fix/e2e runtime java

[Saga4]

• wip java support
• add Java code to optimize with tests
• add Class and Proxy type handlers to Serializer
• Fix Map key collision
• e2e working java
• make tests do full string equality check
• fix code context extraction bugs
• syntax error for code extraction is not allowed
• thorough tests for code replacement
• fix instrumentation
• more tests
• progress on instrumentation of java code
• feat: add JaCoCo test coverage support for Java optimization
• fix: improve Java coverage support and config parsing
• fix: improve JaCoCo plugin insertion for complex Maven pom.xml files
• feat: add multi-module Maven project support for Java tests
• feat: add JUnit 4/TestNG support for Java test framework detection
• fix: improve Java class name extraction regex to avoid false matches
• fix: improve Java test file handling and JaCoCo coverage for multi-module projects
• fix: handle NOT_FOUND coverage status in Java multi-module projects
• Optimize get_optimized_code_for_module
• feat: add inner loop and compile-once-run-many optimization for Java benchmarking
• fix: enable stdout capture in JUnit Console Launcher XML reports
• fix: improve multi-module detection and add JUnit 4 fallback
• feat: support Java optimizations with static fields and helper methods
• fix: continue benchmark looping when some tests fail but timing markers exist
• fix: handle overloaded Java methods correctly in code replacement
• fix: handle Java overloaded methods and class members correctly
• fix: pass function_to_optimize for precise overload matching
• fix: handle null message in JUnit test result parsing
• fix: reduce Java inner_iterations to prevent parsing hang
• fix: cache Java fallback stdout parsing to avoid O(n²) complexity
• fix: add security and validation improvements to Java implementation
• test: add comprehensive security tests for Java implementation
• feat: add import-based test discovery for Java
• fix: comprehensive improvements to Java test discovery
• fix: add pom.xml to java_maven test fixture
• fix: update Java Comparator to read from test_results table
• test: add integration tests for test_results schema validation
• fix: add JSON-aware comparison to Python comparator fallback
• Revert "fix: add JSON-aware comparison to Python comparator fallback"
• fix: avoid dependency conflicts in Java behavior instrumentation
• feat: add Java end-to-end tests and CI workflow
• fix: prevent duplicate and wrong test-to-function associations in Java
• fix: add API key for tests and build codeflash-runtime JAR in CI
• feat: implement Java line profiling for hotspot identification
• fix: improve thread safety in Java line profiler
• fix: resolve circular import in env_utils by deferring registry import
• Fix Java test path duplication when tests_root includes package path
• feat: add concurrency pattern detection for Java optimization
• Add check for codeflash.toml
• Update codeflash/languages/java/import_resolver.py
• fix: skip formatter check for Java projects
• Optimize _add_behavior_instrumentation
• feat: implement Java assertion removal transformer
• fix: use correct variable name in JS/TS instrumentation log
• fix: handle new ClassName().method() style calls in assertion removal
• fix: prevent optimized code from one file being applied to another file
• fix: increase Java test timeout from 15s to 120s
• fix: add Java patterns to instrumented test file cleanup
• fix: handle numbered suffixes in Java instrumented test files
• fix: set tests_project_rootdir to tests_root for Java projects
• debug: add logging to investigate empty test filter issue
• feat: Add verbose logging for Java optimization debugging
• feat: Add verbose logging for existing instrumented tests
• fix: set tests_project_rootdir to tests_root for Java
• fix: prevent Maven running all tests + fix TestFile type annotation
• chore: remove documentation markdown files from PR
• refactor: use DEBUG_MODE from console.py for verbose logging
• style: fix linting and formatting issues in function_optimizer.py
• style: apply linting and formatting fixes
• WIP in kryo
• fix: show actual test file paths in failure log instead of original_file_path
• fix: detect and log Java compilation failures explicitly
• refactor
• fix: route Java/JavaScript/TypeScript to Optimizer instead of Python tracer
• test(05-02): add concurrency-aware assertion removal tests
• test(05-01): extend comparator tests with edge case and error handling coverage
• test(05-01): create decision logic tests for SQLite vs pass-fail-only routing
• better unit test discovery java
• optimize for performance
• test(05-02): add concurrency-aware assertion removal tests
• test(05-01): extend comparator tests with edge case and error handling coverage
• test(05-01): create decision logic tests for SQLite vs pass-fail-only routing
• fix: add warning logging for pass_fail_only masking and overload detection in test discovery
• fix: wire Java formatter into detection pipeline
• feat(06-02): enhance Maven infrastructure with XML parsing, profiles, and custom source dirs
• test: add tests for pass_fail_only warning logging and overload disambiguation
• feat(06-02): enhance build tool detection with project_root and custom source dirs
• chore: restore timeout documentation comments
• chore: restore timeout documentation comments
• Optimize _get_test_module_target_dir
• Fix insturmentation Bugs
• fix: remove duplicate _get_method_call_pattern function definition
• fix: auto-format with prek
• fix: correct return value order in Java test_runner for coverage
• fix: remove pass_fail_only mode to enforce strict correctness
• fix: restore _extract_modules_from_pom_content and _extract_source_dirs_from_pom functions
• ** fix: use Kryo serialization and deep comparison for Java test results**
• fix: correct Java string syntax in line profiler code generation
• Optimize _extract_modules_from_pom_content
• fix pom.xml
• fix: correct Java test file path generation for Maven structure
• fix: handle assertThrows variable assignment in Java instrumentation
• Optimize JavaAssertTransformer._detect_variable_assignment
• Optimize JavaAssertTransformer._generate_exception_replacement
• Fix line profiler
• fix asserts
• fix: update failing unit tests to match current behavior
• fix: update large number comparison test for float precision limits
• fix(java): fix JS import injection and JPMS split-package errors
• fix(java): fix missing import and incorrect parent path in JPMS remapping
• fix(java): fix instrumentation syntax errors from @testonly and nested parens
• fix: Java line profiler timeout and test categorization issues
• fix(java): fix class rename scope and variable scoping in instrumentation
• fix(java): detect parameterized lambdas in instrumentation
• fix(java): apply JAVA_TESTCASE_TIMEOUT for all Java test frameworks
• fix(java): fix line profiler class detection for modified class declarations
• fix(java): fix line profiler class detection and timeout for Java tests
• fix(java): fix benchmarking fallback timeout using same or-vs-max pattern
• do instrument generated regression tests
• Function discovery and other fixes

[CLAassistant]

Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.
1 out of 2 committers have signed the CLA.

✅ mashraf-222
❌ Ubuntu

---

Ubuntu seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.
_{You have signed the CLA already but the status is still pending? Let us recheck it.}