Scaffold the crate
Rust project layout, Cargo.toml, justfile, coverage script, and CI workflow per the rust skill's scaffolding.md and binary.md, adapted for d3j: no tokio (synchronous CPU-bound merge driver), no build.rs versioning, and no release workflow yet — those land in a later milestone. Assisted-by: Claude Sonnet 5 via Claude Code
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..03e4628
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,20 @@
+name: CI
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+
+jobs:
+ ci:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+ with:
+ persist-credentials: false
+ - run: rustup component add clippy rustfmt llvm-tools
+ - run: cargo install grcov cargo-mutants just
+ - uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6
+ - run: cargo fmt --check
+ - run: just clippy coverage
+ - run: just mutants
diff --git a/.gitignore b/.gitignore
index dadea7c..2425919 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
/2607.07987v1.pdf
+/target
diff --git a/Cargo.lock b/Cargo.lock
new file mode 100644
index 0000000..0f92d42
--- /dev/null
+++ b/Cargo.lock
@@ -0,0 +1,1190 @@
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+name = "windows-sys"
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+checksum = "ae137229bcbd6cdf0f7b80a31df61766145077ddf49416a728b02cb3921ff3fc"
+dependencies = [
+ "windows-link",
+]
+
+[[package]]
+name = "winnow"
+version = "0.7.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df79d97927682d2fd8adb29682d1140b343be4ac0f08fd68b7765d9c059d3945"
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+[[package]]
+name = "winnow"
+version = "1.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
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+
+[[package]]
+name = "zmij"
+version = "1.0.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
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diff --git a/Cargo.toml b/Cargo.toml
new file mode 100644
index 0000000..2cc5cf0
--- /dev/null
+++ b/Cargo.toml
@@ -0,0 +1,36 @@
+[package]
+name = "d3j"
+version = "0.1.0"
+edition = "2024"
+
+[[bin]]
+name = "d3j"
+path = "src/bin/d3j/main.rs"
+
+[dependencies]
+clap = { version = "*", features = ["derive", "env"] }
+fs-err = "*"
+miette = { version = "*", features = ["fancy"] }
+serde = { version = "*", features = ["derive"] }
+serde_json = "*"
+thiserror = "*"
+tracing = "*"
+tracing-subscriber = { version = "*", features = ["env-filter"] }
+tree-sitter = "*"
+tree-sitter-java = "*"
+tree-sitter-json = "*"
+tree-sitter-rust = "*"
+
+[dev-dependencies]
+assert_cmd = "*"
+hegeltest = "*"
+predicates = "*"
+tempfile = "*"
+
+[lints.clippy]
+self_named_module_files = "warn"
+unwrap_used = "warn"
+expect_used = "warn"
+panic = "warn"
+indexing_slicing = "warn"
+arithmetic_side_effects = "warn"
diff --git a/bin/coverage b/bin/coverage
new file mode 100755
index 0000000..0a67da7
--- /dev/null
+++ b/bin/coverage
@@ -0,0 +1,69 @@
+#!/usr/bin/env bash
+
+# Measures library line coverage with grcov and fails below the
+# threshold. Uses a separate CARGO_TARGET_DIR so instrumented and
+# normal build artifacts never mix — mixing causes phantom uncovered
+# lines. Override the gate with COVERAGE_THRESHOLD (defaults to 100).
+#
+# Scaffolded into a project as bin/coverage; the `coverage` justfile
+# recipe runs it. See the rust skill's coverage.md and scaffolding.md.
+
+set -euo pipefail
+if [[ "${TRACE-0}" == "1" ]]; then
+ set -o xtrace
+fi
+
+readonly THRESHOLD="${COVERAGE_THRESHOLD:-100}"
+readonly TARGET_DIR="target/coverage"
+
+main() {
+ export RUSTFLAGS="-Cinstrument-coverage"
+ export CARGO_TARGET_DIR="$TARGET_DIR"
+ export LLVM_PROFILE_FILE="$TARGET_DIR/profraw/%p-%m.profraw"
+
+ rm -rf "$TARGET_DIR"
+ cargo test --workspace --quiet
+
+ local report
+ report=$(grcov "$TARGET_DIR/profraw" \
+ --binary-path "./$TARGET_DIR/debug/" \
+ --source-dir . \
+ --output-types covdir \
+ --ignore-not-existing \
+ --keep-only 'src/**' \
+ --ignore 'src/bin/**' \
+ --excl-line 'cov-excl-line|unreachable!' \
+ --excl-start 'cov-excl-start' \
+ --excl-stop 'cov-excl-stop')
+
+ # Per-file breakdown: walk the covdir tree, printing leaf files only.
+ jq --raw-output '
+ def files:
+ to_entries[] | .value |
+ if .children then .children | files
+ else "\(.name): \(.coveragePercent)% (\(.linesCovered)/\(.linesTotal))"
+ end;
+ .children | files
+ ' <<<"$report"
+
+ # A crate with no coverable library lines yet (e.g. a fresh
+ # scaffold) reports 0.0%, which would spuriously fail the gate.
+ local lines_total
+ lines_total=$(jq '.linesTotal' <<<"$report")
+ if [[ "$lines_total" -eq 0 ]]; then
+ echo "coverage: no coverable lines yet, skipping gate"
+ return 0
+ fi
+
+ local coverage
+ coverage=$(jq '.coveragePercent' <<<"$report")
+ echo ""
+ echo "Total: ${coverage}%"
+
+ if [[ "$(echo "$coverage < $THRESHOLD" | bc -l)" -eq 1 ]]; then
+ echo "ERROR: coverage ${coverage}% is below ${THRESHOLD}%" >&2
+ exit 1
+ fi
+}
+
+main "$@"
diff --git a/justfile b/justfile
new file mode 100644
index 0000000..5d2c7b2
--- /dev/null
+++ b/justfile
@@ -0,0 +1,29 @@
+default: all
+
+fmt:
+ cargo fmt --all
+
+check:
+ cargo check --workspace
+
+clippy:
+ cargo clippy --workspace -- -D warnings
+
+coverage:
+ ./bin/coverage
+
+mutants:
+ #!/usr/bin/env bash
+ set -uo pipefail
+ cargo mutants --timeout-multiplier 3 -j4
+ rc=$?
+ # 0 = all caught, 3 = timeouts (infinite loops from mutants, still caught).
+ if [ "$rc" -eq 0 ] || [ "$rc" -eq 3 ]; then
+ exit 0
+ fi
+ exit "$rc"
+
+all: fmt clippy coverage
+
+install:
+ cargo install --locked --path .
diff --git a/src/bin/d3j/main.rs b/src/bin/d3j/main.rs
new file mode 100644
index 0000000..1e713bf
--- /dev/null
+++ b/src/bin/d3j/main.rs
@@ -0,0 +1,11 @@
+use tracing_subscriber::{EnvFilter, fmt, prelude::*};
+
+fn main() -> miette::Result<()> {
+ miette::set_panic_hook();
+ tracing_subscriber::registry()
+ .with(fmt::layer())
+ .with(EnvFilter::from_default_env())
+ .init();
+
+ Ok(())
+}
diff --git a/src/lib.rs b/src/lib.rs
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/src/lib.rs
@@ -0,0 +1 @@
+