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Summary:
The PR upgrades the trunk cli version, some linters (eslint, pmd), and the trunk-io/configs plugin. It also adds java@13.0.11 to the enabled runtimes.

Root Cause Analysis:
Without test logs, it's difficult to pinpoint the exact cause of the flaky tests. However, the changes in this PR could potentially lead to flakiness in a few ways:

1. Linter Version Upgrades: Upgrading linters like eslint and pmd could introduce new rules or change existing rule behavior. This might cause existing code to fail linting checks intermittently, especially if the codebase isn't perfectly compliant with the stricter rules.
2. Trunk CLI Upgrade: The trunk CLI upgrade could also introduce subtle changes in how linters are executed or how results are reported, leading to inconsistent test outcomes.
3. New Java Runtime: Adding a new Java runtime could expose compatibility issues or subtle differences in behavior that cause tests to fail sporadically.

Resolution Plan:

Since I don't have access to the test logs, I can only provide general recommendations.

1. Re-run the tests: The first step is always to re-run the tests to see if the flakiness persists. It's possible that the failures were transient and won't reappear.
2. Examine the test logs: If the tests continue to fail, try to get the test logs. Look for patterns in the failures. Are the same tests failing consistently? Are there any error messages that provide clues about the root cause?
3. Investigate linter changes: If the failures seem related to linting, investigate the changes in eslint and pmd versions. Check their release notes for any breaking changes or new rules that might be affecting the codebase.
4. Consider specific files: If specific files are failing, use the fileContentTool to examine those files and see if the new linter versions are flagging any new issues.
5. Check Java compatibility: If the failures seem related to Java, investigate the compatibility of the codebase with Java 13.0.11. Look for any known issues or differences in behavior that might be causing the tests to fail.

If the user can provide the test logs, I can provide a more specific and actionable resolution plan.

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