fix(config): target nearest config dir for TOML writes

e2e/cli/test_set

@@ -35,6 +35,22 @@ assert "mise set NEW_VAR=new_value" ""
 assert_contains "cat mise.toml" "NEW_VAR"
 assert_not_contains "cat mise.local.toml" "NEW_VAR"
 
+# Test that mise set writes to the nearest config directory, not the lowest
+# precedence TOML file across the entire hierarchy.
+rm -rf parent
+mkdir -p parent/myproject/inner
+touch parent/mise.toml parent/myproject/mise.toml
+assert "cd parent/myproject/inner && mise set SOMETHING=from_inner" ""
+assert_contains "cat parent/myproject/mise.toml" "SOMETHING"
+assert_not_contains "cat parent/mise.toml" "SOMETHING"
+
+# Test that ignored config directories are not selected as write targets.
+ignored_child="$(pwd)/parent/myproject"
+assert "cd parent/myproject/inner && MISE_IGNORED_CONFIG_PATHS=$ignored_child mise set IGNORED_CHILD=skipped" ""
+assert_contains "cat parent/mise.toml" "IGNORED_CHILD"
+assert_not_contains "cat parent/myproject/mise.toml" "IGNORED_CHILD"
+rm -rf parent
+
 # Test --stdin reads multiline value
 assert "printf 'line1\nline2' | mise set --stdin MULTI_LINE" ""
 assert "mise set MULTI_LINE" "line1

src/config/mod.rs

@@ -1170,11 +1170,7 @@ pub fn load_config_paths(config_filenames: &[String], include_ignored: bool) ->
     let mut config_files = dirs
         .iter()
         .flat_map(|dir| {
-            if !include_ignored
-                && env::MISE_IGNORED_CONFIG_PATHS
-                    .iter()
-                    .any(|p| dir.starts_with(p))
-            {
+            if config_dir_is_ignored(dir, include_ignored) {
                 vec![]
             } else {
                 config_filenames
@@ -1192,13 +1188,7 @@ pub fn load_config_paths(config_filenames: &[String], include_ignored: bool) ->
     config_files
         .into_iter()
         .unique_by(|p| file::desymlink_path(p))
-        .filter(|p| {
-            if is_default_config_dir_override_filtered(p) {
-                return false;
-            }
-            include_ignored
-                || !(config_file::is_ignored(&config_trust_root(p)) || config_file::is_ignored(p))
-        })
+        .filter(|p| !config_path_is_ignored(p, include_ignored))
         .collect()
 }
 
@@ -1302,11 +1292,7 @@ fn detect_auto_env_candidate_files() -> Vec<PathBuf> {
     // that wouldn't be loaded even with auto_env enabled
     found
         .into_iter()
-        .filter(|p| {
-            !(is_default_config_dir_override_filtered(p)
-                || config_file::is_ignored(&config_trust_root(p))
-                || config_file::is_ignored(p))
-        })
+        .filter(|p| !config_path_is_ignored(p, false))
         .collect()
 }
 
@@ -1335,10 +1321,7 @@ pub async fn load_config_hierarchy_from_dir(
     let mut config_files = dirs
         .iter()
         .flat_map(|dir| {
-            if env::MISE_IGNORED_CONFIG_PATHS
-                .iter()
-                .any(|p| dir.starts_with(p))
-            {
+            if config_dir_is_ignored(dir, false) {
                 vec![]
             } else {
                 config_filenames
@@ -1357,12 +1340,7 @@ pub async fn load_config_hierarchy_from_dir(
     let paths = config_files
         .into_iter()
         .unique_by(|p| file::desymlink_path(p))
-        .filter(|p| {
-            if is_default_config_dir_override_filtered(p) {
-                return false;
-            }
-            !(config_file::is_ignored(&config_trust_root(p)) || config_file::is_ignored(p))
-        })
+        .filter(|p| !config_path_is_ignored(p, false))
         .collect();
 
     Ok((paths, idiomatic_files))
@@ -1386,6 +1364,21 @@ fn is_default_config_dir_override_filtered(path: &Path) -> bool {
         && path.starts_with(&*env::MISE_DEFAULT_CONFIG_DIR)
 }
 
+fn config_dir_is_ignored(dir: &Path, include_ignored: bool) -> bool {
+    !include_ignored
+        && env::MISE_IGNORED_CONFIG_PATHS
+            .iter()
+            .any(|p| dir.starts_with(p))
+}
+
+fn config_path_is_ignored(path: &Path, include_ignored: bool) -> bool {
+    if is_default_config_dir_override_filtered(path) {
+        return true;
+    }
+    !include_ignored
+        && (config_file::is_ignored(&config_trust_root(path)) || config_file::is_ignored(path))
+}
+
 static GLOBAL_CONFIG_FILES: Lazy<Mutex<Option<IndexSet<PathBuf>>>> = Lazy::new(Default::default);
 static SYSTEM_CONFIG_FILES: Lazy<Mutex<Option<IndexSet<PathBuf>>>> = Lazy::new(Default::default);
 
@@ -1476,30 +1469,37 @@ pub static ALL_TOML_CONFIG_FILES: Lazy<IndexSet<PathBuf>> = Lazy::new(|| {
         .collect()
 });
 
-/// list of all non-global mise.tomls
-pub fn local_toml_config_paths() -> Vec<&'static PathBuf> {
-    ALL_TOML_CONFIG_FILES
-        .iter()
-        .filter(|p| !is_global_config(p))
-        .collect()
-}
-
-/// The last (lowest precedence) local mise.toml or the path to where it should be written to.
-/// This ensures commands write to mise.toml instead of mise.local.toml when both exist.
-/// Note: local_toml_config_paths() returns files in highest-to-lowest precedence order,
-/// so we use .last() to get the lowest precedence file.
+/// The lowest-precedence TOML config in the nearest local config directory, or
+/// the path where it should be written.
 pub fn local_toml_config_path() -> PathBuf {
     static CWD: Lazy<PathBuf> = Lazy::new(|| PathBuf::from("."));
-    local_toml_config_paths()
-        .into_iter()
-        .last()
-        .cloned()
-        .unwrap_or_else(|| {
-            dirs::CWD
-                .as_ref()
-                .unwrap_or(&CWD)
-                .join(&*env::MISE_DEFAULT_CONFIG_FILENAME)
-        })
+    local_toml_config_path_from_dir(dirs::CWD.as_ref().unwrap_or(&CWD))
+}
+
+/// The lowest-precedence TOML config in the nearest directory that has one.
+///
+/// This matches the write-target rule from the docs: choose the highest-precedence
+/// directory first, then the lowest-precedence file inside that directory.
+pub fn local_toml_config_path_from_dir(cwd: &Path) -> PathBuf {
+    if !Settings::no_config() {
+        for dir in all_dirs_from(cwd).unwrap_or_default() {
+            if config_dir_is_ignored(&dir, false) {
+                continue;
+            }
+            let files = TOML_CONFIG_FILENAMES
+                .iter()
+                .flat_map(|f| glob(&dir, f).unwrap_or_default())
+                .unique_by(|p| file::desymlink_path(p))
+                .filter(|p| !config_path_is_ignored(p, false))
+                .collect();
+            if let Some(cf) = first_config_file(&files)
+                && !is_global_config(cf)
+            {
+                return cf.clone();
+            }
+        }
+    }
+    cwd.join(&*env::MISE_DEFAULT_CONFIG_FILENAME)
 }
 
 /// Options for resolving target config file path
@@ -1562,8 +1562,9 @@ pub fn resolve_target_config_path(opts: ConfigPathOptions) -> Result<PathBuf> {
 
     // Default: determine based on current directory
     if opts.prefer_toml {
-        // For mise set, prefer TOML and use local_toml_config_path logic
-        Ok(local_toml_config_path())
+        // For TOML-only commands, choose the nearest config directory and write
+        // to its lowest-precedence TOML file.
+        Ok(local_toml_config_path_from_dir(&cwd))
     } else {
         // For mise use, use existing config_file_from_dir logic which respects ASDF compat
         Ok(config_file_from_dir(&cwd))