dependabot-snyk-pr-management

name	dependabot-snyk-pr-management
description	Interact with Dependabot and Snyk pull requests for dependency upgrades and security fixes. Documents Dependabot commands, javax/jakarta compatibility checks, safe merge workflows, and troubleshooting. Use when managing dependency upgrade PRs or security fix PRs.

Dependabot and Snyk PR Management

Interact with Dependabot and Snyk pull requests for dependency upgrades and security fixes.

When to Use

Use when:

• User asks to "rebase Dependabot PR", "merge Dependabot PR", or similar
• User asks to "update dependencies", "fix Snyk alerts", or similar
• Investigating failed dependency upgrade PRs
• Reviewing security vulnerability PRs from Snyk or Dependabot

Safety Rules

IMPORTANT: Before merging, rebasing, or closing any PR:

1. Verify PR author is app/dependabot or a Snyk bot
2. Check CI status (all checks must pass for merge)
3. Verify javax/jakarta compatibility (see section below)
4. Review changed dependencies and scope
5. Never use git add . — stage explicit files only
6. Never force-push to bot-owned branches without explicit user approval

Dependabot Commands

Dependabot responds to commands in PR comments. All commands are invoked via @dependabot <command>.

Response behavior: Dependabot reacts with 👍 and may take several minutes to process the command.

Common Commands

Command	Purpose	When to Use
@dependabot rebase	Rebase PR onto latest base branch	When PR is behind master or needs to pick up recent fixes
@dependabot recreate	Close and recreate PR from scratch	When PR is in a bad state or has conflicts
@dependabot merge	Merge PR (if all checks pass)	To auto-merge via Dependabot (alternative: gh pr merge --auto)
@dependabot squash and merge	Squash and merge PR	Preferred for dependency bumps to keep history clean
@dependabot cancel merge	Cancel a previously requested merge	If you change your mind
@dependabot close	Close PR without merging	To reject an upgrade
@dependabot reopen	Reopen a closed PR	To reconsider a previously rejected upgrade
@dependabot ignore this dependency	Never upgrade this dependency	For permanently pinned dependencies
@dependabot ignore this major version	Skip this major version	When major version requires code changes
@dependabot ignore this minor version	Skip this minor version	When minor version has issues
@dependabot ignore this patch version	Skip this patch version	When patch version has issues
@dependabot show <dep> ignore conditions	Show current ignore rules for dependency	Before removing ignore rules
@dependabot unignore <dep>	Remove all ignore rules for dependency	Re-enable upgrades for a specific dependency

Note: Ignore commands create repository-level preferences. For team visibility, also update .github/dependabot.yml when adding permanent ignore rules.

Example Usage

Rebase a Dependabot PR:

gh pr comment <PR_NUMBER> --body "@dependabot rebase"

Merge a Dependabot PR (preferred: use GitHub native merge):

# Preferred: GitHub native merge with auto-merge when checks pass
gh pr merge <PR_NUMBER> --squash --auto

# Alternative: delegate to Dependabot
gh pr comment <PR_NUMBER> --body "@dependabot squash and merge"

Ignore a major version:

gh pr comment <PR_NUMBER> --body "@dependabot ignore this major version"

Close and reject an upgrade:

gh pr comment <PR_NUMBER> --body "@dependabot close"

Workflow: Rebase to Trigger Fresh Build

When a Dependabot PR fails due to a flaky test or a fix has been merged to master:

1. Ask Dependabot to rebase:

   gh pr comment <PR_NUMBER> --body "@dependabot rebase"
   

2. Dependabot will:

   • Rebase the PR branch onto latest master
   • Push the rebased commits
   • Trigger all CI checks (Buildkite, CodeQL, Snyk, etc.)

3. Monitor the rebuild:

   gh pr checks <PR_NUMBER> --watch
   

This is the preferred method for re-triggering builds on Dependabot PRs because:

• ✅ Simpler than manual empty commits
• ✅ Picks up latest master changes automatically
• ✅ Dependabot manages the rebase (no local checkout needed)
• ✅ Maintains Dependabot authorship and metadata

Snyk PRs

Snyk creates PRs to fix security vulnerabilities. These PRs are created by the Snyk bot and follow similar patterns to Dependabot.

Snyk PR Workflow

1. Review the vulnerability:

   • Check the Snyk PR description for CVE details
   • Review the severity (critical, high, medium, low)
   • Check if the fix is a direct or transitive dependency upgrade
   • Check javax/jakarta compatibility (see section below)

2. Test the fix:

   • Snyk PRs trigger the same CI checks as any PR
   • Wait for Buildkite, CodeQL, and Snyk checks to pass
   • Run local tests if needed

3. Merge or close:

   • If tests pass and javax-compatible: gh pr merge <PR_NUMBER> --squash
   • If the upgrade forces the jakarta namespace: close and document workaround (pin old version or accept vulnerability)
   • If tests fail: investigate failure (may need code changes)
   • If false positive: close and mark as ignored in Snyk UI

Snyk Commands

Snyk bot does not respond to comments like Dependabot. To manage Snyk PRs:

Merge (preferred):

gh pr merge <PR_NUMBER> --squash

Close:

gh pr close <PR_NUMBER>

Rebase:

Snyk PRs cannot be safely rebased via git commands because:

• Snyk bot owns the branch on the Snyk fork
• Force pushing to bot-owned branches can cause sync conflicts
• The PR cannot be updated from external forks without special permissions

Safe alternatives:

1. Use GitHub UI "Update branch" button (if available)
2. Close the PR and wait for Snyk to create a new one
3. Ask Snyk to recreate via Snyk UI: Project Settings → Integrations → GitHub → Re-test

Dependabot Configuration

Dependabot is configured in .github/dependabot.yml. Always check that file for the complete, authoritative configuration.

Key ecosystems:

• Maven (/mockserver) - Java dependencies, weekly schedule Monday, 10 PR limit
• npm (/.opencode) - OpenCode config dependencies, weekly schedule Monday, 5 PR limit
• GitHub Actions (/) - Workflow dependencies, weekly schedule Monday, 5 PR limit

javax/jakarta compatibility blocks:

The configuration blocks major-version upgrades for dependencies that would force the jakarta namespace before the javax→jakarta migration is scheduled. See the ignore section in .github/dependabot.yml for the authoritative list, which currently includes:

• Spring Framework/Boot - Blocks 6.x+ / 3.x+ (uses jakarta namespace)
• Tomcat, Jetty - Blocks 10.x+ (uses jakarta namespace)
• Servlet - Defensive guard on javax.servlet:* ≥ 5
• Jakarta EE artifacts - Blocks jakarta.xml.bind ≥ 3, jakarta.activation ≥ 2, jakarta.validation ≥ 3

Common Scenarios

Scenario 1: Dependabot PR Fails with Flaky Test

Problem: Buildkite build fails on Dependabot PR due to intermittent test failure.

Solution:

1. Check if the test failure is related to the dependency upgrade:

   gh pr view <PR_NUMBER>
   gh pr checks <PR_NUMBER>
   

2. If unrelated (flaky test), rebase to re-run:

   gh pr comment <PR_NUMBER> --body "@dependabot rebase"
   

3. If still failing, investigate the test failure before merging

Scenario 2: Dependabot PR is Behind Master

Problem: PR shows "This branch is out-of-date with the base branch".

Solution:

gh pr comment <PR_NUMBER> --body "@dependabot rebase"

Scenario 3: Merge Multiple Passing Dependabot PRs

Problem: Many Dependabot PRs have passed checks and are ready to merge.

Solution (SAFE - requires checks and confirmation):

# List all open Dependabot PRs with passing checks
gh pr list --author app/dependabot --state open --json number,title,statusCheckRollup \
  --jq '.[] | select(.statusCheckRollup | all(.conclusion == "SUCCESS" or .conclusion == null)) | {number: .number, title: .title}'

# Review the list, then merge each individually:
gh pr merge <PR_NUMBER> --squash --auto

# Alternative: ask Dependabot to merge (after verifying checks)
gh pr comment <PR_NUMBER> --body "@dependabot squash and merge"

WARNING: Do NOT use a blind loop. Always verify:

• All checks are passing
• javax/jakarta compatibility
• No breaking changes
• PR scope is reasonable

Scenario 4: Dependabot PR Has Merge Conflicts

Problem: Dependabot PR shows merge conflicts.

Solution:

# Ask Dependabot to recreate the PR (resolves conflicts automatically)
gh pr comment <PR_NUMBER> --body "@dependabot recreate"

If recreate fails, close the PR and wait for Dependabot to create a new one.

Scenario 5: Block a Major Version Upgrade

Problem: Dependabot proposes a major version upgrade that requires code changes (e.g., Spring 5 → 6).

Solution:

# Ignore this major version
gh pr comment <PR_NUMBER> --body "@dependabot ignore this major version"

Then update .github/dependabot.yml for team visibility:

ignore:
  - dependency-name: "org.springframework:*"
    update-types: ["version-update:semver-major"]

Scenario 6: Snyk PR Fixes Critical CVE

Problem: Snyk creates PR to fix CVE-2024-12345 (critical severity).

Solution:

1. Check javax/jakarta compatibility first
2. Review the CVE and verify severity
3. Check if tests pass
4. Merge immediately if safe:

   gh pr merge <PR_NUMBER> --squash --auto
   

5. If tests fail or the PR forces the jakarta namespace, investigate before merging

javax / jakarta Compatibility Requirements

MockServer targets Java 17 as the minimum supported version but still uses the javax namespace throughout. When reviewing Dependabot PRs, always check for upgrades that force the jakarta namespace.

See the javax/jakarta compatibility policy in ../../../AGENTS.md and the Snyk policy in ../../../.snyk for version ceilings.

Quick Check: Does This PR Force jakarta?

# Check the PR diff for blocked dependencies
gh pr diff <PR_NUMBER> | grep -E "(springframework|jakarta|jetty|tomcat\.embed)"

How to Handle jakarta-forcing PRs

If Dependabot proposes a dependency that forces the jakarta namespace:

1. Close the PR:

   gh pr comment <PR_NUMBER> --body "@dependabot close"
   

2. Ignore the major version:

   gh pr comment <PR_NUMBER> --body "@dependabot ignore this major version"
   

3. Update .github/dependabot.yml:

   ignore:
     - dependency-name: "<dependency-pattern>"
       versions: [">=<major>"]
   

Troubleshooting

Dependabot Command Not Working

Symptoms: Comment posted but Dependabot doesn't respond.

Causes & Solutions:

• Typo in command - Must be exact: @dependabot rebase, not @dependabot please rebase
• Delayed processing - Wait 2-5 minutes; check for Dependabot's 👍 reaction
• Wrong PR type - Verify PR author is app/dependabot
• Dependabot disabled - Check GitHub repository settings → Security → Dependabot

Debugging:

1. Check for Dependabot's thumbs-up reaction on your comment
2. Look for Dependabot's response comment (may take minutes)
3. Check the PR's "Dependabot commands and options" section
4. Verify the command is supported for this PR type (single-dependency vs grouped update)

Dependabot Rebase Creates Conflicts

Symptoms: Dependabot comments "I couldn't rebase due to conflicts."

Solution:

# Try recreate instead (creates fresh PR from latest base)
gh pr comment <PR_NUMBER> --body "@dependabot recreate"

If recreate also fails, close the PR and wait for Dependabot to create a new one on its next run.

Snyk PR Tests Fail After Upgrade

Symptoms: Snyk upgrades a dependency but tests fail.

Causes:

• Breaking change in upgraded dependency
• Transitive dependency incompatibility
• jakarta-namespace requirement
• Test needs updating for new API

Solution:

1. Review the Snyk PR diff:

   gh pr diff <PR_NUMBER>
   

2. Check release notes for breaking changes
3. Check Java compatibility (see section above)
4. Run tests locally to debug:

   gh pr checkout <PR_NUMBER>
    cd mockserver && ./mvnw clean test
   

5. Either:
   • Fix the code to work with the new version, OR
   • Close the Snyk PR and document the decision (pin old version, accept risk, etc.)

Reference

• Dependabot commands documentation
• Snyk GitHub integration
• MockServer javax/jakarta compatibility policy
• Security and dependency constraints
• Dependabot configuration file