This PR hardens the Java-Thread-Affinity module across native code, affinity selection, and timing paths, while adding explicit architecture docs and quality profiles. It also introduces shared AGENTS.md guidance for AI and human contributors, and a Claude-specific helper file.

Functional changes

• Affinity selection and JNA fallback

  • Refactored Affinity initialiser to:

    • Guard all native initialisation with a try/catch and fall back cleanly to NullAffinity on failure.
    • Use a thread-safe, lazy isJNAAvailable() check that reflects the actual JNA presence and version.
    • Ensure getAffinity() always returns a valid implementation (falls back to NullAffinity if needed).

• Native JNI affinity and timer behaviour

  • Hardened NativeAffinity JNI layer:

    • Added getVersion0() and surfaced it as NativeAffinity.VERSION, initialised at class-load time and logged when the native library is present.
    • Replaced C++ exceptions with Java UnsupportedOperationException / RuntimeException via JNI, including error handling for sched_setaffinity failures and unsupported platforms.
    • Added JNI_OnLoad returning JNI_VERSION_1_8 to make version negotiation explicit.

  • Strengthened JNIClock:

    • Adjusted estimateFrequency loop to always invoke rdtsc0() during spin, avoiding the JIT optimising away calls.
    • Clarified rdtsc0 as a static native method.

• Native build pipeline

  • Reworked affinity/src/main/c/Makefile:

    • Added VERSION and JAVA_HOME parameters (wired from Maven exec-maven-plugin) and propagate them via -DPROJECT_VERSION for getVersion0().
    • Introduced hardened CFLAGS/CXXFLAGS (optimisation, warnings, stack protector, FORTIFY, PIE).
    • Split compilation into object files for each native source and linked them into libCEInternals.so.
    • Ensured macOS-specific source is included only on Darwin and switched sprintf to snprintf.
    • Added clean target that removes both the library and object files.

• Locking and inter-process coordination

  • Updated FileLockBasedLockChecker:

    • Reworked getInstance() to return a fresh instance, avoiding long-lived shared state in tests.
    • Switched all file IO to UTF-8, with better error messages when temp directories cannot be created.
    • Added documentation explaining lock-file semantics and retry behaviour.

  • Tightened LockCheck helper methods (storePid, isLockFree) by making the synchronized flag placement conventional and explicit.

• JNA-based affinity helpers

  • Enriched LinuxHelper, LinuxJNAAffinity, PosixJNAAffinity, WindowsJNAAffinity, OSXJNAAffinity, SolarisJNAAffinity, Utilities, and VersionHelper with class-level Javadoc capturing:

    • Behavioural role (CPU mask handling, pid/tid resolution, libc calls).
    • Thread-local caching semantics for thread IDs.
    • Version parsing and comparison rules.

  • Normalised ThreadLocal naming (THREAD_ID → threadId) to better reflect intent and avoid Checkstyle noise.

  • Ensured LinuxJNAAffinity and PosixJNAAffinity handle missing native helpers gracefully (do not throw from static initialisers, rely on LOADED flags).

• Ticker and affinity APIs

  • Documented BootClassPath, LockInventory, ticker packages, and affinity packages with package-info.java:

    • Public APIs in net.openhft.affinity and net.openhft.ticker now describe purpose, scope, and usage patterns (thread pinning, low-jitter time sources).
    • Internal packages (impl, lockchecker, main, ticker.impl) are explicitly marked as implementation/support code.

  • Adjusted MicroJitterSampler busy-wait loop to use an empty while body without a trailing semicolon in the same line, clarifying intent.

• Tests and safety nets

  • Added/updated tests to cover new behaviour:

    • AffinitySelectionAndFallbackTest and AffinityJnaUnavailableSimulationTest verify default selection on Linux and fallback to NullAffinity when JNA is genuinely absent.

    • LinuxAffinityParityTest exercises JNI vs JNA affinity parity on Linux, validating that masks intersect correctly when set via either path.

    • JNIClockBasicBehaviourTest and updated JNIClockTest validate tick changes, monotonic nanoTime behaviour, concurrent access, and tolerance bounds compared to System.nanoTime.

    • NativeAffinityEdgeCaseTest, NativeAffinityErrorHandlingTest, NativeAffinityLibraryLoadingTest, NativeAffinityVersionTest, and NativeAffinityVersionIntegrationTest cover:

      • Library load state, version reporting, JNI error handling, argument bounds, concurrency, and safe repeated calls.

  • Updated existing tests:

    • AffinityThreadFactoryMain and AffinityThreadFactoryTest now use ExecutorService#execute with proper interruption handling.
    • LinuxJNAAffinityTest method naming aligned with standard Java test naming (linuxJna).
    • LockCheckTest and MultiProcessAffinityTest updated to use explicit UTF-8 encoding for lock files and avoid unnecessary locals.
    • BaseAffinityTest now uses a final TemporaryFolder rule to match JUnit best practices.

  • Added an OSGi test package net.openhft.affinity.osgi with package-info.java describing its role in verifying bundle packaging and service exposure.

• Docs and guidance

  • Introduced root-level AGENTS.md:

    • Defines British English plus ISO-8859-1 policy for all content, including tools to detect non-compliant characters.
    • Documents high-value Javadoc rules (behavioural contracts only, no trivial “gets/sets” comments).
    • Captures CI expectations (mvn -q verify), PR etiquette, security checklist, Nine-Box requirement taxonomy, ADR format, and AsciiDoc conventions.

  • Added affinity/AGENTS.md to inherit repository rules and add module-specific guidelines (affinity purpose, build commands, quality gates, and platform guardrails).

  • Added CLAUDE.md with:

    • Project overview, module structure, build commands, architecture notes, and key classes for Claude Code.
    • Chronicle-wide conventions (language, charset, Javadoc, commits, test expectations, docs-sync behaviour).

• Architecture and requirements docs

  • Added affinity/src/main/docs/decision-log.adoc capturing key architectural choices:

    • JNA as the primary native interface with JNI reserved for specialised paths.
    • File-based inter-process locking for CPU reservations.
    • /proc/cpuinfo-based topology parsing.
    • Recommended isolcpus usage for jitter reduction.

  • Added affinity/src/main/docs/project-requirements.adoc:

    • Reframes and tags functional and non-functional requirements with Nine-Box IDs (AFF-FN-*, AFF-NF-P-*, AFF-OPS-*, AFF-TEST-*, AFF-DOC-*, etc.).
    • Makes platform support, operability, UX, testing, risk, and documentation obligations explicit.

• Miscellaneous functional tweaks

  • FileLockBasedLockChecker.getInstance() now returns a new instance to improve test isolation.
  • AffinityThreadFactoryMain and AffinityThreadFactoryTest slightly adjusted execution patterns but preserve behaviour.
  • LockChecker/LockReference formatting cleaned up while preserving API.

Non-functional / quality changes

• Quality profiles and static analysis

  • Introduced a quality Maven profile in:

    • Root pom.xml.
    • affinity/pom.xml.
    • affinity-test/pom.xml.

  • Each quality profile:

    • Runs Checkstyle (3.6.0) with chronicle-quality-rules and a pinned Checkstyle core (10.26.1), including tests.
    • Runs SpotBugs (4.9.8.1) with chronicle-quality-rules include/exclude filters, effort=Max, threshold=Low, and includeTests=true, bound to process-test-classes.

  • Documented in TODO.md that affinity and affinity-test are now Checkstyle/SpotBugs-clean on Java 21 under the shared Chronicle configuration.

• BOM and dependency alignment

  • affinity-test now imports net.openhft:third-party-bom:3.27ea7.
  • affinity module continues to track 3.27ea2 (unchanged in this diff) but now passes VERSION down to the native build.

• Docs front-matter and AsciiDoc consistency

  • Added common header attributes to:

    • LICENSE.adoc and README.adoc: :toc:, :lang: en-GB, :source-highlighter: rouge.

  • Marked code sections in README.adoc with opts=novalidate where appropriate to avoid spurious AsciiDoc validation warnings.

  • Standardised AsciiDoc formatting guidance in AGENTS.md and ensured the new docs follow the same rules (automatic section numbering, no manual prefixes, correct list indentation).

• Repository TODO and compliance traceability

  • Introduced a repository-scoped TODO.md that:

    • Links this module to the global ARCH_TODO.md, TODO_INDEX.md, ADOC_TODO.md, and ISO 9001 / ISO 27001 checklists.
    • Tracks open work on architecture overviews, decision logs, requirements, security reviews, performance targets, glossary terms, and test strategy.
    • Captures the current Checkstyle/SpotBugs status and notes deferred work via TODO_STATUS.md.

• Security and robustness improvements

  • Native code:

    • Added defensive checks for unsupported platforms, error paths, and buffer bounds.
    • Ensured JNI functions ignore unused parameters explicitly and use safe string formatting.

  • Java:

    • Centralised NullAffinity fallback when JNA or native paths are not available.
    • Improved error messages around temp directory creation and lock-file content parsing.

  • AGENTS.md now includes a security checklist reminding reviewers to assess validation, authorisation, resource exhaustion, timing, and secrets handling on every PR.

Notes for reviewers

• Behavioural scope

  • Affinity semantics are preserved by design: JNA remains the default for affinity control, JNI remains opt-in via NativeAffinity, and NullAffinity is the safety net when native support is missing.

  • The main behaviour changes are:

    • More predictable native library loading and error handling.
    • Clearer and more robust JNA/JNI interplay (including tests that validate JNA vs JNI parity on Linux).

• Risk / impact

  • Risk is primarily around native integration on Linux/macOS; the new tests and error-handling paths are intended to reduce this by:

    • Failing fast with clear Java exceptions instead of C++ runtime errors.
    • Providing a well-defined fallback to JNA and NullAffinity if anything goes wrong in initialisation.