Summary

Standalone fallow dupes ignores duplicates.minLines, duplicates.minTokens, duplicates.threshold, duplicates.mode, and duplicates.skipLocal declared in .fallowrc.jsonc whenever the matching CLI flag is omitted. The Command::Dupes clap definitions use default_value = "5" (etc.), so min_lines: usize is always populated with the clap default — build_dupes_config then overwrites the toml value unconditionally.

Reproduction

mkdir /tmp/repro && cd /tmp/repro
cat > a.ts << 'TS'
function foo() {
  const a = 1
  const b = 2
  const c = 3
  return a + b + c
}
TS
cp a.ts b.ts && sed -i '' 's/foo/bar/' b.ts
cat > .fallowrc.jsonc << 'JSON'
{ "duplicates": { "minLines": 100, "minTokens": 1000 } }
JSON

# Before this PR: still reports the 4-line clone, ignoring config
fallow dupes

The same problem affects mode, threshold, and skipLocal. audit/combined/programmatic paths are not affected because they merge config into their own structs before constructing DupesOptions.

Root cause

crates/cli/src/dupes.rs::build_dupes_config overwrote each toml scalar with the corresponding opts.* value:

min_tokens: opts.min_tokens,           // clap default of 50 wins, always
min_lines: opts.min_lines,             // clap default of 5 wins, always
threshold: opts.threshold,             // clap default of 0.0 wins, always
skip_local: opts.skip_local,           // CLI false stomps config true

Option<T> with default_value is the only way to distinguish user-passed from clap-supplied default with non-Optional types — so we can't fix this without touching the CLI signature.

Fix

• Switch mode, min_tokens, min_lines, threshold on DupesOptions and the Command::Dupes clap args to Option<T> and drop their default_values.
• build_dupes_config now uses opts.x.unwrap_or(toml_dupes.x) for those four fields.
• skip_local adopts the OR-merge already used for cross_language/ignore_imports, so config-driven skipLocal: true is honored.
• DupesResult.threshold is now sourced from the merged dupes_config.threshold (was opts.threshold), so the failure gate honors .fallowrc.jsonc too.
• audit.rs, combined.rs, and programmatic.rs already have explicit values from their own merges; they forward each as Some(...) (no behavior change at those entry points).

Help text now reads:

--min-lines <MIN_LINES>
    Minimum line count for a clone
    (defaults to the value in `.fallowrc.jsonc`, or `5` if unset).

Test plan

• Updated existing build_config_uses_cli_* tests to wrap CLI values in Some(...)
• Added regression tests for each fallback path:
  • falls_back_to_toml_min_lines_when_cli_unset
  • falls_back_to_toml_min_tokens_when_cli_unset
  • falls_back_to_toml_threshold_when_cli_unset
  • falls_back_to_toml_mode_when_cli_unset
  • cli_min_lines_overrides_toml
  • skip_local_or_merges_with_toml
• cargo fmt --all
• cargo clippy --workspace --all-targets -- -D warnings (clean)
• cargo test --workspace (all suites green)
• End-to-end repro project verified — config minLines: 100 now suppresses the toy clone, and --min-lines 100 still overrides config

Compatibility

• CLI surface: --mode, --min-tokens, --min-lines, --threshold still accept the same values; the only observable difference is "flag omitted" no longer wins over config. Users who relied on the old behavior can migrate by either setting duplicates.* = <prior_default> in their config or by passing the flag explicitly.
• Public Rust API (DuplicationOptions): unchanged. Callers still pass concrete values; we forward each as Some(...) internally.