Snyk Fix (All-in-One)

Complete security remediation workflow in a single command. Scans for vulnerabilities, fixes them, validates the fix, and optionally creates a PR.

Workflow: Parse → Scan → Analyze → Fix → Validate → Summary → (Optional) PR

Modes:

• Single Mode (default): Fix one vulnerability type at a time

• Batch Mode: Fix multiple vulnerabilities in priority order

Example Triggers

Single Mode (One Issue)

User Request Behavior

"fix security issues" Auto-detect scan type, fix highest priority issue (all instances)

"fix code vulnerabilities" SAST scan only, fix highest priority code issue (all instances in file)

"fix dependency vulnerabilities" SCA scan only, fix highest priority dependency issue

"fix SNYK-JS-LODASH-1018905" Fix specific Snyk issue by ID

"fix CVE-2021-44228" Find and fix specific CVE

"fix vulnerabilities in lodash" Fix highest priority issue in lodash package

"fix security issues in server.ts" Code scan on file, fix highest priority issue (all instances)

"fix XSS vulnerabilities" Fix all XSS vulnerabilities in highest priority file

"fix path traversal" Fix all path traversal vulnerabilities

Batch Mode (Multiple Issues)

User Request Behavior

"fix all security issues" Fix ALL vulnerabilities by priority (Critical → Low)

"fix all critical vulnerabilities" Fix only Critical severity issues

"fix all high and critical" Fix Critical and High severity issues

"fix all code vulnerabilities" Fix all SAST issues in the project

"fix all dependency issues" Fix all SCA issues in the project

"fix top 5 vulnerabilities" Fix the 5 highest priority issues

"fix all issues in src/" Fix all vulnerabilities in specified directory

Batch Mode Overview

Batch mode fixes multiple vulnerabilities in a single session. Use when the user says "all", "batch", or specifies a severity filter.

Batch Mode Workflow

1. Scan entire project (SAST + SCA)
2. Filter by severity/type if specified
3. Group vulnerabilities by type and priority
4. For each group (in priority order): a. Fix all instances of that vulnerability type b. Validate the fix c. Track results
5. Generate comprehensive summary
6. Prompt for single PR with all fixes

Batch Mode Limits

Setting Value Notes

Max vulnerabilities 20 To avoid overwhelming changes

Max files modified 15 To keep PRs reviewable

Timeout per fix 3 attempts Same as single mode

Stop on failure Configurable Can continue or stop

Batch Priority Order

• Critical with known exploit

• Critical without exploit

• High with known exploit

• High without exploit

• Medium severity

• Low severity

Within same priority: Code (SAST) issues before SCA issues (code fixes are typically more urgent).

Phase 1: Input Parsing

Parse user input to extract:

• mode: Single (default) or Batch (if user says "all", "batch", or specifies count/severity filter)

• scan_type: Explicit (code , sca , both ) or infer from context

• target_vulnerability: Specific issue ID, CVE, package name, file reference, or vulnerability type

• target_path: File or directory to focus on (defaults to project root)

• severity_filter: For batch mode - which severities to include

• max_fixes: For batch mode - maximum vulnerabilities to fix (default: 20)

Mode Detection Rules

Batch Mode Indicators:

• User says "all" (e.g., "fix all vulnerabilities")

• User specifies severity filter (e.g., "fix all high and critical")

• User specifies count (e.g., "fix top 5")

• User says "batch" explicitly

Single Mode (default):

• User specifies a single vulnerability ID

• User mentions one vulnerability type

• User references a specific file

• No batch indicators present

Scan Type Detection Rules (in priority order)

• Explicit code: User says "code", "sast", "static" → Code scan

• Explicit sca: User says "sca", "dependency", "package", "npm", "pip", "maven" → SCA scan

• Vulnerability ID provided:

• Starts with SNYK- → run both scans to locate it

• Contains CVE- → run both scans to find it

• Vulnerability type provided: User mentions type like "XSS", "SQL injection", "path traversal" → Code scan

• File reference: User mentions .ts , .js , .py , etc. file → Code scan on that file

• Package reference: User mentions known package name (e.g., "lodash", "express") → SCA scan

• Default (no hints): Run BOTH scans, select highest priority issue

Phase 1B: Batch Mode Planning (Skip if Single Mode)

Only execute this phase if Batch Mode was detected in Phase 1.

Step 1B.1: Run Full Project Scan

Run comprehensive scans to discover all vulnerabilities:

Run both scans:

• mcp_snyk_snyk_code_scan with path = project root
• mcp_snyk_snyk_sca_scan with path = project root

Step 1B.2: Filter Results

Apply user-specified filters:

Filter Example Result

Severity "critical only" Only Critical vulns

Severity "high and critical" Critical + High

Type "code vulnerabilities" Only SAST results

Type "dependency issues" Only SCA results

Path "in src/" Only vulns in src/

Count "top 5" First 5 by priority

Step 1B.3: Group and Prioritize

Group vulnerabilities for efficient fixing:

• Group by type: Same vulnerability ID in same file (code) or same package (SCA)

• Sort by priority: Critical > High > Medium > Low

• Within priority: Prefer issues with available fixes

Step 1B.4: Generate Fix Plan

Display the batch fix plan to user:

Batch Fix Plan

Mode: Batch Remediation Filter: [severity/type/path filter if any] Total Vulnerabilities: [count]

Fix Order

Estimated Changes: [X files, Y packages]

Proceed with batch fix? (yes/no/adjust)

Wait for user confirmation before proceeding.

If user says "adjust", allow them to modify the plan (exclude items, change order, etc.).

Step 1B.5: Execute Batch Fixes

For each vulnerability group in the plan:

• Execute the appropriate fix phase (Phase 3 for Code, Phase 4 for SCA)

• Validate the fix (Phase 5)

• Track result (success/failure/partial)

• If failure and stop_on_failure=true : Stop and report

• If failure and stop_on_failure=false : Continue to next item

After all fixes attempted, proceed to Phase 6B (Batch Summary).

Phase 2: Discovery

Goal: Run scan(s) and identify the vulnerability type to fix, including ALL instances of that type in the same file (for code vulnerabilities)

Step 2.1: Run Security Scan(s)

Based on scan type detection:

• Code only: Run mcp_snyk_snyk_code_scan with path set to project root or specific file

• SCA only: Run mcp_snyk_snyk_sca_scan with path set to project root

• Both: Run both scans in parallel

Step 2.2: Select Target Vulnerability Type

If user specified a vulnerability:

• Search scan results for matching issue (by ID, CVE, package name, vulnerability type, or description)

• If NOT found: Report "Vulnerability not found in scan results" and STOP

• If found: Note whether it's a Code or SCA issue

If user did NOT specify a vulnerability:

• From ALL scan results, select the highest priority vulnerability TYPE using this priority:

• Critical severity with known exploit

• Critical severity

• High severity with known exploit

• High severity

• Medium severity

• Low severity

• Within same priority: prefer issues with available fixes/upgrades

Step 2.3: Group All Instances (Code Vulnerabilities Only)

IMPORTANT for Code vulnerabilities: After selecting the vulnerability type, find ALL instances of that same vulnerability type in the same file:

• Same vulnerability ID (e.g., javascript/PT , javascript/XSS , python/SQLi )

• In the same file

Example: If scan finds:

High Path Traversal src/api/files.ts:45 javascript/PT High Path Traversal src/api/files.ts:112 javascript/PT
High XSS src/api/files.ts:78 javascript/XSS

And Path Traversal is selected as highest priority, target BOTH lines 45 and 112.

Step 2.4: Document Target

For Code vulnerabilities:

Target Vulnerability

• Type: Code (SAST)
• ID: [Snyk ID] (e.g., javascript/PT)
• Severity: [Critical | High | Medium | Low]
• Title: [vulnerability title]
• CWE: [CWE-XXX if available]
• Instances to Fix: [count]

For SCA vulnerabilities:

Target Vulnerability

• Type: SCA (Dependency)
• ID: [Snyk Issue ID]
• Severity: [Critical | High | Medium | Low]
• Package: [package@current_version]
• Title: [vulnerability title]
• Fix Version: [minimum version that fixes]
• Dependency Path: [direct | transitive via X → Y → Z]

Phase 3: Remediation (Code Vulnerabilities)

Skip to Phase 4 if this is an SCA vulnerability.

Step 3.1: Understand the Vulnerability

• Read the affected file and ALL vulnerable locations

• Identify the vulnerability type:

• Injection (SQL, Command, LDAP, etc.)

• XSS (Cross-Site Scripting)

• Path Traversal

• Sensitive Data Exposure

• Insecure Deserialization

• Security Misconfiguration

• Cryptographic Issues

• Other (check Snyk description)

• Review Snyk's remediation guidance if provided

• Look for patterns across instances (often the same fix approach applies)

Step 3.2: Plan the Fix

Before implementing, document the approach:

Fix Plan

• Vulnerability Type: [type]
• Root Cause: [why the code is vulnerable]
• Fix Approach: [what will be changed]
• Security Mechanism: [what protection is being added]
• Instances Affected: [count] locations in [file]

Common fix patterns:

Vulnerability Fix Pattern

SQL Injection Parameterized queries / prepared statements

Command Injection Input validation + shell escaping or avoid shell

Path Traversal Canonicalize path + validate against allowed base

XSS Output encoding / sanitization appropriate to context

Sensitive Data Exposure Remove/mask data, use secure headers

Hardcoded Secrets Move to environment variables / secrets manager

Step 3.3: Apply the Fix to ALL Instances

• Fix ALL identified instances of the vulnerability type in the file

• Apply consistent fix pattern across all instances

• Make the minimal code change needed at each location

• Prefer standard library/framework security features over custom solutions

• Consider creating a shared helper function if:

• 3+ instances exist with identical fix pattern

• The helper improves readability without over-engineering

• Add comments explaining security-relevant changes if non-obvious

• Do NOT refactor unrelated code

• Do NOT change business logic

Order of fixes: Fix from bottom of file to top (highest line number first) to avoid line number shifts affecting subsequent fixes.

Continue to Phase 5 (Validation).

Phase 4: Remediation (SCA Vulnerabilities)

Skip to Phase 5 if this is a Code vulnerability (already handled in Phase 3).

Step 4.1: Analyze Dependency Path

• Document the full dependency path (direct → transitive → vulnerable)

• Identify manifest files to modify (package.json , requirements.txt , etc.)

• Determine if vulnerable package is direct or transitive

For transitive dependencies:

• Identify which direct dependency pulls in the vulnerable transitive

• Check if upgrading the direct dependency will pull in the fixed transitive

• If app directly imports the transitive: note this for breaking change analysis

Step 4.2: Check for Breaking Changes

Search codebase for potential impact:

Search for imports of the package

grep -r "from 'package'" --include=".ts" --include=".js" grep -r "require('package')" --include=".ts" --include=".js"

If complex breaking changes detected:

• Add TODO comments with migration notes

• Note in summary that manual review is needed

Step 4.3: Apply Minimal Upgrade

• Edit ONLY the necessary dependency in the manifest

• Use the LOWEST version that fixes the vulnerability

• Preserve file formatting and comments

Example (package.json):

// Before "lodash": "^4.17.15"

// After - minimal fix "lodash": "^4.17.21"

Step 4.4: Regenerate Lockfile

Run the appropriate install command:

Package Manager Command

npm (major upgrade) npm install <pkg>@<version>

npm (minor/patch) npm install

yarn yarn install or yarn upgrade <pkg>@<version>

pip pip install -r requirements.txt

maven mvn dependency:resolve

If installation fails:

• If sandbox/permission issue: retry with elevated permissions

• If dependency conflict: try a different version or note as unfixable

• Revert manifest changes if resolution completely fails

• Document the failure reason

Phase 5: Validation

Step 5.1: Re-run Security Scan

• Run mcp_snyk_snyk_code_scan or mcp_snyk_snyk_sca_scan on the same target

• Verify ALL targeted vulnerability instances are NO LONGER reported

For Code vulnerabilities - If any instances still present:

• Review the fix attempt for that specific instance

• Try alternative approach

• Maximum 3 total attempts per instance, then report partial success/failure

For SCA vulnerabilities - If vulnerability still present:

• Check if lockfile was properly updated

• Try explicit version install: npm install <pkg>@<exact_version>

• Maximum 3 attempts, then STOP and report failure

If NEW vulnerabilities introduced:

For Code:

• Code fixes must be clean — no new vulnerabilities allowed

• Attempt to fix any new issues introduced by your fix

• Iterate until clean (max 3 total attempts)

• If unable to produce clean fix: Revert ALL changes and report failure

For SCA:

• Check severity trade-off:

• New severity LOWER than fixed: Accept (net security improvement)

• New severity EQUAL OR HIGHER: Try higher version (up to 3 iterations)

• If no clean version exists: Revert and report as unfixable

Step 5.1a: Identify Additional Issues Fixed (SCA Only)

A single upgrade often fixes multiple vulnerabilities:

• Compare pre-fix and post-fix scan results

• Identify ALL vulnerabilities resolved by this upgrade

• Record each: ID, severity, title

Step 5.2: Run Tests

• Execute project tests (npm test , pytest , etc.)

• If tests fail due to the fix:

• Prefer adjusting the fix over changing tests

• Only modify tests if the fix legitimately changes expected behavior

• Apply mechanical fixes only (renamed imports, etc.)

• Maximum 2 attempts to resolve test failures

Step 5.3: Run Linting

• Run project linter if configured

• Fix any formatting issues introduced

Phase 6: Summary & PR Prompt

Step 6.1: Display Remediation Summary

For Code vulnerabilities (single or multiple instances):

Remediation Summary

What Was Fixed

[2-3 sentence plain-English explanation of the vulnerability and how it was fixed. No code snippets.]

Validation

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Should I create a PR for this fix? (yes / no)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

For SCA vulnerabilities:

Remediation Summary

Additional Issues Fixed by This Upgrade

Total issues fixed: [count]

What Was Fixed

[2-3 sentence plain-English explanation of the vulnerability and how it was fixed.]

Validation

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Should I create a PR for this fix? (yes / no)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Rules for this summary:

• Do NOT include code snippets (before/after)

• Do NOT list remaining issues in codebase

• Keep "What Was Fixed" to 2-3 sentences max

• Use visual separator (━) around PR prompt to make it stand out

Step 6.2: Send Feedback to Snyk

After successful fix, report the remediation using mcp_snyk_snyk_send_feedback :

• fixedExistingIssuesCount: [total issues fixed]

• preventedIssuesCount: 0

• path: [absolute project path]

Step 6.3: Wait for User Response

IMPORTANT: Do NOT proceed until the user explicitly confirms.

Phase 6B: Batch Summary (Batch Mode Only)

Only execute this phase after completing all batch fixes.

Step 6B.1: Generate Comprehensive Summary

Batch Remediation Summary

Overall Results

Issues Fixed by Severity

Detailed Results

Code Vulnerabilities Fixed

Dependency Vulnerabilities Fixed

Files Modified

• src/db.ts
• src/api/render.ts
• src/files.ts
• package.json
• package-lock.json

Validation Results

Issues NOT Fixed

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Should I create a single PR for all these fixes? (yes / no)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Step 6B.2: Send Batch Feedback

Report all fixes to Snyk:

Run mcp_snyk_snyk_send_feedback with:

• path: [project root]
• fixedExistingIssuesCount: [total issues fixed across all vulns]
• preventedIssuesCount: 0

Step 6B.3: Batch PR Handling

If user confirms PR for batch fixes:

Branch naming for batch:

• fix/security-batch-YYYYMMDD

• fix/security-critical-high-batch

Commit strategy:

• Option 1: Single commit with all changes

• Option 2: One commit per vulnerability type (cleaner history)

Default to Option 1 unless user prefers separate commits.

PR Body for Batch:

Security Fixes (Batch)

This PR addresses multiple security vulnerabilities identified by Snyk.

Summary

• Code vulnerabilities fixed: [count]
• Dependency vulnerabilities fixed: [count]
• Total CVEs resolved: [count]

Code Fixes

Dependency Upgrades

Validation

• Snyk scans pass
• Tests pass
• No new vulnerabilities introduced

Review Notes

Each fix was validated independently before inclusion in this batch.

Phase 7: Create PR (If Confirmed)

Only execute if user says "yes" to PR prompt.

Step 7.1: Check Git Status

git status

Verify:

• There are uncommitted changes (staged or unstaged)

• The changes are related to the security fix

If no changes found: Report "No uncommitted changes to commit" and STOP

Step 7.2: Create Branch

Format: fix/security-<identifier>

Examples:

• fix/security-SNYK-JS-LODASH-1018905

• fix/security-cwe-79-xss

• fix/security-path-traversal-server

• fix/security-lodash-upgrade

git checkout -b fix/security-<identifier>

Step 7.3: Stage and Commit

Stage only files related to the security fix:

git add <files>

Do NOT stage:

• Unrelated changes

• IDE/editor files

• Build artifacts

Create commit:

git commit -m "fix(security): <description>

Resolves: [Snyk ID or CVE] Severity: [Critical/High/Medium/Low]"

Step 7.4: Push Branch

git push -u origin fix/security-<identifier>

Step 7.5: Create Pull Request

gh pr create
--title "Security: <title>"
--body "<body>"
--base main

PR Body Template:

Security Fix

Vulnerability Details

• ID: [Snyk ID or CVE]
• Severity: [Critical | High | Medium | Low]
• Type: [SCA | Code]

Changes Made

[Description of the fix]

Files Changed

• [list files]

Validation

• Snyk scan passes
• Tests pass
• No new vulnerabilities introduced

IMPORTANT:

• Do NOT use --label flags (labels may not exist in repo)

Step 7.6: Output Confirmation

PR Created Successfully

• PR URL: [URL]
• Branch: fix/security-<identifier>
• Title: [PR title]
• Status: Ready for review

Next Steps

1. Review the PR at the URL above
2. Request reviews from team members
3. Merge when approved

Error Handling

Authentication Errors

• Run mcp_snyk_snyk_auth and retry once

• If still failing: STOP and ask user to authenticate manually

Scan Timeout/Failure

• Retry once

• If still failing: STOP and report the error

Vulnerability Not Found

• If user specified a vulnerability that doesn't appear in scan results

• Report clearly and STOP (don't guess or fix something else)

Unfixable Code Vulnerability

If the vulnerability cannot be fixed automatically:

• Document why it cannot be fixed (complex refactoring needed, unclear fix, etc.)

• Add TODO comment in the affected file with context

• Report to user with manual remediation suggestions

• Do NOT leave partial/broken fixes

SCA - No Fix Available

If no upgrade path exists:

• Document this clearly

• Suggest alternatives (replace package, patch, accept risk)

• Do NOT make changes

Partial Success (Code)

If some instances are fixed but others fail:

• Keep the successful fixes

• Document which instances remain unfixed and why

• Add TODO comments for unfixed instances

• Report partial success in summary with clear breakdown

Rollback Triggers

Revert ALL changes if:

• Unable to produce clean fix after 3 attempts (new vulnerabilities introduced)

• Tests fail and cannot be reasonably fixed

• Fix would require changing business logic

• Dependency resolution completely fails

Git/PR Errors

Error Resolution

Not a git repository STOP - cannot create PR

Branch already exists Generate unique branch name with timestamp

SSH key error Retry command

Not authenticated (gh) Suggest gh auth login

Constraints

Single Mode

• One vulnerability TYPE per run - Fix all instances of ONE vulnerability type (Code) or ONE dependency issue (SCA)

• Minimal changes - Only modify what's necessary

• No new vulnerabilities - Fixes must be clean (or net improvement for SCA)

• Preserve functionality - Tests must pass

• No scope creep - Don't refactor or "improve" other code

• Consistent fixes - Apply the same fix pattern across all instances (Code)

• User confirmation for PR - Never auto-create PRs

• Always prompt for PR - Every successful fix MUST end with the PR prompt question

Batch Mode Additional Constraints

• User approval required - Must confirm batch plan before starting

• Max 20 vulnerabilities - Keep batch fixes manageable

• Max 15 files - Keep PRs reviewable

• Validate each fix - Each vulnerability fix is validated before proceeding to next

• Partial success allowed - Can complete batch even if some fixes fail

• Single PR for batch - All batch fixes go into one PR (unless user requests otherwise)

• Detailed tracking - Track success/failure for each item in batch

Completion Checklist

Single Mode Checklist

Before ending the conversation, verify ALL are complete:

• Vulnerability type identified and documented (including all instances for code vulns)

• Fix applied successfully

• Re-scan shows ALL instances resolved (or net improvement for SCA)

• Tests pass (or failures documented)

• Summary displayed to user (with instance count if multiple)

• Snyk feedback sent with correct count

• PR prompt asked ← Do NOT skip this step

• PR created (if user confirmed)

Batch Mode Checklist

Before ending the conversation, verify ALL are complete:

• Full project scan completed (SAST + SCA)

• Batch plan generated and shown to user

• User approved the batch plan

• Each vulnerability in plan was attempted

• Each fix was validated before proceeding to next

• Results tracked for all items (success/partial/failed)

• Comprehensive batch summary displayed

• Total fix count sent to Snyk feedback

• PR prompt asked with all batch changes

• Single PR created with all fixes (if user confirmed)