[FLINK-39803][e2e] Ignore jdk25 native access and deprecated method warnings

[snuyanzin]

What is the purpose of the change

When using restricted or terminally deprecated methods, the JVM prints warnings on JDK 25 like below:

  WARNING: A terminally deprecated method in java.lang.System has been called
  WARNING: java.lang.System::setSecurityManager has been called by org.apache.flink.runtime.security.NoOpSecurityManager
  WARNING: A restricted method in sun.misc.Unsafe has been called
  WARNING: sun.misc.Unsafe::objectFieldOffset has been called by org.apache.flink.core.memory.MemorySegment
  WARNING: Use --enable-native-access to avoid a warning for callers in this module
  WARNING: Restricted methods will be blocked in a future release unless native access is enabled

These are printed into the .out file of the processes, and cause e2e tests to fail since we check for empty .out files.

These warnings cannot be suppressed without {{--enable-native-access}}, which would require changes across the entire module structure. They also occur in third-party libraries (e.g. Netty, Kryo), so we cannot simply

Additionally, empty lines appearing in .out files can cause false positives and should also be excluded.

Brief change log

common.sh

Verifying this change

e2e

Does this pull request potentially affect one of the following parts:

• Dependencies (does it add or upgrade a dependency): ( no)
• The public API, i.e., is any changed class annotated with @Public(Evolving): ( no)
• The serializers: ( no )
• The runtime per-record code paths (performance sensitive): ( no )
• Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn, ZooKeeper: ( no)
• The S3 file system connector: ( no )

Documentation

• Does this pull request introduce a new feature? ( no)
• If yes, how is the feature documented? (not applicable )

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Was generative AI tooling used to co-author this PR?

• Yes (please specify the tool below)

[flinkbot]

CI report:

• 10b1fd6 Azure: SUCCESS

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[snuyanzin]

Thanks for taking a look