Deterministic test infrastructure with injectable clocks and project reorganization

[wallstop]

Summary

Introduce an injectable ClockFn abstraction and in-memory ChannelSocket transport to enable fully deterministic, fast, and platform-independent integration tests — replacing real UDP sockets, thread::sleep(), and #[serial] test ordering throughout the test suite. Also reorganizes scripts and LLM skills into domain-based subdirectories.

Clock injection & deterministic time control

• Add ClockFn type alias (Arc<dyn Fn() -> Instant + Send + Sync>) and ProtocolConfig::clock field for injectable time sources
• Add ChaosSocket::with_clock() builder method for deterministic chaos/network-condition testing
• Replace all Instant::now() calls in Protocol and ChaosSocket with the injected clock (falling back to system time)
• Breaking: ProtocolConfig no longer implements Copy (due to Arc-based clock field)

New test infrastructure

• ChannelSocket: in-memory NonBlockingSocket using mpsc channels — eliminates all real UDP I/O from tests
• TestClock: manually-advanceable virtual clock with advance(duration), as_protocol_clock(), and as_chaos_clock() helpers
• Deterministic test utilities: synchronize_sessions_deterministic(), poll_with_advance(), run_p2p_frame_advancement_test_deterministic()

Test suite migration

• Converted all resilience, p2p, p2p_enum, and spectator tests from real sockets + thread::sleep + #[serial] to ChannelSocket + TestClock
• Removed serial_test dependency and all #[serial] attributes from migrated tests
• Removed #[cfg_attr(miri, ignore)] from timing-dependent chaos socket tests (now virtual-time-based)

Scripts & skills reorganization

• Reorganized scripts/ into build/, ci/, docs/, verification/ subdirectories
• Reorganized .llm/skills/ into 8 category subdirectories (rust-language, testing, formal-verification, etc.)
• Added 8 new workflow skills (code-review, adversarial-review, dev-pipeline, investigation, etc.)
• Added .llm/design-history/ and .llm/templates/ask-user-question.md

Documentation & CI

• Updated user guide with custom clock documentation, new config presets, and expanded API reference
• Updated all wiki pages with corrected examples, API signatures, and verification status
• Updated all CI workflows and pre-commit hooks for new script paths
• Expanded devcontainer with additional VS Code extensions and editor settings
• Added logo banner SVG

Test plan

• cargo nextest run --no-capture — all tests pass with deterministic infrastructure
• cargo clippy --all-targets --features tokio,json — no warnings
• CI workflows resolve scripts at new paths
• Pre-commit hooks work with reorganized script layout
• Verify no #[serial] tests remain in migrated test files

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR introduces deterministic time control and in-memory networking primitives to make integration tests fast and reproducible, while also reorganizing repository scripts/LLM skills and updating docs/CI paths accordingly.

Changes:

• Add injectable clock support (ClockFn + ProtocolConfig::clock) and propagate it through session/protocol setup to enable virtual-time testing.
• Introduce deterministic integration-test infrastructure (ChannelSocket, TestClock, deterministic polling/synchronization helpers) and migrate selected tests away from UDP + sleeps + serial ordering.
• Reorganize scripts/ and .llm/skills/ into domain subdirectories and update docs/workflows/pre-commit hooks to the new paths.

Reviewed changes

Copilot reviewed 96 out of 140 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
wiki/assets/logo-banner.svg	Adds new wiki banner asset.
wiki/Spec-Divergences.md	Updates spec↔code links/paths and verification command path.
wiki/Migration.md	Updates migration examples (builder ?, desync handling, Session trait).
wiki/Home.md	Small homepage snippet updates (test count).
wiki/Fortress-vs-GGRS.md	Updates examples/claims to match new APIs and stats.
wiki/Formal-Specification.md	Updates formal spec text and message-shape snippets.
wiki/Determinism-Model.md	Updates determinism doc examples to match new APIs.
wiki/Contributing.md	Updates script paths after scripts reorg.
tests/verification/property.rs	Adjusts checksum exchange polling logic (removed sleep).
tests/sessions/p2p_enum.rs	Migrates enum-input P2P test to deterministic helper; removes serial.
tests/network/multi_process.rs	Updates internal skill link path after skills reorg.
tests/config.rs	Adjusts Copy/Clone expectations; adds ProtocolConfig Clone test.
tests/common/mod.rs	Exposes/re-exports ChannelSocket + TestClock + deterministic helpers.
src/sessions/builder.rs	Clones protocol_config where Copy is no longer available.
src/lib.rs	Re-exports ClockFn from sessions config.
specs/tla/README.md	Updates verification script paths and skill links.
scripts/verification/verify-tla.sh	Relocates script and fixes project root resolution.
scripts/verification/verify-kani.sh	Relocates script and fixes project root resolution.
scripts/verification/verify-all.sh	Relocates script and fixes project root resolution.
scripts/verification/check-kani-coverage.sh	Updates paths to relocated Kani scripts.
scripts/verification/check-kani-coverage.py	Updates project root and verify-kani.sh path.
scripts/tests/test_validate_wiki_output.py	Updates import path for moved docs scripts.
scripts/tests/test_sync_wiki.py	Updates sys.path/import path for moved docs scripts.
scripts/tests/test_check_wiki_consistency.py	Updates sys.path/import path for moved docs scripts.
scripts/tests/test_check_llm_skills.sh	Updates path to moved check-llm-skills.sh.
scripts/tests/test_check_links.py	Updates sys.path/import path for moved docs scripts.
scripts/tests/test_cargo_linker.py	Updates sys.path to import from scripts/build.
scripts/hooks/regenerate-skills-index.py	Recurses skills subdirs and uses relative paths in index links.
scripts/docs/verify-markdown-code.sh	Updates usage header and project root derivation.
scripts/docs/validate-wiki-output.py	Updates usage header and project root derivation.
scripts/docs/sync-wiki.py	Updates usage header examples to new script path.
scripts/docs/check-wiki-consistency.py	Updates usage header and sync script path.
scripts/docs/check-rustdoc-links.py	Imports shared cargo linker helper from scripts/build.
scripts/docs/check-llm-skills.sh	Updates repo-root derivation for new location.
scripts/docs/check-links.sh	Updates usage header and repo-root derivation.
scripts/docs/check-links.py	Updates docstring and project-root derivation.
scripts/docs/check-code-fence-syntax.sh	Updates usage header examples to new script path.
scripts/docs/init.py	Marks scripts/docs as a Python package.
scripts/ci/verify-sccache.sh	Updates usage header to new path.
scripts/ci/test-verify-sccache.sh	Fixes workflow-dir path after scripts reorg.
scripts/ci/docker-network-tests.sh	Updates usage header and project root derivation.
scripts/ci/check-tools.sh	New devcontainer tool verification script.
scripts/ci/check-shell-portability.sh	Updates usage header and project root derivation.
scripts/build/run-cargo-fmt.py	New pre-commit wrapper to run fmt and stage only formatted Rust files.
scripts/build/run-cargo-clippy.py	New pre-commit wrapper to run clippy with linker fallback env.
scripts/build/check-cargo-hack.py	New optional feature-powerset check wrapper for pre-commit.
scripts/build/cargo_linker.py	New shared helper to disable custom linker flags when lld isn’t available.
scripts/build/init.py	Marks scripts/build as a Python package.
docs/specs/spec-divergences.md	Updates verification script path.
docs/contributing.md	Updates script paths after scripts reorg.
docker/README.md	Updates docker test script path after scripts reorg.
Cargo.toml	Bumps crate version to 0.7.0.
Cargo.lock	Updates crate version to 0.7.0.
CLAUDE.md	Adds clarifying-question template reference and test-output rule.
CHANGELOG.md	Adds 0.7.0 entry for clock injection / ProtocolConfig Copy break; updates script paths.
AGENTS.md	Adds clarifying-question template reference and test-output rule.
.typos.toml	Updates reference path after skills reorg.
.pre-commit-config.yaml	Updates hook entries and file globs for reorganized scripts dirs.
.llm/templates/ask-user-question.md	New template for concise clarifying questions.
.llm/skills/workflows/user-facing-docs.md	New workflow skill for public-doc updates.
.llm/skills/workflows/review-readiness.md	New workflow skill for pre-review gating.
.llm/skills/workflows/design-decisions.md	New workflow skill for design decision logging.
.llm/skills/workflows/code-review.md	New structured review workflow guidance.
.llm/skills/workflows/adversarial-review.md	New adversarial review guidance.
.llm/skills/workflows/adversarial-handoff.md	New escalation/handoff workflow.
.llm/skills/testing/testing.md	Adds “no tail/head on test output” guidance.
.llm/skills/testing/network-chaos-testing.md	New chaos testing skill (moved/expanded).
.llm/skills/testing/mutation-testing.md	New mutation testing skill.
.llm/skills/testing/fuzzing.md	New fuzzing skill.
.llm/skills/rust-language/zero-copy.md	New Rust zero-copy skill.
.llm/skills/rust-language/type-driven-design.md	New type-driven design skill.
.llm/skills/rust-language/text-parsing.md	New text parsing skill.
.llm/skills/rust-language/rust-pitfalls.md	New Rust pitfalls skill.
.llm/skills/rust-language/rust-idioms.md	New Rust idioms skill.
.llm/skills/rust-language/rust-design-patterns.md	New Rust design patterns skill.
.llm/skills/rust-language/refactoring.md	New refactoring skill.
.llm/skills/rust-language/no-std.md	New no_std skill.
.llm/skills/rust-language/ffi.md	New FFI skill.
.llm/skills/rust-language/defensive-programming.md	New defensive programming (zero-panic) skill.
.llm/skills/rust-language/concurrency.md	New concurrency skill.
.llm/skills/rust-language/async-rust.md	New async Rust skill.
.llm/skills/rust-language/api-design.md	New public API design skill.
.llm/skills/publishing-organization/changelog.md	New changelog practices skill.
.llm/skills/performance-quality/performance.md	Updates reference to moved cargo_linker helper path.
.llm/skills/performance-quality/binary-size.md	New binary size optimization skill.
.llm/skills/formal-verification/verification.md	Updates verification script path reference.
.llm/skills/formal-verification/kani.md	Updates verify-kani/check-kani-coverage path references.
.llm/skills/determinism-rollback/dst.md	New deterministic simulation testing (DST) skill.
.llm/skills/ci-cd-tooling/wiki-sync.md	Updates wiki sync script paths and relative-link rules after skills reorg.
.llm/skills/ci-cd-tooling/markdown.md	Updates docs script paths and relative-link rules after skills reorg.
.llm/skills/ci-cd-tooling/github-actions.md	New GitHub Actions best practices skill.
.llm/skills/ci-cd-tooling/doc-code-sync.md	New doc↔code consistency skill.
.llm/skills/ci-cd-tooling/ci-debugging.md	Updates Kani coverage script path reference.
.llm/design-history/sync-layer.txt	Adds sync-layer decision-log entry.
.llm/design-history/network.txt	Adds network decision-log entries.
.llm/design-history/README.md	Documents design-history format.
.llm/context.md	Updates core repo guidance (test output, moved skill links, new workflow links).
.github/workflows/wiki-sync.yml	Updates docs script paths in wiki sync workflow.
.github/workflows/publish.yml	Updates sccache verify script path.
.github/workflows/ci-verification.yml	Updates verification script paths and sccache script path.
.github/workflows/ci-security.yml	Updates sccache verify script path.
.github/workflows/ci-rust.yml	Updates verification script paths and sccache script path.
.github/workflows/ci-network.yml	Updates docker test script path and sccache script path.
.github/workflows/ci-llm-lint.yml	Updates check-llm-skills script path.
.github/workflows/ci-docs.yml	Updates docs script paths (wiki/links/code-fence/markdown verify).
.github/workflows/ci-benchmarks.yml	Updates sccache verify script path.
.github/copilot-instructions.md	Adds clarifying-question template reference.
.devcontainer/welcome.sh	Updates verification script paths shown to users.
.devcontainer/devcontainer.json	Updates postCreate tool-check command and adds editor extensions/settings.
.devcontainer/README.md	Updates verification/tool-check script paths.
.config/nextest.toml	Removes serial test-group config now that port conflicts are reduced.

[Copilot]

Pull request overview

Copilot reviewed 114 out of 158 changed files in this pull request and generated 1 comment.

[Copilot]

This test module still relies on real UDP sockets (bind_socket_with_retry) and #[serial] ordering, which conflicts with the PR description’s claim of eliminating real UDP I/O / serial_test via ChannelSocket + virtual time. If the intent is full migration, consider switching this test to ChannelSocket (and dropping #[serial]), or update the PR description/scope to reflect that some P2P checksum tests still use OS sockets (including Windows retry sleeps inside bind_socket_with_retry).