { "id": "BUG-3", "severity": "Medium", "category": "logic", "file": "...", "claim": "...", "reason": "..." }
  ],
  "dependencies": [],
  "summary": {
    "total_reported": 0, "confirmed": 0, "dismissed": 0,
    "by_severity": { "CRITICAL": 0, "HIGH": 0, "MEDIUM": 0, "LOW": 0 },
    "by_stride": { "Tampering": 0, "InfoDisclosure": 0, "ElevationOfPrivilege": 0, "Spoofing": 0, "DoS": 0, "Repudiation": 0, "N/A": 0 },
    "by_category": { "security": 0, "logic": 0, "error-handling": 0 }
  }
}

Rules for JSON output:

• Non-security findings: stride: "N/A", cwe: "N/A", omit reachability/CVSS/PoC fields.
• Security findings without CRITICAL/HIGH severity: omit CVSS and PoC fields.
• dependencies array: populated only if --deps was used and .bug-hunter/dep-findings.json exists.
• This JSON enables CI/CD gating, dashboard ingestion, and downstream patch generation.

Also write the final markdown report to .bug-hunter/report.md as the canonical human-readable output. Generate it from the JSON artifacts with:

node "$SKILL_DIR/scripts/render-report.cjs" report ".bug-hunter/findings.json" ".bug-hunter/referee.json" > ".bug-hunter/report.md"

Self-Test Mode

To validate the pipeline works end-to-end, run /bug-hunter SKILL_DIR/test-fixture/ on the included test fixture. This directory contains a small Express app with 6 intentionally planted bugs (2 Critical, 3 Medium, 1 Low). Expected results:

• Recon should classify 3 files as CRITICAL, 1 as HIGH
• Hunters should find all 6 bugs (possibly more false positives)
• Skeptic should challenge at least 1 false positive
• Referee should confirm all 6 planted bugs

If the pipeline finds fewer than 5 of the 6 planted bugs, the prompts need tuning. If it reports more than 3 false positives that survive to the Referee, the Skeptic prompt needs tightening.

The test fixture source files ship with the skill. If using --fix mode on the fixture, initialize its git repo first: bash SKILL_DIR/scripts/init-test-fixture.sh

Error handling

| Step | Failure | Fallback | |------|---------|----------| | Triage | script error | Skip triage, Recon does full classification with FILE_BUDGET=40 default | | Recon | timeout/error | Skip Recon, Hunters use triage scanOrder (or Glob-based discovery if no triage) | | Optional scout pass | timeout/error | Disable scout, continue with deep Hunter | | Deep Hunter | timeout/error | Retry once on narrowed chunk, otherwise report partial coverage | | Orchestration backend | launch failure | Fall back to next backend (subagent → teams → interactive_shell → local-sequential) | | Gap-fill Hunter | timeout/error | Note missed files, continue | | Payload guard | validation fails | Do not launch subagent; fix payload and retry | | Chunk orchestrator | timeout/error | Retry with exponential backoff, then mark chunk failed | | Skeptic | timeout/error | Use single Skeptic or accept all findings as-is | | Referee | timeout/error | Use Skeptic's accepted list as final result | | Git safety (Step 8a) | not a git repo | Warn user, skip branching | | Git safety (Step 8a) | stash/branch fails | Warn, continue without safety net | | Fix lock | lock held | Stop Phase 2, report concurrent fixer run | | Test baseline (Step 8c) | timeout/not found | Set BASELINE=null, skip test verification | | Fixer | timeout/error | Mark unfixed bugs as SKIPPED | | Post-fix tests | new failures | Auto-revert failed fix commit, mark FIX_REVERTED | | Post-fix re-scan | timeout/error | Skip re-scan, note "fixer output not re-verified" | | Worktree prepare | git worktree add fails | Fall back to WORKTREE_MODE=false (direct edit mode) for this run | | Worktree harvest | no commits found, dirty | Stash uncommitted work, mark bugs as FIX_FAILED (reason: fixer-did-not-commit) | | Worktree harvest | branch switched | Mark all bugs in batch as FIX_FAILED (reason: branch-switched) | | Worktree cleanup | git worktree remove fails | Force-remove directory, run git worktree prune | | Stale worktrees | from previous crash | cleanup-all at Step 8a-wt removes them before starting | | Fix lock release | release fails | Warn user to clear .bug-hunter/fix.lock manually |

New in This Update

This release is a reliability hardening pass — 11 bugs fixed, 10 previously-failing tests now pass, and the full pipeline is more robust end-to-end.

• High severity works everywhere. All JSON schemas, severity ranking, and payload-guard templates now recognize High — previously only Critical, Medium, and Low were accepted, silently dropping valid findings.
• Confidence threshold is fully wired. --confidence-threshold now propagates from the CLI through the orchestrator to record-findings. Previously the flag was parsed but never forwarded, always defaulting to 75.
• Shell injection fixed in doc-lookup. Library names passed to chub CLI are now properly shell-quoted — prevents command injection via crafted library names.
• SIGKILL timer leak fixed. The failsafe kill timer in runCommandOnce is now cleared on normal exit — previously it could fire after the child had already exited.
• Modern Bun lockfile support. dep-scan.cjs now detects bun.lock (text format, Bun 1.2+) alongside the legacy bun.lockb binary format.
• Worktree commit parsing hardened. Edge case where git log lines with no space separator caused truncated hashes and wrong m...