Fix Rust test discovery, docs, binaries, CI, and clippy

.github/workflows/ci.yml

@@ -61,6 +61,8 @@ jobs:
         uses: dtolnay/rust-toolchain@1.97.0
         with:
           targets: aarch64-apple-darwin
+      - name: Test
+        run: cargo test -- --test-threads=8
       - name: Build
         run: cargo build --release --target aarch64-apple-darwin
       - uses: actions/upload-artifact@v4
@@ -76,6 +78,8 @@ jobs:
         uses: dtolnay/rust-toolchain@1.97.0
         with:
           targets: x86_64-apple-darwin
+      - name: Test
+        run: cargo test -- --test-threads=8
       - name: Build
         run: cargo build --release --target x86_64-apple-darwin
       - uses: actions/upload-artifact@v4
@@ -91,6 +95,8 @@ jobs:
         uses: dtolnay/rust-toolchain@1.97.0
         with:
           targets: x86_64-pc-windows-msvc
+      - name: Test
+        run: cargo test -- --test-threads=8
       - name: Build
         run: cargo build --release --target x86_64-pc-windows-msvc
       - uses: actions/upload-artifact@v4

.gitignore

@@ -29,6 +29,6 @@ PLAN_NEXT.md
 PLAN_COMPLETED.md
 plan/
 
-# Wikifier runtime cache (state files like file_health.md ARE versioned)
+# Wikifier runtime cache. Generated maps of the old Python package are not versioned.
 .wikifier_staging/
 .coordinationhub/

AGENTS.md

@@ -43,6 +43,6 @@ Shards are one snapshot each under `.chisel/shards/<shard>/`, configured by `CHI
 
 Scores are heuristics. Read `_meta.uniform_components` before trusting a composite risk score. `flakiness_trend` is present when a covering test has dated results in the current week and in an older week of the last 28 days. It does not change risk weights. `record_result` stores `recorded_at`.
 
-Test filenames that produce edges include `test_*.py`, `*_test.py`, `*.test.ts`, `*.spec.ts`, `*_test.go`, and `*_test.rs`.
+Test filenames that produce edges include `test_*.py`, `*_test.py`, `*.test.ts`, `*.spec.ts`, `*_test.go`, `*_test.rs`, and any `.rs` file under the top-level `tests/` directory. Rust functions marked `#[test]`, `#[tokio::test]`, `#[rstest]`, or `#[test_case]` are test units even when the file is not named like a test.
 
 `CHISEL_EXTRACTOR` or `extractor` in `.chisel/extensions.toml` names an executable. That program may use its own libraries. Chisel does not link them. The toml file is ignored unless the process was started with `--allow-repo-extractor` or `CHISEL_ALLOW_REPO_EXTRACTOR=1`. A tool argument cannot turn it on. The path must stay inside the project. `CHISEL_EXTRACTOR` overrides the file. A bad run falls back to the built-in scanner. A git ref that starts with `-` is rejected.

ARCHITECTURE.md

@@ -1,11 +1,49 @@
 # Architecture
 
-Chisel is a zero-dependency Rust program. `AGENTS.md` is the agent contract.
+Chisel is a zero-dependency Rust program. `AGENTS.md` is the agent contract. `plan.md` records the layout and the rules that stay in force.
 
-`src/engine` analyzes the worktree, answers queries, and records advisory locks. `src/extract` scans source files. `src/store.rs` reads and writes one snapshot, `.chisel/store`, with a temp file, fsync, and rename. It does not open `chisel.db` and it rejects `:memory:` and `file:` paths.
+The crate exposes two binaries. `chisel` is `src/main.rs`. `chisel-mcp` is `src/bin/chisel-mcp.rs`. Both call `cli::entry`. When the program name is `chisel-mcp`, the entry inserts `serve-mcp` and speaks stdio MCP. `chisel serve` is HTTP only: `GET /health`, `GET /tools`, and `POST /call` on `127.0.0.1:8377`. There is no `/mcp` path.
 
-Git is a subprocess. HTTP is `GET /health`, `GET /tools`, and `POST /call` on `127.0.0.1:8377`. There is no `/mcp` path. MCP is stdio Content-Length JSON-RPC from `chisel serve-mcp` or the `chisel-mcp` name of the same binary.
+## Flow
 
-Status values: `no_data`, `no_changes`, `no_edges`, `git_error`, `stale_db`, `error`, `unsupported`, `auto_queued`.
+1. `analyze` lists code files through git (or a walk when ignored files are included), extracts units, and writes one snapshot.
+2. Test files come from `looks_like_test` in `src/engine/mod.rs`. That is the only filename classifier. Rust files under the top-level `tests/` directory are test files. Functions with a `#[test]`-family attribute are test units even inside a source file.
+3. Edges are calls and imports from those test units to code units. `suggest-tests`, `diff-impact`, `test-gaps`, and `risk-map` read the snapshot.
+4. `update` recomputes changed files. A no-op update sets `edge_rebuild_skipped` and does not run `git blame` or per-function `git log -L`.
+5. `risk-map` and `test-gaps` skip paths that `looks_like_test` accepts. A source file that also holds `#[test]` functions stays in those answers. The test functions themselves are not listed as untested code.
 
-Do not pip-install this project. Do not store analysis in SQLite.
+## Modules
+
+| Module | Responsibility |
+|---|---|
+| `src/cli.rs` | Flags, subcommands, `chisel run`, `chisel watch`. |
+| `src/engine/analyze.rs` | Full and incremental scans, test units, edges. |
+| `src/engine/query.rs` | Read tools: impact, suggestions, risk, gaps, triage. |
+| `src/engine/locks.rs` | Advisory lock rows in the snapshot. |
+| `src/extract` | Python syntax units, brace-language units, import and call deps. |
+| `src/syntax.rs` | Built-in Python and JavaScript syntax tree used by the scanners. |
+| `src/store.rs` | One snapshot file. Write to a temp file, fsync, rename. |
+| `src/git.rs` | Porcelain via `std::process`. A ref that starts with `-` is rejected. |
+| `src/impact.rs` | Churn, coupling, coverage gap, risk score. |
+| `src/json.rs` | Parser, serializer, Python-compatible rounding for scores. |
+| `src/hash.rs` | SHA-256 for file content. |
+| `src/http.rs` | The small JSON HTTP server. |
+| `src/mcp.rs` | Content-Length framing and the tool bridge. |
+| `src/fswatch.rs` | OS change notification. `collect_files` is only compiled for the kqueue path. |
+| `src/lock.rs` | Cross-process shared and exclusive locks. |
+| `src/schemas.rs` | Tool list. Missing required arguments are `status: "error"`. |
+| `src/next_steps.rs` | Hint rows attached to tool results. |
+
+Shards are one snapshot each under `.chisel/shards/<shard>/`. Writes use the longest path prefix. Unscoped reads aggregate. Cross-shard test edges are written to the parent snapshot and overlaid for impact, suggestions, diff, risk coverage, and stale tests.
+
+## Storage and git
+
+`.chisel/store` is the snapshot. Chisel does not open `chisel.db`. `:memory:` and `file:` storage paths are rejected. `CHISEL_PROJECT_DIR` and `CHISEL_STORAGE_DIR` apply when the CLI flags are absent.
+
+Git is a subprocess. Locks are advisory records. They do not lock source files.
+
+## Status
+
+`no_data`, `no_changes`, `no_edges`, `git_error`, `stale_db`, `error`, `unsupported`, `auto_queued`. `no_data` and `stale_db` exit 0. `error` and `git_error` exit 1.
+
+Do not pip-install this project. Do not store analysis in SQLite. Do not add a crates.io dependency.

CLAUDE.md

@@ -1,9 +1,11 @@
 # Chisel
 
-The product is the Rust crate in `src/`. Read `AGENTS.md` for how to call it.
+The product is the Rust crate in `src/`. Read `AGENTS.md` for how to call it and `ARCHITECTURE.md` for the module map.
 
-Build with `cargo build --release`. The binary is `chisel`. `chisel-mcp` is the same program. Storage is the snapshot `.chisel/store`. Chisel does not open `chisel.db`. `:memory:` and `file:` storage paths are rejected.
+Build with `cargo build --release`. The `chisel` binary is `src/main.rs`. The `chisel-mcp` binary is `src/bin/chisel-mcp.rs`. Both call the same entry point. Storage is the snapshot `.chisel/store`. Chisel does not open `chisel.db`. `:memory:` and `file:` storage paths are rejected.
 
-Do not pip-install Chisel. Do not use SQLite as the store.
+Do not pip-install Chisel. Do not use SQLite as the store. `Cargo.toml` dependency tables stay empty. There is no `build.rs`.
+
+`looks_like_test` in `src/engine/mod.rs` is the only test-file classifier. Rust files under `tests/` are tests. `#[test]` functions are test units.
 
 Status values: `no_data`, `no_changes`, `no_edges`, `git_error`, `stale_db`, `error`, `unsupported`, `auto_queued`. `no_data` and `stale_db` exit 0. `error` and `git_error` exit 1.

COMPLETE_PROJECT_DOCUMENTATION.md

@@ -1,9 +1,107 @@
 # Chisel
 
-The program you run is the Rust binary from `src/`. Read `AGENTS.md`.
+Updated: 2026-11-03.
+
+Purpose: inventory of this repository. The program you run is the Rust binary from `src/`. Read `AGENTS.md` for calls and `ARCHITECTURE.md` for how the pieces fit.
 
 Storage is the snapshot `.chisel/store`. Chisel does not open `chisel.db`. `:memory:` and `file:` paths are rejected. Do not pip-install Chisel and do not use SQLite as the store.
 
 Status values: `no_data`, `no_changes`, `no_edges`, `git_error`, `stale_db`, `error`, `unsupported`, `auto_queued`.
 
 `no_data` and `stale_db` exit 0. `error` and `git_error` exit 1.
+
+`library.md`, `file_health.md`, and `file_health.json` were removed. They were generated maps of the deleted Python package. Nothing in this tree regenerates them. `monitored_paths.txt` was removed because it held one machine's absolute path and the binary does not read it.
+
+## Root
+
+| Path | Purpose |
+|---|---|
+| `README.md` | How to build and call the binary. |
+| `AGENTS.md` | Agent contract: status values, flags, scale limits. |
+| `CLAUDE.md` | Short orientation for agents that load this file first. |
+| `ARCHITECTURE.md` | Module map and the analyze-to-query flow. |
+| `plan.md` | Current layout and the dependency rule. Not a Python port schedule. |
+| `CONTRIBUTING.md` | Build and test commands. |
+| `CHANGELOG.md` | Release notes. Older entries mention the Python package. |
+| `LLM_Development.md` | Historical session log. |
+| `Cargo.toml` | Package `chisel`. Empty dependency tables. Two binaries. |
+| `Cargo.lock` | Lockfile for the empty dependency graph. |
+| `rust-toolchain.toml` | Pinned Rust channel. |
+| `LICENSE` | MIT. |
+| `.gitignore` | Build output, `.chisel/`, and the old `plan/` directory. |
+| `exclude_patterns.txt` | Paths a watcher should skip. Not read by the Rust binary. |
+| `GROK_CONNECTORS.md` | How to point an MCP client at `chisel-mcp`. |
+| `skills/SKILL.md` | Skill text for calling the binary. |
+| `.grok/skills/chisel/SKILL.md` | Same skill, installed for this workspace. |
+
+## `src/`
+
+| Path | Purpose |
+|---|---|
+| `src/lib.rs` | Crate root. |
+| `src/main.rs` | `chisel` binary. |
+| `src/bin/chisel-mcp.rs` | `chisel-mcp` binary. |
+| `src/cli.rs` | Argv and dispatch, including `--version`. |
+| `src/engine/mod.rs` | Engine type and `looks_like_test`. |
+| `src/engine/analyze.rs` | `analyze` and `update`. |
+| `src/engine/query.rs` | Read tools. |
+| `src/engine/locks.rs` | Advisory locks. |
+| `src/extract/mod.rs` | Scanner entry. |
+| `src/extract/python.rs` | Python units. |
+| `src/extract/brace.rs` | Brace languages, including Rust `#[test]`. |
+| `src/extract/deps.rs` | Imports and calls. |
+| `src/syntax.rs` | Python and JavaScript syntax tree. |
+| `src/store.rs` | Snapshot file. |
+| `src/git.rs` | Git subprocess. |
+| `src/impact.rs` | Risk math. |
+| `src/json.rs` | JSON. |
+| `src/hash.rs` | SHA-256. |
+| `src/http.rs` | HTTP server. |
+| `src/mcp.rs` | Stdio MCP. |
+| `src/fswatch.rs` | OS directory watch. |
+| `src/lock.rs` | Process locks. |
+| `src/schemas.rs` | Tool schemas. |
+| `src/schemas_data.json` | Schema payload compiled into `schemas.rs`. |
+| `src/next_steps.rs` | Follow-up hints. |
+
+## `tests/`
+
+| Path | Purpose |
+|---|---|
+| `tests/scale.rs` | Behaviour checks against temp git repos and the binary. |
+| `tests/oracle_parity.rs` | Binary output against frozen oracle JSON. |
+| `tests/surface_contract.rs` | Tool list shape. |
+| `tests/extract_parity.rs` | Language fixtures, including Rust `#[test]` unit types. |
+| `tests/durability.rs` | Snapshot publish under a killed writer. |
+| `tests/rust_layout.rs` | Cargo layout fixture and a dogfood run on this repo. |
+| `tests/fixtures/oracle/` | Frozen JSON for the Python-era oracle. |
+| `tests/fixtures/languages/` | Small samples per language. |
+| `tests/fixtures/rust_crate/` | `src/lib.rs`, `src/a.rs`, `tests/a.rs`, and a `Cargo.toml`. |
+
+## Other trees
+
+| Path | Purpose |
+|---|---|
+| `.github/workflows/ci.yml` | Test on Linux, macOS, and Windows. Release builds for the publish targets. |
+| `.github/workflows/publish.yml` | Tagged release builds. |
+| `docs/AGENT_PLAYBOOK.md` | Short pointer at `AGENTS.md`. |
+| `docs/CUSTOM_EXTRACTORS.md` | External extractor program. |
+| `docs/EXTRACTOR_ECOSYSTEM.md` | Where an external extractor fits. |
+| `docs/LLM_CONTRACT.md` | Pointer at the status contract. |
+| `docs/ZERO_DEPS.md` | Empty dependency tables. |
+| `docs/chisel-demo.png` | Screenshot used by the README. |
+| `examples/github-actions/chisel.yml` | Example workflow that builds this binary with Cargo. |
+| `findings/` | Closed review notes. |
+| `journal/2026/` | Dated notes from June 2026. |
+| `Logged_issues/` | One closed issue note. |
+| `wiki-local/` | Local notes. They still mention `schemas.py` in places. The Rust schemas are `src/schemas.rs`. |
+
+## Removed in this pass
+
+| Path | Why |
+|---|---|
+| `library.md` | Wikifier map of `chisel/*.py`. Those modules are gone, and this repo cannot regenerate the file. |
+| `file_health.md` | Same age, same deleted tree. |
+| `file_health.json` | Machine-readable copy of that matrix. |
+| `pending_updates.md` | Empty. |
+| `monitored_paths.txt` | Held `/home/aron/Documents/coding_projects/Chisel`. The binary does not read it. |

Cargo.toml

@@ -5,14 +5,15 @@ edition = "2021"
 description = "Test impact analysis and code intelligence for LLM agents"
 license = "MIT"
 publish = false
+autobins = false
 
 [[bin]]
 name = "chisel"
 path = "src/main.rs"
 
 [[bin]]
 name = "chisel-mcp"
-path = "src/main.rs"
+path = "src/bin/chisel-mcp.rs"
 
 [dependencies]
 

LLM_Development.md

@@ -4,6 +4,17 @@ Chronological record of development activity on the Chisel project.
 
 ---
 
+## 2026-11-03 -- Cargo test discovery, docs, CI, version
+
+- One test-file classifier. Rust files under `tests/` and `#[test]`-family functions are test units.
+- Removed `library.md`, `file_health.md`, `file_health.json`, and `pending_updates.md`. They described the deleted Python package or were empty. `plan.md`, `ARCHITECTURE.md`, `CLAUDE.md`, and `COMPLETE_PROJECT_DOCUMENTATION.md` now describe the Rust tree.
+- `chisel` and `chisel-mcp` no longer share `src/main.rs`. `collect_files` is compiled only for the kqueue path.
+- CI runs `cargo test` on macOS and Windows as well as Linux.
+- `--version` prints the package version. Removed `monitored_paths.txt` (it held one local absolute path).
+- Cleared the clippy warnings reported by `cargo clippy --all-targets`.
+
+---
+
 ## 2026-04-14 -- Review Thirteen fixes (kimi_review_2): risk_map crash, suggest_tests/diff_impact working_tree timeouts
 
 ### Summary

README.md

@@ -157,7 +157,7 @@ The same binary has been run on flask, requests, cJSON, quixbugs, and the Probat
 
 - **Zero dependencies** — the Rust binary links only the standard library. No crates.io crates. System `git` is required at runtime.
 - **Multi-language** — Python, JavaScript/TypeScript, Go, Rust, C#, Java, Kotlin, C/C++, Swift, PHP, Ruby, Dart
-- **Framework-aware** — pytest, Jest, Go test, Rust #[test], Playwright, xUnit/NUnit/MSTest, JUnit (incl. parameterized), XCTest + Swift Testing, PHPUnit, RSpec, Minitest, gtest, Dart test
+- **Framework-aware** — pytest, Jest, Go test, Rust `#[test]` (including `#[tokio::test]` and `#[rstest]`, in `tests/*.rs` and in source files), Playwright, xUnit/NUnit/MSTest, JUnit (incl. parameterized), XCTest + Swift Testing, PHPUnit, RSpec, Minitest, gtest, Dart test
 - **Incremental** — `update` recomputes changed files and newer commits. A no-op update sets `edge_rebuild_skipped` and does not run `git blame` or per-function `git log -L`. Above 2000 code files, file-level churn still runs and per-function `git log -L` does not (`unit_churn_skipped`).
 - **gitignore-aware** — ignored trees (vendored deps, build output, fixtures) are never scanned; untracked files still are (`CHISEL_INCLUDE_IGNORED=1` to override)
 - **Branch-aware** — `diff_impact` auto-detects feature branch vs main. Feature-branch co-change comes from `merge-base..HEAD`. `main` and `master` keep that list empty.