npm - coverme-scanner - Versions diffs - 1.0.18 → 1.0.20 - Mend

coverme-scanner 1.0.18 → 1.0.20

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (13) hide show

package/dist/prompts/cross-validator.md +44 -0
package/dist/prompts/mitigation-validator.md +68 -0
package/dist/prompts/orchestration.md +125 -33
package/dist/prompts/security-scanner.md +63 -2
package/dist/report/generator.d.ts.map +1 -1
package/dist/report/generator.js +7 -6
package/dist/report/generator.js.map +1 -1
package/package.json +1 -1
package/src/prompts/cross-validator.md +44 -0
package/src/prompts/mitigation-validator.md +68 -0
package/src/prompts/orchestration.md +125 -33
package/src/prompts/security-scanner.md +63 -2
package/src/report/generator.ts +7 -6

package/dist/prompts/cross-validator.md CHANGED Viewed

@@ -223,4 +223,48 @@ Focus: Find what was MISSED
 - Don't ignore context from CLAUDE.md
 - Don't miss the forest for the trees
+## CRITICAL: Things That Are NOT False Positives
+### Command Injection from Config Files
+**DO NOT dismiss as false positive!**
+```javascript
+execSync(`pm2 start ${configValue}`)  // STILL VULNERABLE!
+```
+Even if the value comes from a config file (models.json, config.yaml), if that file is:
+- Writable by users (admin panel, API)
+- Not validated against a strict schema
+- Could be modified by an attacker with file access
+Then it IS a real command injection. The attack vector is just indirect.
+**Only dismiss if:**
+- Config file is hardcoded at build time (not runtime loaded)
+- Config values are validated against strict regex/enum
+- execFile() is used instead of execSync() with proper argument array
+### Secrets in Git History
+**DO NOT dismiss just because file is now gitignored!**
+If a secret file was EVER committed, it may still be in git history.
+```bash
+git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+```
+If this returns results, the secret is STILL EXPOSED even if currently gitignored.
+### CORS Without Whitelist
+**DO NOT dismiss as "internal only"!**
+```javascript
+res.header('Access-Control-Allow-Origin', req.headers.origin);  // VULNERABLE
+```
+This reflects ANY origin. Even if the server is "internal", browser-based attacks can still:
+- Steal data via malicious website
+- Perform CSRF-like attacks
+- Exfiltrate to attacker-controlled domains
+### Missing Security Configuration
+**These are real findings, not false positives:**
+- `helmet()` without custom CSP configuration
+- Missing `npm audit` in CI pipeline
+- No Dependabot/Renovate for dependency updates
+- Logs without rotation/retention policy
 START VALIDATION NOW. Be critical but fair.

package/dist/prompts/mitigation-validator.md CHANGED Viewed

@@ -178,6 +178,74 @@ The finding is incorrect:
 3. Is it localhost/development credentials only?
 4. Is there environment variable loading that overrides?
+### Race Condition / TOCTOU Findings (CRITICAL - Often False Positives)
+**Check for atomic operations that FULLY mitigate the race:**
+1. **Redis Lua Scripts** = FULL MITIGATION
+   - `redis.call()` inside Lua script is atomic
+   - SETNX, GETSET, INCR are atomic
+   - Look for: `eval`, `evalsha`, `script load`
+   ```javascript
+   // This is ATOMIC - no race condition!
+   redis.eval(`
+     local current = redis.call('GET', key)
+     if current < limit then
+       redis.call('INCR', key)
+       return 1
+     end
+     return 0
+   `)
+   ```
+2. **Database Transactions** = FULL MITIGATION
+   - `BEGIN...COMMIT` with proper isolation
+   - `SELECT FOR UPDATE` locks rows
+   - Prisma `$transaction()`, TypeORM `transaction()`
+   - Look for: `transaction`, `FOR UPDATE`, `SERIALIZABLE`
+3. **Atomic Compare-and-Swap** = FULL MITIGATION
+   - `WATCH/MULTI/EXEC` in Redis
+   - `findOneAndUpdate` with conditions in MongoDB
+   - `UPDATE ... WHERE version = ?` (optimistic locking)
+4. **Mutex/Locking** = FULL MITIGATION
+   - `redis-lock`, `redlock`
+   - Database advisory locks
+   - File locks (flock)
+**If ANY of these patterns exist, mark as MITIGATED, not "partial"!**
+### Intentional Design Decisions (Check Comments!)
+**Before reporting, check if there are comments explaining WHY:**
+1. **Search for explanatory comments near the code:**
+   ```
+   grep -B5 -A5 "intentional|by design|deliberately|on purpose|security note" <file>
+   ```
+2. **Common patterns that are INTENTIONAL:**
+   - PKCE code reuse to prevent double-click race conditions
+   - Longer token expiry for better UX (with other mitigations)
+   - Allowing certain "unsafe" operations for admin users
+   - Development-only bypasses with environment checks
+3. **If comment explains the decision:**
+   ```json
+   {
+     "verdict": "false_positive",
+     "reason": "Intentional design decision documented in code",
+     "evidence": ["Comment at line 45: 'Intentionally allow reuse to prevent double-submit'"]
+   }
+   ```
+### Open Redirect Findings
+1. **Check for whitelist validation:**
+   ```
+   grep -r "isValidRedirect|allowedDomains|whitelist|validateUrl" <file>
+   ```
+2. If whitelist exists and covers the redirect parameter = MITIGATED
+3. Check if validation function is actually called before redirect
 ## Output Format
 ```json

package/dist/prompts/orchestration.md CHANGED Viewed

@@ -158,6 +158,32 @@ CHECK FOR:
 - API versioning issues
 - Excessive data exposure in responses
+**CORS MISCONFIGURATION** (MEDIUM):
+Look for these vulnerable patterns:
+```javascript
+// VULNERABLE - reflects ANY origin
+res.header('Access-Control-Allow-Origin', req.headers.origin);
+res.header('Access-Control-Allow-Origin', '*');
+// VULNERABLE - no whitelist validation
+app.use(cors({ origin: true }));
+```
+Only mark as safe if there's explicit whitelist validation:
+```javascript
+const allowedOrigins = ['https://app.example.com'];
+if (allowedOrigins.includes(origin)) { ... }
+```
+**HELMET MISCONFIGURATION** (MEDIUM):
+```javascript
+app.use(helmet());  // Using defaults only - INSUFFICIENT!
+```
+Check that helmet() includes:
+- Custom `contentSecurityPolicy` with proper directives
+- `hsts: { maxAge: 31536000, includeSubDomains: true, preload: true }`
+- Proper `referrerPolicy`
+Report as MEDIUM if using only defaults without customization.
 **FAIL-OPEN vs FAIL-CLOSED PATTERNS** (CRITICAL):
 - IP whitelist empty/missing = allow all (should deny all)
 - Auth middleware errors = request passes through (should block)
@@ -207,6 +233,14 @@ CHECK FOR:
 - Ansible vault passwords in plaintext
 - CI/CD pipeline secrets in yaml files (.github/workflows, .gitlab-ci.yml)
+**SECRETS IN GIT HISTORY** (CRITICAL CHECK!):
+Run these commands to check if secrets were EVER committed:
+```bash
+git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+git log --all -p -S "AWS_SECRET" -S "PRIVATE_KEY" --source
+```
+If secrets appear in history, they are EXPOSED even if now gitignored!
 **PRIVILEGE ESCALATION RISKS**:
 - Containers/processes running as root
 - Missing securityContext in K8s (runAsNonRoot, readOnlyRootFilesystem)
@@ -220,6 +254,20 @@ CHECK FOR:
 - Missing config = silent fallback to insecure defaults
 - No validation of secret strength/format at startup
+**DEPENDENCY SECURITY** (HIGH if missing):
+Check for presence of:
+- `npm audit` or `yarn audit` in CI pipeline
+- Dependabot/Renovate configuration (.github/dependabot.yml, renovate.json)
+- SBOM generation (cyclonedx, syft)
+- Snyk/Trivy/Grype scanning
+Report as HIGH if NONE of these exist - supply chain risk!
+**LOGGING & MONITORING**:
+- Log rotation configured? (maxFiles, maxsize in Winston/Pino)
+- Log retention policy defined?
+- Sensitive data redacted from logs?
+Report as LOW if log rotation missing - disk exhaustion risk.
 For EACH finding, output the FULL JSON format.
 ---
@@ -577,63 +625,107 @@ Output as list of strings.
 ## PHASE 7: BUILD CONSENSUS & GENERATE OUTPUT
-1. **Apply Mitigation Results** (from Phase 3):
-   - Remove findings marked as `mitigated` or `false_positive`
-   - Adjust severity for findings marked as `partial`
-   - Add mitigation notes to confirmed findings
+### CRITICAL: Actually Remove False Positives!
-2. Calculate confidence: (confirmations / total_validators) * 100
-3. Remove findings with confidence < 50%
-4. Add missed issues from Validator C
-5. Sort: severity DESC, confidence DESC
+The final report should ONLY contain findings that are:
+1. **Confirmed** by mitigation validation (no existing protection found)
+2. **Partial** mitigations (some protection but incomplete)
-### Include Mitigation Summary
+**DO NOT INCLUDE** findings that are:
+- `mitigated` - full protection exists elsewhere
+- `false_positive` - not actually a vulnerability
+- Intentional design decisions with documented comments
+- Race conditions protected by atomic operations (Lua, transactions)
-For each finding that passed validation, include:
-```json
-{
-  "id": "SEC-001",
-  "mitigationStatus": "confirmed",
-  "mitigationChecks": [
-    "No input validation found between user input and SQL query",
-    "No ORM - raw SQL used",
-    "No middleware protection on this route"
-  ]
-}
-```
+### Step-by-Step Process:
-### SAVE OUTPUT AS JSON
+1. **Start with all Phase 1 findings**
+2. **Apply Mitigation Validator results (Phase 3):**
+   - `mitigated` → REMOVE from findings, add to `mitigatedFindings` array
+   - `false_positive` → REMOVE from findings, add to `falsePositives` array
+   - `partial` → KEEP but downgrade severity if specified
+   - `confirmed` → KEEP with original severity
+3. **Apply Cross-Validator results (Phase 4):**
+   - Additional false positives → REMOVE from findings
+   - Duplicates → Merge into single finding
+4. **Calculate final counts AFTER removals:**
+   - Only count findings that remain in the `findings` array
+   - Do NOT count mitigated or false positive findings
+5. **Add missed issues from Validator C**
+6. **Sort remaining findings:** severity DESC, confidence DESC
+### Final JSON Structure
 ```json
 {
   "projectName": "project-name",
   "scanDate": "{{SCAN_DATE}}",
   "summary": {
-    "total": 0,
-    "critical": 0,
-    "high": 0,
-    "medium": 0,
-    "low": 0,
-    "info": 0
+    "total": 10,
+    "critical": 1,
+    "high": 3,
+    "medium": 4,
+    "low": 2,
+    "info": 0,
+    "mitigatedCount": 5,
+    "falsePositiveCount": 3
   },
   "findings": [
-    "all findings with full fields including mitigationStatus"
+    "ONLY confirmed and partial findings - NOT mitigated or false positives!"
   ],
   "mitigatedFindings": [
-    {"id": "SEC-005", "reason": "Protected by Zod schema validation", "originalSeverity": "high"}
+    {
+      "id": "SEC-005",
+      "title": "Original finding title",
+      "originalSeverity": "high",
+      "reason": "Protected by Zod schema validation at src/routes/user.ts:23",
+      "mitigationType": "input_validation"
+    }
+  ],
+  "falsePositives": [
+    {
+      "id": "BIZ-004",
+      "title": "TOCTOU Race Condition",
+      "reason": "Redis Lua script provides atomic operation - no race condition possible",
+      "evidence": ["Lua script at src/services/rate-limit.js:95-113"]
+    },
+    {
+      "id": "AUTH-003",
+      "title": "PKCE Code Reuse",
+      "reason": "Intentional design decision documented in code comment",
+      "evidence": ["Comment: 'Allow reuse to prevent double-click race condition'"]
+    }
   ],
   "positiveObservations": [
     "Good pattern 1",
     "Good pattern 2"
   ],
-  "falsePositives": [
-    {"id": "...", "reason": "..."}
-  ],
+  "validationSummary": {
+    "totalInitialFindings": 18,
+    "mitigated": 5,
+    "falsePositives": 3,
+    "confirmed": 8,
+    "partial": 2,
+    "accuracy": "Only 56% of initial findings were actual issues"
+  },
   "agentsUsed": ["Security Core", "Auth & Session", "Mitigation Validator"],
   "scanDuration": 0
 }
 ```
+### Sanity Check Before Saving
+Before saving, verify:
+1. `findings` array does NOT contain any item from `mitigatedFindings` or `falsePositives`
+2. `summary.total` equals `findings.length`
+3. Severity counts match actual findings in array
+4. No duplicate IDs across findings/mitigated/falsePositives
 Save as: .coverme/scan.json
 Then generate PDF report:

package/dist/prompts/security-scanner.md CHANGED Viewed

@@ -145,12 +145,21 @@ Before reporting ANY secret/credential finding as critical or high:
    - If file matches .gitignore patterns = NOT exposed in repo
    - Mark as "info" severity, not "critical"
-3. **Identify environment context**:
+3. **CRITICAL: Check git HISTORY for secrets!**
+   Even if a file is currently gitignored, it may have been committed in the past:
+   ```bash
+   git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+   git log --all -p -S "AWS_SECRET" --source --all
+   ```
+   If the secret was EVER committed, it's CRITICAL - secrets in git history are exposed!
+4. **Identify environment context**:
    - `localhost`, `127.0.0.1`, `example.com` = development/example credentials
    - `.env.example`, `*.example.json` = template files, not real secrets
    - Mark these as "info" with note: "Development/example credentials"
-4. **Severity mapping for secrets**:
+5. **Severity mapping for secrets**:
+   - In git history (even if now removed) = CRITICAL
    - Tracked in git + real credentials = CRITICAL
    - Tracked in git + example/dev credentials = LOW
    - NOT tracked (gitignored) + real credentials = INFO (local only)
@@ -161,10 +170,62 @@ Always include in finding:
 {
   "gitTracked": true/false,
   "gitignored": true/false,
+  "inGitHistory": true/false,
   "appearsToBeDev": true/false
 }
 ```
+## Command Injection: Config Files Are NOT Safe!
+**DO NOT assume config file values are safe:**
+```javascript
+// STILL VULNERABLE even though pm2Name comes from config!
+const pm2Name = config.models[modelId].pm2Name;
+execSync(`pm2 start ${pm2Name}`);  // Command injection!
+```
+Config files (models.json, config.yaml) are attack vectors if:
+- File can be modified via admin panel/API
+- File permissions allow non-root writes
+- No schema validation on config values
+**Only mark as safe if:**
+- Using execFile() with argument array (not string interpolation)
+- Config values validated against strict whitelist/regex
+- Config is hardcoded at build time (not runtime loaded)
+## Security Misconfiguration Checks
+### Helmet Without Proper CSP
+```javascript
+app.use(helmet());  // Defaults only - NOT sufficient!
+```
+Report as MEDIUM if helmet() is called without:
+- Custom `contentSecurityPolicy` configuration
+- `hsts: { preload: true }` for HTTPS enforcement
+- Proper `referrerPolicy`
+### CORS Without Whitelist
+```javascript
+// VULNERABLE - reflects any origin!
+res.header('Access-Control-Allow-Origin', req.headers.origin);
+res.header('Access-Control-Allow-Origin', '*');
+```
+Report as MEDIUM unless there's explicit domain whitelist validation.
+### Missing Dependency Security
+Check for absence of:
+- `npm audit` in CI/CD pipeline (.github/workflows, .gitlab-ci.yml)
+- Dependabot/Renovate configuration
+- SBOM generation
+Report as HIGH if none exist - supply chain attacks are critical.
+### Missing Log Rotation
+Check Winston/Pino/Bunyan configs for:
+- `maxFiles` or `maxsize` settings
+- Log retention policy
+Report as LOW if missing - can lead to disk exhaustion.
 ## Files to Focus On
 Priority order:

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package/dist/report/generator.js CHANGED Viewed

@@ -564,6 +564,7 @@ async function generateHtmlReport(result, outputPath, falsePositives = []) {
     const templatePath = path.join(__dirname, '..', 'templates', 'report.html');
     const templateHtml = fs.readFileSync(templatePath, 'utf-8');
     const { grade, value } = calculateScore(result);
+    const counts = getSeverityCounts(result.summary);
     const criticalFindings = result.findings.filter(f => f.severity === 'critical');
     const highFindings = result.findings.filter(f => f.severity === 'high');
     const mediumFindings = result.findings.filter(f => f.severity === 'medium');
@@ -582,11 +583,11 @@ async function generateHtmlReport(result, outputPath, falsePositives = []) {
         }),
         scoreGrade: grade,
         scoreValue: value,
-        criticalCount: result.summary?.critical || 0,
-        highCount: result.summary?.high || 0,
-        mediumCount: result.summary?.medium || 0,
-        lowCount: result.summary?.low || 0,
-        infoCount: result.summary?.info || 0,
+        criticalCount: counts.critical,
+        highCount: counts.high,
+        mediumCount: counts.medium,
+        lowCount: counts.low,
+        infoCount: counts.info,
         executiveSummary: generateExecutiveSummary(result),
         criticalFindings,
         highFindings,
@@ -601,7 +602,7 @@ async function generateHtmlReport(result, outputPath, falsePositives = []) {
         positiveCount: result.positiveObservations?.length || 0,
         falsePositives,
         falsePositiveCount: falsePositives.length,
-        lowInfoCount: (result.summary?.low || 0) + (result.summary?.info || 0),
+        lowInfoCount: counts.low + counts.info,
         positiveObservations: result.positiveObservations || [],
         scanDuration: `${Math.round((result.scanDuration || 0) / 1000)}s`,
         agentCount: result.agentCount || result.agentsUsed?.length || 0,

package/dist/report/generator.js.map CHANGED Viewed

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "coverme-scanner",
-  "version": "1.0.18",
+  "version": "1.0.20",
   "description": "AI-powered code scanner with multi-agent verification for Claude Code. One command scans everything.",
   "main": "dist/index.js",
   "bin": {

package/src/prompts/cross-validator.md CHANGED Viewed

@@ -223,4 +223,48 @@ Focus: Find what was MISSED
 - Don't ignore context from CLAUDE.md
 - Don't miss the forest for the trees
+## CRITICAL: Things That Are NOT False Positives
+### Command Injection from Config Files
+**DO NOT dismiss as false positive!**
+```javascript
+execSync(`pm2 start ${configValue}`)  // STILL VULNERABLE!
+```
+Even if the value comes from a config file (models.json, config.yaml), if that file is:
+- Writable by users (admin panel, API)
+- Not validated against a strict schema
+- Could be modified by an attacker with file access
+Then it IS a real command injection. The attack vector is just indirect.
+**Only dismiss if:**
+- Config file is hardcoded at build time (not runtime loaded)
+- Config values are validated against strict regex/enum
+- execFile() is used instead of execSync() with proper argument array
+### Secrets in Git History
+**DO NOT dismiss just because file is now gitignored!**
+If a secret file was EVER committed, it may still be in git history.
+```bash
+git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+```
+If this returns results, the secret is STILL EXPOSED even if currently gitignored.
+### CORS Without Whitelist
+**DO NOT dismiss as "internal only"!**
+```javascript
+res.header('Access-Control-Allow-Origin', req.headers.origin);  // VULNERABLE
+```
+This reflects ANY origin. Even if the server is "internal", browser-based attacks can still:
+- Steal data via malicious website
+- Perform CSRF-like attacks
+- Exfiltrate to attacker-controlled domains
+### Missing Security Configuration
+**These are real findings, not false positives:**
+- `helmet()` without custom CSP configuration
+- Missing `npm audit` in CI pipeline
+- No Dependabot/Renovate for dependency updates
+- Logs without rotation/retention policy
 START VALIDATION NOW. Be critical but fair.

package/src/prompts/mitigation-validator.md CHANGED Viewed

@@ -178,6 +178,74 @@ The finding is incorrect:
 3. Is it localhost/development credentials only?
 4. Is there environment variable loading that overrides?
+### Race Condition / TOCTOU Findings (CRITICAL - Often False Positives)
+**Check for atomic operations that FULLY mitigate the race:**
+1. **Redis Lua Scripts** = FULL MITIGATION
+   - `redis.call()` inside Lua script is atomic
+   - SETNX, GETSET, INCR are atomic
+   - Look for: `eval`, `evalsha`, `script load`
+   ```javascript
+   // This is ATOMIC - no race condition!
+   redis.eval(`
+     local current = redis.call('GET', key)
+     if current < limit then
+       redis.call('INCR', key)
+       return 1
+     end
+     return 0
+   `)
+   ```
+2. **Database Transactions** = FULL MITIGATION
+   - `BEGIN...COMMIT` with proper isolation
+   - `SELECT FOR UPDATE` locks rows
+   - Prisma `$transaction()`, TypeORM `transaction()`
+   - Look for: `transaction`, `FOR UPDATE`, `SERIALIZABLE`
+3. **Atomic Compare-and-Swap** = FULL MITIGATION
+   - `WATCH/MULTI/EXEC` in Redis
+   - `findOneAndUpdate` with conditions in MongoDB
+   - `UPDATE ... WHERE version = ?` (optimistic locking)
+4. **Mutex/Locking** = FULL MITIGATION
+   - `redis-lock`, `redlock`
+   - Database advisory locks
+   - File locks (flock)
+**If ANY of these patterns exist, mark as MITIGATED, not "partial"!**
+### Intentional Design Decisions (Check Comments!)
+**Before reporting, check if there are comments explaining WHY:**
+1. **Search for explanatory comments near the code:**
+   ```
+   grep -B5 -A5 "intentional|by design|deliberately|on purpose|security note" <file>
+   ```
+2. **Common patterns that are INTENTIONAL:**
+   - PKCE code reuse to prevent double-click race conditions
+   - Longer token expiry for better UX (with other mitigations)
+   - Allowing certain "unsafe" operations for admin users
+   - Development-only bypasses with environment checks
+3. **If comment explains the decision:**
+   ```json
+   {
+     "verdict": "false_positive",
+     "reason": "Intentional design decision documented in code",
+     "evidence": ["Comment at line 45: 'Intentionally allow reuse to prevent double-submit'"]
+   }
+   ```
+### Open Redirect Findings
+1. **Check for whitelist validation:**
+   ```
+   grep -r "isValidRedirect|allowedDomains|whitelist|validateUrl" <file>
+   ```
+2. If whitelist exists and covers the redirect parameter = MITIGATED
+3. Check if validation function is actually called before redirect
 ## Output Format
 ```json

package/src/prompts/orchestration.md CHANGED Viewed

@@ -158,6 +158,32 @@ CHECK FOR:
 - API versioning issues
 - Excessive data exposure in responses
+**CORS MISCONFIGURATION** (MEDIUM):
+Look for these vulnerable patterns:
+```javascript
+// VULNERABLE - reflects ANY origin
+res.header('Access-Control-Allow-Origin', req.headers.origin);
+res.header('Access-Control-Allow-Origin', '*');
+// VULNERABLE - no whitelist validation
+app.use(cors({ origin: true }));
+```
+Only mark as safe if there's explicit whitelist validation:
+```javascript
+const allowedOrigins = ['https://app.example.com'];
+if (allowedOrigins.includes(origin)) { ... }
+```
+**HELMET MISCONFIGURATION** (MEDIUM):
+```javascript
+app.use(helmet());  // Using defaults only - INSUFFICIENT!
+```
+Check that helmet() includes:
+- Custom `contentSecurityPolicy` with proper directives
+- `hsts: { maxAge: 31536000, includeSubDomains: true, preload: true }`
+- Proper `referrerPolicy`
+Report as MEDIUM if using only defaults without customization.
 **FAIL-OPEN vs FAIL-CLOSED PATTERNS** (CRITICAL):
 - IP whitelist empty/missing = allow all (should deny all)
 - Auth middleware errors = request passes through (should block)
@@ -207,6 +233,14 @@ CHECK FOR:
 - Ansible vault passwords in plaintext
 - CI/CD pipeline secrets in yaml files (.github/workflows, .gitlab-ci.yml)
+**SECRETS IN GIT HISTORY** (CRITICAL CHECK!):
+Run these commands to check if secrets were EVER committed:
+```bash
+git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+git log --all -p -S "AWS_SECRET" -S "PRIVATE_KEY" --source
+```
+If secrets appear in history, they are EXPOSED even if now gitignored!
 **PRIVILEGE ESCALATION RISKS**:
 - Containers/processes running as root
 - Missing securityContext in K8s (runAsNonRoot, readOnlyRootFilesystem)
@@ -220,6 +254,20 @@ CHECK FOR:
 - Missing config = silent fallback to insecure defaults
 - No validation of secret strength/format at startup
+**DEPENDENCY SECURITY** (HIGH if missing):
+Check for presence of:
+- `npm audit` or `yarn audit` in CI pipeline
+- Dependabot/Renovate configuration (.github/dependabot.yml, renovate.json)
+- SBOM generation (cyclonedx, syft)
+- Snyk/Trivy/Grype scanning
+Report as HIGH if NONE of these exist - supply chain risk!
+**LOGGING & MONITORING**:
+- Log rotation configured? (maxFiles, maxsize in Winston/Pino)
+- Log retention policy defined?
+- Sensitive data redacted from logs?
+Report as LOW if log rotation missing - disk exhaustion risk.
 For EACH finding, output the FULL JSON format.
 ---
@@ -577,63 +625,107 @@ Output as list of strings.
 ## PHASE 7: BUILD CONSENSUS & GENERATE OUTPUT
-1. **Apply Mitigation Results** (from Phase 3):
-   - Remove findings marked as `mitigated` or `false_positive`
-   - Adjust severity for findings marked as `partial`
-   - Add mitigation notes to confirmed findings
+### CRITICAL: Actually Remove False Positives!
-2. Calculate confidence: (confirmations / total_validators) * 100
-3. Remove findings with confidence < 50%
-4. Add missed issues from Validator C
-5. Sort: severity DESC, confidence DESC
+The final report should ONLY contain findings that are:
+1. **Confirmed** by mitigation validation (no existing protection found)
+2. **Partial** mitigations (some protection but incomplete)
-### Include Mitigation Summary
+**DO NOT INCLUDE** findings that are:
+- `mitigated` - full protection exists elsewhere
+- `false_positive` - not actually a vulnerability
+- Intentional design decisions with documented comments
+- Race conditions protected by atomic operations (Lua, transactions)
-For each finding that passed validation, include:
-```json
-{
-  "id": "SEC-001",
-  "mitigationStatus": "confirmed",
-  "mitigationChecks": [
-    "No input validation found between user input and SQL query",
-    "No ORM - raw SQL used",
-    "No middleware protection on this route"
-  ]
-}
-```
+### Step-by-Step Process:
-### SAVE OUTPUT AS JSON
+1. **Start with all Phase 1 findings**
+2. **Apply Mitigation Validator results (Phase 3):**
+   - `mitigated` → REMOVE from findings, add to `mitigatedFindings` array
+   - `false_positive` → REMOVE from findings, add to `falsePositives` array
+   - `partial` → KEEP but downgrade severity if specified
+   - `confirmed` → KEEP with original severity
+3. **Apply Cross-Validator results (Phase 4):**
+   - Additional false positives → REMOVE from findings
+   - Duplicates → Merge into single finding
+4. **Calculate final counts AFTER removals:**
+   - Only count findings that remain in the `findings` array
+   - Do NOT count mitigated or false positive findings
+5. **Add missed issues from Validator C**
+6. **Sort remaining findings:** severity DESC, confidence DESC
+### Final JSON Structure
 ```json
 {
   "projectName": "project-name",
   "scanDate": "{{SCAN_DATE}}",
   "summary": {
-    "total": 0,
-    "critical": 0,
-    "high": 0,
-    "medium": 0,
-    "low": 0,
-    "info": 0
+    "total": 10,
+    "critical": 1,
+    "high": 3,
+    "medium": 4,
+    "low": 2,
+    "info": 0,
+    "mitigatedCount": 5,
+    "falsePositiveCount": 3
   },
   "findings": [
-    "all findings with full fields including mitigationStatus"
+    "ONLY confirmed and partial findings - NOT mitigated or false positives!"
   ],
   "mitigatedFindings": [
-    {"id": "SEC-005", "reason": "Protected by Zod schema validation", "originalSeverity": "high"}
+    {
+      "id": "SEC-005",
+      "title": "Original finding title",
+      "originalSeverity": "high",
+      "reason": "Protected by Zod schema validation at src/routes/user.ts:23",
+      "mitigationType": "input_validation"
+    }
+  ],
+  "falsePositives": [
+    {
+      "id": "BIZ-004",
+      "title": "TOCTOU Race Condition",
+      "reason": "Redis Lua script provides atomic operation - no race condition possible",
+      "evidence": ["Lua script at src/services/rate-limit.js:95-113"]
+    },
+    {
+      "id": "AUTH-003",
+      "title": "PKCE Code Reuse",
+      "reason": "Intentional design decision documented in code comment",
+      "evidence": ["Comment: 'Allow reuse to prevent double-click race condition'"]
+    }
   ],
   "positiveObservations": [
     "Good pattern 1",
     "Good pattern 2"
   ],
-  "falsePositives": [
-    {"id": "...", "reason": "..."}
-  ],
+  "validationSummary": {
+    "totalInitialFindings": 18,
+    "mitigated": 5,
+    "falsePositives": 3,
+    "confirmed": 8,
+    "partial": 2,
+    "accuracy": "Only 56% of initial findings were actual issues"
+  },
   "agentsUsed": ["Security Core", "Auth & Session", "Mitigation Validator"],
   "scanDuration": 0
 }
 ```
+### Sanity Check Before Saving
+Before saving, verify:
+1. `findings` array does NOT contain any item from `mitigatedFindings` or `falsePositives`
+2. `summary.total` equals `findings.length`
+3. Severity counts match actual findings in array
+4. No duplicate IDs across findings/mitigated/falsePositives
 Save as: .coverme/scan.json
 Then generate PDF report:

package/src/prompts/security-scanner.md CHANGED Viewed

@@ -145,12 +145,21 @@ Before reporting ANY secret/credential finding as critical or high:
    - If file matches .gitignore patterns = NOT exposed in repo
    - Mark as "info" severity, not "critical"
-3. **Identify environment context**:
+3. **CRITICAL: Check git HISTORY for secrets!**
+   Even if a file is currently gitignored, it may have been committed in the past:
+   ```bash
+   git log --all --full-history -- "**/secrets*" "**/credentials*" "**/*.env"
+   git log --all -p -S "AWS_SECRET" --source --all
+   ```
+   If the secret was EVER committed, it's CRITICAL - secrets in git history are exposed!
+4. **Identify environment context**:
    - `localhost`, `127.0.0.1`, `example.com` = development/example credentials
    - `.env.example`, `*.example.json` = template files, not real secrets
    - Mark these as "info" with note: "Development/example credentials"
-4. **Severity mapping for secrets**:
+5. **Severity mapping for secrets**:
+   - In git history (even if now removed) = CRITICAL
    - Tracked in git + real credentials = CRITICAL
    - Tracked in git + example/dev credentials = LOW
    - NOT tracked (gitignored) + real credentials = INFO (local only)
@@ -161,10 +170,62 @@ Always include in finding:
 {
   "gitTracked": true/false,
   "gitignored": true/false,
+  "inGitHistory": true/false,
   "appearsToBeDev": true/false
 }
 ```
+## Command Injection: Config Files Are NOT Safe!
+**DO NOT assume config file values are safe:**
+```javascript
+// STILL VULNERABLE even though pm2Name comes from config!
+const pm2Name = config.models[modelId].pm2Name;
+execSync(`pm2 start ${pm2Name}`);  // Command injection!
+```
+Config files (models.json, config.yaml) are attack vectors if:
+- File can be modified via admin panel/API
+- File permissions allow non-root writes
+- No schema validation on config values
+**Only mark as safe if:**
+- Using execFile() with argument array (not string interpolation)
+- Config values validated against strict whitelist/regex
+- Config is hardcoded at build time (not runtime loaded)
+## Security Misconfiguration Checks
+### Helmet Without Proper CSP
+```javascript
+app.use(helmet());  // Defaults only - NOT sufficient!
+```
+Report as MEDIUM if helmet() is called without:
+- Custom `contentSecurityPolicy` configuration
+- `hsts: { preload: true }` for HTTPS enforcement
+- Proper `referrerPolicy`
+### CORS Without Whitelist
+```javascript
+// VULNERABLE - reflects any origin!
+res.header('Access-Control-Allow-Origin', req.headers.origin);
+res.header('Access-Control-Allow-Origin', '*');
+```
+Report as MEDIUM unless there's explicit domain whitelist validation.
+### Missing Dependency Security
+Check for absence of:
+- `npm audit` in CI/CD pipeline (.github/workflows, .gitlab-ci.yml)
+- Dependabot/Renovate configuration
+- SBOM generation
+Report as HIGH if none exist - supply chain attacks are critical.
+### Missing Log Rotation
+Check Winston/Pino/Bunyan configs for:
+- `maxFiles` or `maxsize` settings
+- Log retention policy
+Report as LOW if missing - can lead to disk exhaustion.
 ## Files to Focus On
 Priority order:

package/src/report/generator.ts CHANGED Viewed

@@ -667,6 +667,7 @@ export async function generateHtmlReport(
   const templateHtml = fs.readFileSync(templatePath, 'utf-8');
   const { grade, value } = calculateScore(result);
+  const counts = getSeverityCounts(result.summary);
   const criticalFindings = result.findings.filter(f => f.severity === 'critical');
   const highFindings = result.findings.filter(f => f.severity === 'high');
@@ -688,11 +689,11 @@ export async function generateHtmlReport(
     }),
     scoreGrade: grade,
     scoreValue: value,
-    criticalCount: result.summary?.critical || 0,
-    highCount: result.summary?.high || 0,
-    mediumCount: result.summary?.medium || 0,
-    lowCount: result.summary?.low || 0,
-    infoCount: result.summary?.info || 0,
+    criticalCount: counts.critical,
+    highCount: counts.high,
+    mediumCount: counts.medium,
+    lowCount: counts.low,
+    infoCount: counts.info,
     executiveSummary: generateExecutiveSummary(result),
     criticalFindings,
     highFindings,
@@ -707,7 +708,7 @@ export async function generateHtmlReport(
     positiveCount: result.positiveObservations?.length || 0,
     falsePositives,
     falsePositiveCount: falsePositives.length,
-    lowInfoCount: (result.summary?.low || 0) + (result.summary?.info || 0),
+    lowInfoCount: counts.low + counts.info,
     positiveObservations: result.positiveObservations || [],
     scanDuration: `${Math.round((result.scanDuration || 0) / 1000)}s`,
     agentCount: (result as any).agentCount || result.agentsUsed?.length || 0,