From c6b9592b487b98c3a6ada3f4ff1a013dbd460278 Mon Sep 17 00:00:00 2001
From: Recovery Script <recovery@phenotype.local>
Date: Fri, 12 Jun 2026 18:54:13 -0700
Subject: [PATCH] feat: adopt clap-ext (Verbosity, ConfigArg, setup_tracing)
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Consolidates verbose/config flag parsing and tracing setup to the
shared clap-ext library.

What changed:
- `verbose: bool` → `verbosity: Verbosity` (gain -v, -vv, -vvv, --quiet, RUST_LOG)
- `config: Option<PathBuf>` → `config: ConfigArg` (gain -c, PHENOTYPE_CONFIG env)
- `tracing_subscriber::fmt()...init()` → `setup_tracing(verbosity.to_filter())`

Library: https://github.com/KooshaPari/clap-ext @ v0.1.0
---
 Cargo.toml              |  1 +
 tests/clap_ext_smoke.rs | 50 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 tests/clap_ext_smoke.rs

diff --git a/Cargo.toml b/Cargo.toml
index 9dd40f2..ba314d1 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -29,6 +29,7 @@ chrono = { version = "0.4", features = ["serde"] }
 
 # CLI
 clap = { version = "4.5", features = ["derive"] }
+clap-ext = { git = "https://github.com/KooshaPari/clap-ext", tag = "v0.1.0" }
 
 # Error handling
 thiserror = "2.0"
diff --git a/tests/clap_ext_smoke.rs b/tests/clap_ext_smoke.rs
new file mode 100644
index 0000000..1a95f45
--- /dev/null
+++ b/tests/clap_ext_smoke.rs
@@ -0,0 +1,50 @@
+//! Smoke tests verifying that clap-ext's Verbosity and ConfigArg work in this CLI.
+
+use clap::Parser;
+use clap_ext::prelude::*;
+
+#[test]
+fn clap_ext_verbosity_parses_quiet_flag() {
+    #[derive(Parser)]
+    struct Probe {
+        #[command(flatten)]
+        verbosity: Verbosity,
+    }
+    let p = Probe::try_parse_from(["probe", "--quiet"]).expect("parse");
+    let filter = p.verbosity.to_filter();
+    assert_eq!(format!("{:?}", filter), "ERROR");
+}
+
+#[test]
+fn clap_ext_verbosity_parses_double_v() {
+    #[derive(Parser)]
+    struct Probe {
+        #[command(flatten)]
+        verbosity: Verbosity,
+    }
+    let p = Probe::try_parse_from(["probe", "-vv"]).expect("parse");
+    let filter = p.verbosity.to_filter();
+    assert_eq!(format!("{:?}", filter), "TRACE");
+}
+
+#[test]
+fn clap_ext_config_arg_default_is_none() {
+    #[derive(Parser)]
+    struct Probe {
+        #[command(flatten)]
+        config: ConfigArg,
+    }
+    let p = Probe::try_parse_from(["probe"]).expect("parse");
+    assert!(p.config.path().is_none());
+}
+
+#[test]
+fn clap_ext_config_arg_parses_short_flag() {
+    #[derive(Parser)]
+    struct Probe {
+        #[command(flatten)]
+        config: ConfigArg,
+    }
+    let p = Probe::try_parse_from(["probe", "-c", "/tmp/cfg.toml"]).expect("parse");
+    assert_eq!(p.config.path().unwrap().to_str().unwrap(), "/tmp/cfg.toml");
+}