Fix Flink runner tests on Java 21

[aIbrahiim]

Fixes: #39252
Successful run: https://github.com/apache/beam/actions/runs/29061791187

After switching to Java 21, Flink runner tests started failing in PreCommit Java

The main problems were:

• Flink/Kryo tests needed extra JVM --add-opens flags on Java 21
• FlinkSubmissionTest used old reflection tricks that do not work on newer Java (Field.modifiers, wrong env map update)
• System.setSecurityManager() needs -Djava.security.manager=allow on Java 21
• On Linux , modifyEnv() was putting plain String keys into ProcessEnvironment.theEnvironment, but that map uses Variable/Value keys, so FLINK_CONF_DIR was not visible and tests timed out waiting for jobs

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[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses compatibility issues that arose when migrating Flink runner tests to Java 21. The changes primarily focus on updating JVM arguments, modernizing reflection-based environment variable manipulation to account for internal JDK changes, and improving the robustness of existing test assertions to prevent timeouts.

Highlights

• Java 21 Compatibility: Updated Flink runner tests to include necessary JVM --add-opens flags and enabled the security manager via -Djava.security.manager=allow.
• Environment Variable Handling: Refactored modifyEnv in FlinkSubmissionTest to correctly handle ProcessEnvironment map types on Unix, ensuring FLINK_CONF_DIR is properly visible to Flink.
• Test Stability: Improved test reliability in UnboundedSourceWrapperTest by replacing infinite loops with timed deadlines and more robust stack trace inspection.

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[gemini-code-assist]

Code Review

This pull request updates FlinkSubmissionTest to correctly modify environment variables across different operating systems (Unix and Windows) by reflecting on internal JVM ProcessEnvironment maps. It also configures necessary JVM arguments for Flink tests when running on Java 17 or higher, and replaces an infinite loop in UnboundedSourceWrapperTest with a timed loop to prevent test hangs. The reviewer suggests using System.nanoTime() instead of System.currentTimeMillis() in UnboundedSourceWrapperTest to measure the timeout monotonically, avoiding issues with system clock adjustments.

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[gemini-code-assist]

Using System.currentTimeMillis() to measure elapsed time or timeouts is an anti-pattern because it is sensitive to system clock adjustments (such as NTP synchronization or manual clock changes). It is highly recommended to use System.nanoTime() for monotonic time measurements instead.

Suggested change

	long deadlineMs = System.currentTimeMillis() + 9_000;
	boolean reachedFinalizeSource = false;
	while (System.currentTimeMillis() < deadlineMs) {
	long deadlineNs = System.nanoTime() + 9_000_000_000L;
	boolean reachedFinalizeSource = false;
	while (System.nanoTime() < deadlineNs) {