chore: upgrade kotatsu, adopt renamed codec entries and KOTATSU_ANNOTATE

[16bit-ykiko]

What changed

Bumps the kotatsu pin from c516e3a (#181) to 340a32a (#196) and migrates every call site to the new API surface:

• Codec entry points now follow kotatsu's payload-based naming: json::to_json → json::to_string, json::from_json/json::parse → json::from_string, toml::parse<T>(text) → toml::from_string<T>(text), toml::from_toml<Config>(text, out) → toml::from_string<Config>(text, out). bincode::to_bytes/from_bytes are unchanged. No flatbuffers migration — clice has no codec::fbs call sites; the codec just stays enabled.
• Annotations: the old kota::meta::defaulted<T> / annotation<T, attrs::skip> wrappers were removed upstream, so Config/ProjectConfig/TrackerConfig/ConfigRule, the three feature options structs, and the cache-metadata struct in workspace.cpp now use the KOTATSU_ANNOTATE(defaulted = true, ...) / KOTATSU_ANNOTATE(skip = true) macro. The macro expands to the same annotation<T, spec<Tag>> wrapper, so field access (.value, aggregate inheritance) and decode semantics are unchanged.
• Every user-facing config option now carries a description = "..." attribute (validated against actual usage; options that are declared but not consumed yet are marked "not yet implemented"). The internal cache struct keeps defaulted only.
• .clang-format: ports kotatsu's StatementMacros: KOTATSU_ANNOTATE (keeps <T> field; on its own line) and BreakAdjacentStringLiterals: true (stacks long description literals). The latter reflows adjacent string literals in ~10 test files — content-identical, formatting only.

Tests

All four suites locally on Debug: unit 1167/1167 (7 skipped), integration 340 passed / 2 skipped, smoke 3/3, snap 395 passed / 68 skipped. Unit suite re-run after the final doc-string fixes.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: d1d6aaa1-ea39-42f9-ad71-ec5c387f15b2

📥 Commits

Reviewing files that changed from the base of the PR and between 1a3246e and 9738f31.

📒 Files selected for processing (1)

• cmake/package.cmake

🚧 Files skipped from review as they are similar to previous changes (1)

• cmake/package.cmake

---

📝 Walkthrough

Walkthrough

The pull request migrates JSON and TOML operations to Kotatsu string-based codec APIs, replaces defaulted<T> configuration fields with annotated native fields, updates the Kotatsu dependency pin, and reformats adjacent string literals across source and test files.

Changes

Kotatsu migration and formatting

Layer / File(s)	Summary
Annotated configuration contracts src/feature/feature.h, src/server/state/config.h, src/server/state/workspace.cpp	Configuration fields now use native types with KOTATSU_ANNOTATE defaults, descriptions, and skip metadata.
Codec API migration src/driver/inspect.cc, src/server/..., src/support/..., benchmarks/scan_benchmark.cpp, tests/unit/server/config_tests.cpp, cmake/package.cmake	JSON and TOML parsing and serialization now use from_string and to_string. The Kotatsu dependency pin also changes.
Formatting and source fixtures .clang-format, src/..., tests/unit/...	Adjacent string literals, diagnostics, logs, command strings, source fixtures, and Markdown expectations are reformatted without changing their values or behavior.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Possibly related PRs

• clice-io/clice#435: Shares Kotatsu codec migration in benchmark and configuration test code.
• clice-io/clice#449: Shares Kotatsu API migration in benchmark and serialization call sites.
• clice-io/clice#576: Shares configuration option changes in feature.h, config.h, and inspect.cc.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 36.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the Kotatsu upgrade, renamed codec APIs, and KOTATSU_ANNOTATE migration.
Description check	✅ Passed	The description covers the changes and provides detailed local test results; the optional Related issue section is not needed.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch chore/upgrade-kotatsu

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/server/state/config.h`:
- Around line 44-112: Update all stale defaulted<T> member accesses to use
native direct field access instead of .value. In src/server/state/config.h lines
44-112, adjust ProjectConfig and TrackerConfig accesses in production code and
tests; in src/feature/feature.h lines 89-128 and 233-258, adjust
CodeCompletionOptions, HoverOptions, and InlayHintsOptions accesses. Replace
both reads and writes while preserving existing fallback and configuration
behavior.

🪄 Autofix

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: fe717f8f-e1ca-4677-a62d-34ecbb758a9c

📥 Commits

Reviewing files that changed from the base of the PR and between 604b5b1 and 1a3246e.

📒 Files selected for processing (33)

• .clang-format
• benchmarks/scan_benchmark.cpp
• cmake/package.cmake
• src/command/command.cpp
• src/driver/inspect.cc
• src/feature/feature.h
• src/semantic/resolver.cpp
• src/server/compiler/compiler.cpp
• src/server/compiler/indexer.cpp
• src/server/protocol/serialize.h
• src/server/service/feature_router.cpp
• src/server/service/format.cpp
• src/server/state/config.cpp
• src/server/state/config.h
• src/server/state/session_store.cpp
• src/server/state/workspace.cpp
• src/server/transport/agentic.h
• src/server/transport/lsp_client.cpp
• src/server/transport/master_server.cpp
• src/server/worker/stateful_worker.cpp
• src/server/worker/worker_pool.cpp
• src/support/cache_store.cpp
• src/support/glob_pattern.cpp
• src/syntax/annotation.cpp
• src/syntax/dependency_graph.cpp
• tests/unit/command/command_tests.cpp
• tests/unit/server/compile_graph_integration_tests.cpp
• tests/unit/server/compiler_tests.cpp
• tests/unit/server/config_tests.cpp
• tests/unit/server/module_worker_tests.cpp
• tests/unit/server/pch_worker_tests.cpp
• tests/unit/server/stateful_worker_tests.cpp
• tests/unit/support/markup_tests.cpp