From 6e23cba84631119265e04bba5caeec676219efc2 Mon Sep 17 00:00:00 2001
From: Long Ho <holevietlong@gmail.com>
Date: Fri, 29 May 2026 13:41:16 -0400
Subject: [PATCH] Propagate global flags to subcommands

---
 crates/codescythe_cli/e2e.rs  | 62 +++++++++++++++++++++++++++++++++++
 crates/codescythe_cli/main.rs | 34 +++++++++++++------
 2 files changed, 86 insertions(+), 10 deletions(-)

diff --git a/crates/codescythe_cli/e2e.rs b/crates/codescythe_cli/e2e.rs
index 1132b91..f2d6f97 100644
--- a/crates/codescythe_cli/e2e.rs
+++ b/crates/codescythe_cli/e2e.rs
@@ -312,6 +312,68 @@ fn cli_queries_dependency_paths() {
     assert!(svg.contains("src/module.ts:used"), "{svg}");
 }
 
+#[cfg(unix)]
+#[test]
+fn cli_query_honors_global_directory_and_config_flags() {
+    let cli = runfile("crates/codescythe_cli/codescythe");
+    let fixture = env::temp_dir().join(format!(
+        "codescythe-e2e-query-global-flags-{}",
+        SystemTime::now()
+            .duration_since(UNIX_EPOCH)
+            .expect("system time should be after UNIX_EPOCH")
+            .as_nanos()
+    ));
+    fs::create_dir_all(fixture.join("app")).unwrap();
+    fs::create_dir_all(fixture.join(".agents/plugins")).unwrap();
+    fs::write(
+        fixture.join("custom-codescythe.json"),
+        r#"{
+          "project": "app/**/*.ts",
+          "ignore": [".agents", ".agents/**"]
+        }"#,
+    )
+    .unwrap();
+    fs::write(
+        fixture.join("app/main.ts"),
+        "import { used } from './module';\nconsole.log(used);\n",
+    )
+    .unwrap();
+    fs::write(fixture.join("app/module.ts"), "export const used = 1;\n").unwrap();
+    std::os::unix::fs::symlink(
+        fixture.join("missing-symlink-target"),
+        fixture.join(".agents/plugins/broken"),
+    )
+    .unwrap();
+
+    let output = Command::new(&cli)
+        .args([
+            "-C",
+            path_arg(&fixture),
+            "-c",
+            path_arg(&fixture.join("custom-codescythe.json")),
+            "query",
+            "somepath",
+            "--json",
+            "app/main.ts",
+            "app/module.ts:used",
+        ])
+        .output()
+        .expect("failed to run codescythe query");
+
+    assert!(output.status.success(), "{}", output_text(&output));
+    assert!(
+        output.stderr.is_empty(),
+        "unexpected stderr: {}",
+        String::from_utf8_lossy(&output.stderr)
+    );
+    let query: Value = serde_json::from_slice(&output.stdout).expect("query stdout should be JSON");
+    assert_eq!(query["kind"], "somepath");
+    assert_eq!(query["paths"][0]["nodes"][0]["path"], "app/main.ts");
+    assert_eq!(query["paths"][0]["nodes"][1]["path"], "app/module.ts");
+
+    fs::remove_dir_all(&fixture).unwrap();
+}
+
 #[test]
 fn cli_explains_exports_and_doctors_config() {
     let cli = runfile("crates/codescythe_cli/codescythe");
diff --git a/crates/codescythe_cli/main.rs b/crates/codescythe_cli/main.rs
index c58430b..ed91968 100644
--- a/crates/codescythe_cli/main.rs
+++ b/crates/codescythe_cli/main.rs
@@ -115,12 +115,18 @@ fn main() -> ExitCode {
 
 fn run() -> Result<bool> {
     let args = Args::parse();
+    let global_config = args.config;
+    let global_directory = args.directory;
     if let Some(command) = args.command {
-        return run_command(command);
+        return run_command(
+            command,
+            global_config.as_deref(),
+            global_directory.as_deref(),
+        );
     }
 
-    let config = args.config.as_deref();
-    let cwd = analysis_root(args.directory.as_deref(), config)?;
+    let config = global_config.as_deref();
+    let cwd = analysis_root(global_directory.as_deref(), config)?;
 
     if args.fix {
         let result = codescythe::run_and_fix_with_options(
@@ -191,11 +197,15 @@ fn run() -> Result<bool> {
         || !analysis.issues.unresolved.is_empty())
 }
 
-fn run_command(command: Command) -> Result<bool> {
+fn run_command(
+    command: Command,
+    global_config: Option<&Path>,
+    global_directory: Option<&Path>,
+) -> Result<bool> {
     match command {
         Command::Doctor(args) => {
-            let config = args.config.as_deref();
-            let cwd = analysis_root(args.directory.as_deref(), config)?;
+            let config = args.config.as_deref().or(global_config);
+            let cwd = analysis_root(args.directory.as_deref().or(global_directory), config)?;
             let result = codescythe::doctor(&cwd, config)?;
             if args.json {
                 let started = start_profile_timer();
@@ -206,17 +216,21 @@ fn run_command(command: Command) -> Result<bool> {
             }
             Ok(!result.warnings.is_empty() || !result.unresolved_imports.is_empty())
         }
-        Command::Query(args) => run_query_command(args),
+        Command::Query(args) => run_query_command(args, global_config, global_directory),
     }
 }
 
-fn run_query_command(args: QueryArgs) -> Result<bool> {
+fn run_query_command(
+    args: QueryArgs,
+    global_config: Option<&Path>,
+    global_directory: Option<&Path>,
+) -> Result<bool> {
     let (kind, args) = match args.command {
         QueryCommand::Somepath(args) => (codescythe::QueryKind::Somepath, args),
         QueryCommand::Allpaths(args) => (codescythe::QueryKind::Allpaths, args),
     };
-    let config = args.config.as_deref();
-    let cwd = analysis_root(args.directory.as_deref(), config)?;
+    let config = args.config.as_deref().or(global_config);
+    let cwd = analysis_root(args.directory.as_deref().or(global_directory), config)?;
     let result = codescythe::query(
         &cwd,
         config,