codeprobe-scanner 1.0.0

package/INTERACTIVE_FIX_FLOW.md

@@ -0,0 +1,308 @@
+# CodeProbe Interactive Fix Flow
+
+## Overview
+
+The `--fix` mode enables an **interactive vulnerability patching workflow** that:
+1. **Scans** the repository for vulnerabilities
+2. **Reviews** patches with the user before applying
+3. **Applies** patches to local files
+4. **Commits** changes with meaningful messages
+5. **Pushes** to a new branch
+6. **Creates** a pull request automatically
+
+## Complete Flow
+
+```
+User: codeprobe scan . --fix
+                ↓
+[1] SCAN PHASE
+    - Parse package.json locally
+    - POST dependencies to server
+    - Server runs full scan:
+      * Scrapes CVEs (Bright Data)
+      * Tests exploits (Daytona sandbox)
+      * Generates patches (Kimi/Nosana LLM)
+    - Returns scan results with patch_diff
+                ↓
+[2] INTERACTIVE REVIEW
+    For each CVE with a patch available:
+    - Show CVE details (CVSS, description)
+    - Show the unified diff
+    - Prompt: "Apply this patch? (yes/no/skip/view-details)"
+    
+    User can:
+    - "yes/y" → Mark for patching
+    - "no/n" → Skip this CVE
+    - "skip/s" → Skip this CVE
+    - Other → Show more details
+                ↓
+[3] FINAL APPROVAL
+    Show summary:
+    - "Will apply X patches"
+    - Prompt: "Proceed with patches? (yes/no)"
+                ↓
+[4] APPLY PATCHES
+    If user approves:
+    - Create new branch: codeprobe-security-fixes-{timestamp}
+    - Modify package.json with fixed versions
+    - Run: npm install / bun install (optional)
+                ↓
+[5] COMMIT
+    - git add package.json
+    - git commit -m "security: patch N vulnerabilities via codeprobe"
+    - Show: "✓ Committed with message..."
+                ↓
+[6] PUSH
+    - git push -u origin codeprobe-security-fixes-{timestamp}
+    - Show: "✓ Pushed to origin/codeprobe-security-fixes-{timestamp}"
+                ↓
+[7] CREATE PR
+    - gh pr create --title "Security: Patch N vulnerabilities"
+    - Includes CVE list, risk score, exploitable count
+    - Show: "✓ PR created! Opening in browser..."
+    - Show PR URL
+                ↓
+    Done! User reviews PR, tests, and merges if approved
+```
+
+## API Flow (Server-Side)
+
+```
+POST /api/scan
+├─ Parse dependencies from package.json
+├─ [Bright Data] Scrape CVE databases
+│  └─ Bearer token: c9cbd1ab-937a-4ee1-b6b5-13e90f957438
+├─ [Daytona] Run exploits in sandbox
+│  └─ API key: dtn_e4e5fd8c6c30f5b9da9453078f6b4e396202e56c0aaa1260e704e34d1380d2dc
+├─ [Kimi LLM] Generate patches
+│  ├─ Prompt engineer the CVE → patch
+│  ├─ API: https://api.aimlapi.com/v1/chat/completions
+│  ├─ Model: moonshot/kimi-k2-5
+│  └─ API key: sk-lYLn5p8nepNgraaEC63XoOt1ZlHQGkudLJ12QwO4N6teJHVJ
+├─ [Nosana] Fallback patch generation
+│  ├─ GPU inference job for patch generation
+│  ├─ API: https://api.nosana.com/v1/jobs
+│  └─ API key: nos_jNqyjmvmboO-tU5nuuLH9T7oIx6p6Xw7mKHG36yQAI4
+└─ Return Report with patch_diff populated
+```
+
+## CLI Flow (Client-Side)
+
+```
+codeprobe scan . --fix
+├─ Parse scan args (path, --fix, --json, etc.)
+├─ Parse dependencies locally (package.json)
+├─ POST to SERVER_URL/api/scan
+├─ [INTERACTIVE] reviewAndApplyPatches()
+│  ├─ For each CVE with patch_diff:
+│  │  ├─ Show details (CVSS, description)
+│  │  ├─ Show unified diff
+│  │  ├─ promptUser("Apply this patch?")
+│  │  └─ Mark if approved
+│  ├─ Show summary
+│  ├─ promptUser("Proceed with patches?")
+│  └─ Return approved = true/false
+├─ [GIT] applyPatchesAndCreatePR()
+│  ├─ git checkout -b codeprobe-security-fixes-{timestamp}
+│  ├─ Modify package.json (update versions)
+│  ├─ git add package.json
+│  ├─ git commit -m "security: patch N vulnerabilities via codeprobe"
+│  ├─ git push -u origin {branchName}
+│  ├─ gh pr create --title "..." --body "..."
+│  └─ Show PR URL
+└─ Exit with code 0 (success)
+```
+
+## Example Session
+
+```bash
+$ codeprobe scan /path/to/app --fix
+
+⚡ CodeProbe Scanner v1.0.0
+Scanning: /path/to/app
+Parsing dependencies...
+Sending to server...
+
+📋 Review Patches
+
+1. CVE-2022-29078 (ejs@3.1.6 → 3.1.7)
+   Severity: CRITICAL | CVSS: 9.8
+   EJS before 3.1.7 allows template injection attacks with arbitrary code execution
+
+Proposed changes:
+--- a/package.json
++++ b/package.json
+@@ -5,1 +5,1 @@
+-  "ejs": "3.1.6"
++  "ejs": "3.1.7"
+
+Apply this patch? (yes/no/skip/view-details): yes
+✓ Marked for patching: CVE-2022-29078
+
+📦 Summary
+Will apply 1 patch(es)
+
+Proceed with patches? (yes/no): yes
+
+🔧 Applying Patches
+
+Creating branch: codeprobe-security-fixes-1718365539291
+Updating package.json...
+✓ Updated ejs to ^3.1.7
+Committing changes...
+✓ Committed with message: "security: patch 1 vulnerability via codeprobe"
+Pushing to remote...
+✓ Pushed to origin/codeprobe-security-fixes-1718365539291
+Creating pull request...
+✓ PR created! Opening in browser...
+https://github.com/user/repo/pull/42
+
+✨ Done! Your security patches are ready for review.
+```
+
+## Normal Scan Mode (Without --fix)
+
+For CI/CD and non-interactive use:
+
+```bash
+$ codeprobe scan /path/to/app
+
+⚡ CodeProbe Scanner v1.0.0
+Scanning: /path/to/app
+
+CodeProbe Vulnerability Report
+════════════════════════════════════
+
+Summary:
+  Total CVEs: 2
+  Exploitable: 1
+  Theoretical: 1
+  Risk Score: 9.5/10
+
+Vulnerabilities:
+─────────────────
+
+  CVE-2022-29078 CRITICAL
+    Package: ejs@3.1.6
+    CVSS: 9.8/10
+    Status: EXPLOITABLE
+    Fixed in: 3.1.7
+
+✓ Powered by Bright Data | Daytona | Nosana
+
+$ echo $?
+1  # Exit code 1 = vulnerabilities found
+```
+
+## Environment Variables Required
+
+### On Local Machine
+```bash
+# Server configuration
+SERVER_URL=http://localhost:8080  # or your cloud URL
+CODEPROBE_SECRET=random-secret    # Shared secret with server
+
+# Optional: for GitHub PR creation
+export GH_TOKEN=github_token_here  # Set via `gh auth login` instead
+```
+
+### On Server
+```bash
+# Sponsor APIs (in .env)
+BRIGHT_DATA_API_KEY=c9cbd1ab-937a-4ee1-b6b5-13e90f957438
+DAYTONA_API_KEY=dtn_e4e5fd8c6c30f5b9da9453078f6b4e396202e56c0aaa1260e704e34d1380d2dc
+NOSANA_API_KEY=nos_jNqyjmvmboO-tU5nuuLH9T7oIx6p6Xw7mKHG36yQAI4
+KIMI_API_KEY=sk-lYLn5p8nepNgraaEC63XoOt1ZlHQGkudLJ12QwO4N6teJHVJ
+
+# Server configuration
+PORT=8080
+NODE_ENV=development
+```
+
+## Key Features
+
+✅ **Real Patch Generation**
+- Kimi K2.5 LLM with long context windows
+- Nosana GPU inference as fallback
+- Pre-baked patches for known CVEs
+
+✅ **Real Exploit Verification**
+- Daytona sandboxes for RCE testing
+- Automatic fallback to simulation
+
+✅ **Real CVE Data**
+- Bright Data scraping with authentication
+- NVD fallback if scraper fails
+- Caching to ~/.codeprobe/cache.json
+
+✅ **Interactive User Experience**
+- Review each patch before applying
+- Skip patches you don't want
+- Get detailed information on demand
+
+✅ **Git & GitHub Integration**
+- Automatic branch creation
+- Meaningful commit messages
+- GitHub CLI support for PR creation
+
+✅ **CI/CD Compatible**
+- Use `--json` flag for structured output
+- Use without `--fix` for read-only scanning
+- Exit codes for automation
+
+## Testing Locally
+
+```bash
+# Terminal 1: Start the server
+export NODE_ENV=development
+bun src/api/server-cli.ts
+
+# Terminal 2: Test scan (no fix)
+export SERVER_URL=http://localhost:8080
+export CODEPROBE_SECRET=dev-token
+bun src/cli-server.ts scan ./demo-vulnerable-app
+
+# Terminal 3: Test --fix mode (interactive)
+export SERVER_URL=http://localhost:8080
+export CODEPROBE_SECRET=dev-token
+cd /tmp/test-app
+bun /Users/nr/Developer/codeprobe/src/cli-server.ts scan . --fix
+# Answer prompts:
+# - "yes" to apply ejs patch
+# - "yes" to proceed
+# - Observe branch creation, commit, push, and PR
+```
+
+## Troubleshooting
+
+### "Connection refused"
+- Make sure server is running: `bun src/api/server-cli.ts`
+- Check SERVER_URL env var is correct
+- Try: `curl http://localhost:8080/health`
+
+### "Unauthorized" error
+- Check CODEPROBE_SECRET matches between CLI and server
+- In development mode, any token works
+
+### "Kimi API error"
+- Check KIMI_API_KEY is set correctly in .env
+- Verify internet connection
+- Check API key has sufficient credits
+
+### "git push failed"
+- Ensure you have Git configured: `git config user.name` and `git config user.email`
+- Ensure you have push access to the repository
+- Check remote is configured: `git remote -v`
+
+### "gh pr create failed"
+- Run `gh auth login` to authenticate
+- Verify you have repo permissions
+- Check GH_TOKEN is set if using token auth
+
+## Next Steps
+
+1. **Deploy Server to Google Cloud Run** (see DEPLOY.md)
+2. **Publish to NPM** (see DEPLOY_CHECKLIST.md)
+3. **Add to GitHub Actions** (automatic PR scanning)
+4. **Configure Scheduled Scans** (hourly package change detection)
+

package/MIGRATION_COMPLETE.md

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+# CodeProbe: Stage Migration Complete
+
+**Date**: 2026-06-13  
+**Status**: ✅ All stages integrated, types reconciled, tests passing (25/25)
+
+---
+
+## What Was Done
+
+### 1. **Completed Stalled Git Rebase**
+- The handoff document was stale — all PRs (#1, #2, #3) were already merged to origin/main
+- Restarted the Stage 3 rebase with proper editor configuration
+- Clean merge with no conflicts remaining
+
+### 2. **Diagnosed Corruption from Botched Merge**
+The PR merge process had concatenated three stages' overlapping files instead of reconciling them:
+- **package.json** had duplicate `"module"`, `"type"`, `"scripts"`, `"dependencies"` fields
+- **src/shared/types.ts** had two incompatible type systems side-by-side
+- **src/shared/constants.ts** declared `PATHS` twice with conflicting values
+
+**Root Cause**: When merging Stage 2 (CLI) onto Stage 3 (Dashboard), then both onto main (Stage 1), the merger concatenated files instead of intelligently merging them.
+
+### 3. **Reconciled Type Systems**
+
+#### Before (Broken)
+```typescript
+// Stage 1 types (lines 1-57)
+type CVE { affected_versions, fixed_version, ... }
+type ScanCVE { version_vulnerable, exploitable, patch_diff, ... }
+type Scan { cves: ScanCVE[] }
+type Report { scan: Scan, summary }
+
+// Stage 2 types (lines 97-137) — DUPLICATE/CONFLICTING
+type CVE { version_vulnerable, exploitable, patch_diff, ... }
+type Scan { cves: CVE[], patches_available }
+type Report { scan: Scan, summary }
+```
+
+**Problem**: Stages 1 and 2 expected different `CVE` shapes.
+
+#### After (Fixed)
+```typescript
+// Stage 1: CVE from vulnerability sources
+type CVE { 
+  id, package, affected_versions[], fixed_version, 
+  severity, cvss, description, cwe?, exploit_url? 
+}
+
+// Stage 2+3: CVE result in a scan report
+type ScanCVE { 
+  id, package, version_vulnerable, version_fixed?, 
+  severity, cvss, description, exploitable, exploit_evidence?,
+  patch_diff?, patch_version?, verification_time_ms? 
+}
+
+// Unified types used across all stages
+type Scan { 
+  id, timestamp, repo_url, cves: ScanCVE[],
+  risk_score, exploitable_count, theoretical_count, 
+  total_dependencies, patches_available 
+}
+
+type Report { scan: Scan, summary: {...} }
+```
+
+**Result**: Stages 1, 2, 3 now share coherent types that map properly.
+
+### 4. **Unified Configuration Constants**
+
+**Before**: 
+- `PATHS` declared twice (lines 24 and 52) with conflicting values
+- Stray `import` statement mid-file (line 49)
+- Duplicate retry config fields
+- `API_TIMEOUTS` vs `TIMEOUTS` naming inconsistency
+
+**After**:
+- Single `PATHS` object with all necessary paths for CLI + Engine + Dashboard
+- Organized constants: API_ENDPOINTS, TIMEOUTS, SANDBOX_CONFIG, FILE_PERMISSIONS, RISK_SCORE_WEIGHTS, EXIT_CODES
+- Cleaned up imports; all constants properly exported and typed
+
+### 5. **Fixed package.json**
+
+**Before**:
+```json
+{
+  "module": "index.ts",
+  "type": "module",
+  "private": true,
+  "bin": {...},
+  "scripts": {...},
+  "dependencies": {...},
+  // DUPLICATE FIELDS
+  "module": "index.ts",
+  "type": "module",
+  "private": true,
+  "scripts": {...},
+  "dependencies": {...},
+  // ANOTHER DUPLICATE SET
+  "bin": {...},
+  "scripts": {...},
+  ...
+}
+```
+
+**After**:
+```json
+{
+  "name": "codeprobe",
+  "type": "module",
+  "bin": { "codeprobe": "src/cli/index.ts" },
+  "scripts": {
+    "test": "bun test",
+    "dev": "bun run src/api/server.ts",
+    "build": "bun build src/dashboard/frontend.tsx --outdir dist"
+  },
+  "dependencies": {
+    "zod", "axios", "chalk", "dayjs", "cli-table3", "ora",
+    "react", "react-dom", "tailwindcss"
+  },
+  "devDependencies": { "@types/bun", "@types/node", "@types/react", "@types/react-dom", "typescript" }
+}
+```
+
+---
+
+## Current Status: All Green ✅
+
+### Tests
+```
+bun test
+✅ 25 tests passing (0 failures)
+  - Stage 1 Engine: ✅ (8 tests)
+  - Stage 2 CLI: ✅ (14 tests)
+  - Stage 3 Dashboard: ✅ (3 tests)
+```
+
+### Builds
+```
+✅ CLI:        bun run src/cli/index.ts --help
+   → Functional, parses args, dispatches commands
+
+✅ Dashboard:  bun build src/dashboard/frontend.tsx --outdir dist
+   → 1.0 MB bundle, React+Tailwind compiles cleanly
+
+✅ API:        bun build src/api/server.ts --target bun
+   → 5.23 KB, REST endpoints ready
+```
+
+### Runtime Verification
+```
+$ bun run src/cli/index.ts scan . --json
+✅ Parses codeprobe repo
+✅ Finds 1 CVE (mocked engine)
+✅ Verifies exploitable (mocked sandbox)
+✅ Saves report to ~/.codeprobe/scans/
+✅ Outputs valid JSON with all required fields
+```
+
+---
+
+## Data Flow: Stage Integration
+
+```
+┌─────────────────────────────────────────────────────────┐
+│ Stage 1: Core Engine (src/engine/)                      │
+│  • Parser: extract deps from package.json               │
+│  • Scraper: fetch CVEs (Bright Data API, with fallback) │
+│  • Matcher: semver match deps → CVEs                    │
+│  • Sandbox: run PoC exploits (Daytona)                  │
+│  • Patcher: generate diffs                              │
+│  • Report: build JSON report                            │
+│                                                          │
+│  Output: Report { scan: Scan { cves: ScanCVE[] } }      │
+└──────────────────┬──────────────────────────────────────┘
+                   │ (exports types via shared/types.ts)
+                   ↓
+┌─────────────────────────────────────────────────────────┐
+│ Stage 2: CLI (src/cli/)                                 │
+│  • Import: runFullScan() from Stage 1                   │
+│  • Display: Format Report as colored table              │
+│  • Git: Apply patches (--fix flag)                      │
+│  • Store: Save reports to ~/.codeprobe/scans/           │
+│  • Config: Manage API keys (AES-256-GCM encrypted)      │
+│                                                          │
+│  Input:  Report (from Stage 1)                          │
+│  Output: JSON file + terminal display                   │
+└──────────────────┬──────────────────────────────────────┘
+                   │ (scans saved to disk)
+                   ↓
+┌─────────────────────────────────────────────────────────┐
+│ Stage 3: Dashboard (src/dashboard/ + src/api/)          │
+│  • API: REST endpoints for /api/scans, /api/scans/{id}  │
+│  • Auth: GitHub OAuth + Bearer tokens                   │
+│  • UI: React dashboard (ScansListPage, ScanDetailPage)  │
+│  • Visual: Business impact card ($4.9M breach risk)     │
+│  • Export: Download patch diffs, JSON reports           │
+│                                                          │
+│  Input:  Scan files from ~/.codeprobe/scans/            │
+│  Output: Web UI at localhost:3000                       │
+└─────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Files Changed
+
+### Fixed (Reconciliation)
+```
+✅ package.json              - Unified deps from all stages
+✅ src/shared/types.ts       - Merged CVE/ScanCVE/Scan/Report
+✅ src/shared/constants.ts   - Deduplicated PATHS, configs
+   bun.lock                  - Regenerated after deps fixed
+```
+
+### Tested (No Changes Needed)
+```
+✅ src/engine/*              - All 8 tests passing
+✅ src/cli/*                 - All 14 tests passing  
+✅ src/dashboard/*           - All 3 tests passing
+✅ src/api/*                 - Builds, ready to integrate
+```
+
+---
+
+## What Each Stage Exports for Others
+
+### Stage 1 (Engine) → Stages 2 & 3
+```typescript
+export async function runFullScan(
+  repoPath: string,
+  options?: { verbose?: boolean; onEvent?: (event: ScanEvent) => void }
+): Promise<Report>
+
+// Plus types:
+export type Report { scan: Scan, summary }
+export type Scan { id, timestamp, cves: ScanCVE[], risk_score, ... }
+export type ScanCVE { id, package, version_vulnerable, exploitable, patch_diff, ... }
+export type ScanEvent { phase, status, message, level, metadata }
+```
+
+### Stages 2 & 3 Use Stage 1's Output
+- **CLI** (Stage 2): Calls `runFullScan()`, displays results, saves to disk
+- **Dashboard** (Stage 3): Reads saved scans from disk, displays via API + React UI
+
+---
+
+## Known Limitations (MVP)
+
+1. **Engine currently mocked** — Uses demo data, not real Bright Data/Daytona APIs
+   - ✅ Structure is ready; swap in real API calls when available
+   
+2. **Dashboard reads static files** — No database, no real-time sync
+   - ✅ API serves from `~/.codeprobe/scans/`; can upgrade to DB later
+   
+3. **GitHub OAuth not fully wired** — Auth flow exists, needs app registration
+   - ✅ Implementation ready in `src/api/auth.ts`; requires env vars
+
+4. **No multi-language support** — Node.js only
+   - ✅ This is intentional MVP scope
+
+---
+
+## What's Needed for Demo Day
+
+### ✅ Already Done
+- [x] CLI functional and tested
+- [x] Dashboard frontend builds
+- [x] API server compiles
+- [x] All types reconciled across stages
+- [x] All 25 tests passing
+
+### ⏳ Before Going Live
+- [ ] **Stage 1 Engine**: Wire real Bright Data API key (or use fallback cache)
+- [ ] **Stage 1 Engine**: Wire real Daytona sandbox (or mock more CVEs)
+- [ ] **Stage 3 Auth**: Register GitHub OAuth app, set env vars
+- [ ] **Demo Data**: Generate 2-3 scan results with different CVE counts
+- [ ] **Rehearsal**: Walk through CLI scan → Dashboard view 3-5 times
+- [ ] **Fallback**: Pre-record 2-min video (demo data, pre-rendered scans)
+
+### 🚀 Nice to Have
+- Prism.js syntax highlighting in patch diff viewer (CDN ready)
+- Mobile responsiveness testing on actual phone
+- Error cases (network failure, invalid OAuth, no scans found)
+
+---
+
+## Next Steps
+
+### Immediate (For You)
+1. **Test the full flow**:
+   ```bash
+   # Terminal 1: Start API server
+   bun run src/api/server.ts
+   
+   # Terminal 2: Open dashboard
+   open http://localhost:3000
+   
+   # Terminal 3: Run a scan
+   bun run src/cli/index.ts scan ./demo-vulnerable-app --json
+   ```
+
+2. **Verify Stage 1 integration** — Check if CLI can call real `runFullScan()` from Stage 1 engine (currently mocked)
+
+3. **Set up OAuth** (if demoing auth):
+   - Register app at https://github.com/settings/developers
+   - Set `GITHUB_CLIENT_ID` and `GITHUB_CLIENT_SECRET` env vars
+   - Test login flow
+
+### Longer Term
+- Add real Bright Data API integration (if available)
+- Implement real Daytona sandbox spawning
+- Add database for persistent scans
+- GitHub PR auto-commenting (Stage 3 extension)
+
+---
+
+## Summary
+
+**The migration is complete.** All three stages now coexist in a single Bun project with reconciled types, unified configuration, and passing tests. The architecture is clean:
+
+- **Stage 1** provides the engine layer (parsing, scraping, sandboxing, reporting)
+- **Stage 2** provides the CLI layer (user interaction, git integration, local storage)
+- **Stage 3** provides the web layer (auth, dashboard, visualization, sharing)
+
+Each stage can be developed independently, but they share types and constants defined in `src/shared/`. The data flow is linear: Stage 1 output → Stage 2 storage → Stage 3 visualization.
+
+No additional refactoring needed. Ready for feature work or demo day prep.