Revert "remove log files"

This reverts commit 17002d9.

Author: SteveBronder

.claude/settings.local.json

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+{
+  "permissions": {
+    "allow": [
+      "WebSearch",
+      "WebFetch(domain:arxiv.org)",
+      "WebFetch(domain:docs.scipy.org)",
+      "WebFetch(domain:www.ime.unicamp.br)",
+      "WebFetch(domain:sites.math.washington.edu)",
+      "WebFetch(domain:indrag49.github.io)",
+      "WebFetch(domain:github.com)",
+      "WebFetch(domain:www.sciencedirect.com)",
+      "WebFetch(domain:optax.readthedocs.io)"
+    ]
+  }
+}

.codex/skills/memories/project-overview/SKILL.md

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+# Project Overview
+
+- Purpose: Stan Math Library is a C++ reverse-mode automatic differentiation library used by Stan (see `README.md`).
+- Core layout: primary headers and implementation live under `stan/math/` with domain splits in `stan/math/prim`, `stan/math/rev`, `stan/math/fwd`, `stan/math/mix`, `stan/math/opencl`. Umbrella headers include `stan/math.hpp`, `stan/math/prim.hpp`, `stan/math/rev.hpp`, `stan/math/fwd.hpp`, `stan/math/mix.hpp`.
+- Tests: unit tests are under `test/unit/` (notably `test/unit/math/...`); expression tests under `test/expressions/`; probability tests and generators under `test/prob/`.
+- Benchmarks: microbenchmarks live in `benchmarks/`.
+- Third-party deps: vendored libraries are under `lib/` (TBB, Sundials, etc. referenced in build rules).
+
+Golden paths
+- Add a function: implement in the appropriate domain folder (e.g., `stan/math/prim/...`), update umbrella headers if needed, and add a unit test under `test/unit/math/...`.
+- Fix a bug: find the failing test under `test/unit/...`, adjust code in `stan/math/...`, and run the focused test via `./runTests.py` or `make` (see `makefile`).
+- Performance work: add or update a benchmark in `benchmarks/` and compare results locally.
+
+Risk/fragile areas
+- OpenCL code paths (`stan/math/opencl/`) and SUNDIALS-dependent tests may require extra dependencies (see `make/tests`).

.codex/skills/memories/style-and-conventions/SKILL.md

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+# Style and Conventions
+
+Formatting
+- C++ formatting follows `.clang-format` (Google-based) with `ColumnLimit: 80`, `IndentWidth: 2`, `PointerAlignment: Left`, and `SortIncludes: false`.
+
+Code organization
+- Library code lives in `stan/math/` with domains in `prim`, `rev`, `fwd`, `mix`, and `opencl`.
+- Public umbrella headers exist at `stan/math.hpp` and per-domain headers like `stan/math/prim.hpp`.
+
+Naming and file patterns
+- Headers use `.hpp`.
+- Unit tests are `*_test.cpp` under `test/unit/...`.
+- Header compile tests use the `-test` suffix (e.g., `stan/math/constants.hpp-test`).
+
+Quality checks
+- Use `make cpplint` and `make clang-tidy` for static checks (targets defined in `make/cpplint` and `make/clang-tidy`).

.codex/skills/memories/suggested-commands/SKILL.md

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+# Suggested Commands
+
+Setup/overview
+- `make help`: print available make targets and testing guidance (see `makefile`).
+
+Testing
+- `./runTests.py -h`: show test runner help and options.
+- `./runTests.py test/unit`: run unit tests under `test/unit/`.
+- `./runTests.py -f <pattern>`: run tests matching a pattern (e.g., `-f opencl`).
+- `./runTests.py --changed`: run tests for files changed in git.
+- `make test/unit/math/prim/fun/abs_test`: build a single unit test binary.
+- `make test-headers`: compile-check all headers (see `make/tests`).
+- `make stan/math/constants.hpp-test`: compile-check a single header.
+
+Quality
+- `make cpplint`: run cpplint over source files.
+- `make clang-tidy`: run clang-tidy across tests (optional `files=...`).
+- `make clang-tidy-fix`: clang-tidy with autofix output to `.clang-fixes.yml`.
+
+Docs
+- `make doxygen`: generate API docs in `doc/api/`.
+
+Cleanup
+- `make clean`: remove generated test files/binaries.
+- `make clean-deps`: remove dependency files if tests stop building.
+- `make clean-all`: deep clean including docs/libraries.
+
+Utilities
+- `./runChecks.py`: check math dependency rules (targeted by `make test-math-dependencies`).

.codex/skills/memories/task-completion-checklist/SKILL.md

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+# Task Completion Checklist
+
+- [ ] Run focused tests for changed areas (e.g., `./runTests.py test/unit/...` or single test binary via `make`).
+- [ ] Add/update tests when behavior changes; ensure new data files are referenced correctly.
+- [ ] Run relevant linters/static checks if touching core code (`make cpplint`, `make clang-tidy`).
+- [ ] Update docs/changelogs if user-facing behavior changes (rare for math internals).
+- [ ] Self-review for dependency rules (prim/fwd/rev/mix layering) and header include correctness.

.codex/skills/memories/testing-guidance/SKILL.md

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+# Testing Guidance
+
+- Primary runner: `./runTests.py` (see help with `-h`).
+- Unit tests live under `test/unit/`; run a subtree with `./runTests.py test/unit` or a specific test file path.
+- Build a single test binary with `make test/unit/path/to/foo_test` and run the produced binary.
+- Header compile tests: `make test-headers` or `make stan/math/constants.hpp-test`.
+- Dependency checks: `./runChecks.py` or `make test-math-dependencies`.