Support enable/disable skill via config/api. (#9328)

In config.toml:
```
[[skills.config]]
path = "/Users/xl/.codex/skills/my_skill/SKILL.md"
enabled = false
```

API:
skills/list, skills/config/write

codex-rs/core/src/config/edit.rs

@@ -9,6 +9,7 @@ use std::path::Path;
 use std::path::PathBuf;
 use tempfile::NamedTempFile;
 use tokio::task;
+use toml_edit::ArrayOfTables;
 use toml_edit::DocumentMut;
 use toml_edit::Item as TomlItem;
 use toml_edit::Table as TomlTable;
@@ -36,6 +37,8 @@ pub enum ConfigEdit {
     RecordModelMigrationSeen { from: String, to: String },
     /// Replace the entire `[mcp_servers]` table.
     ReplaceMcpServers(BTreeMap<String, McpServerConfig>),
+    /// Set or clear a skill config entry under `[[skills.config]]`.
+    SetSkillConfig { path: PathBuf, enabled: bool },
     /// Set trust_level under `[projects."<path>"]`,
     /// migrating inline tables to explicit tables.
     SetProjectTrustLevel { path: PathBuf, level: TrustLevel },
@@ -298,6 +301,9 @@ impl ConfigDocument {
                 value(*acknowledged),
             )),
             ConfigEdit::ReplaceMcpServers(servers) => Ok(self.replace_mcp_servers(servers)),
+            ConfigEdit::SetSkillConfig { path, enabled } => {
+                Ok(self.set_skill_config(path.as_path(), *enabled))
+            }
             ConfigEdit::SetPath { segments, value } => Ok(self.insert(segments, value.clone())),
             ConfigEdit::ClearPath { segments } => Ok(self.clear_owned(segments)),
             ConfigEdit::SetProjectTrustLevel { path, level } => {
@@ -387,6 +393,113 @@ impl ConfigDocument {
         true
     }
 
+    fn set_skill_config(&mut self, path: &Path, enabled: bool) -> bool {
+        let normalized_path = normalize_skill_config_path(path);
+        let mut remove_skills_table = false;
+        let mut mutated = false;
+
+        {
+            let root = self.doc.as_table_mut();
+            let skills_item = match root.get_mut("skills") {
+                Some(item) => item,
+                None => {
+                    if enabled {
+                        return false;
+                    }
+                    root.insert(
+                        "skills",
+                        TomlItem::Table(document_helpers::new_implicit_table()),
+                    );
+                    let Some(item) = root.get_mut("skills") else {
+                        return false;
+                    };
+                    item
+                }
+            };
+
+            if document_helpers::ensure_table_for_write(skills_item).is_none() {
+                if enabled {
+                    return false;
+                }
+                *skills_item = TomlItem::Table(document_helpers::new_implicit_table());
+            }
+            let Some(skills_table) = skills_item.as_table_mut() else {
+                return false;
+            };
+
+            let config_item = match skills_table.get_mut("config") {
+                Some(item) => item,
+                None => {
+                    if enabled {
+                        return false;
+                    }
+                    skills_table.insert("config", TomlItem::ArrayOfTables(ArrayOfTables::new()));
+                    let Some(item) = skills_table.get_mut("config") else {
+                        return false;
+                    };
+                    item
+                }
+            };
+
+            if !matches!(config_item, TomlItem::ArrayOfTables(_)) {
+                if enabled {
+                    return false;
+                }
+                *config_item = TomlItem::ArrayOfTables(ArrayOfTables::new());
+            }
+
+            let TomlItem::ArrayOfTables(overrides) = config_item else {
+                return false;
+            };
+
+            let existing_index = overrides.iter().enumerate().find_map(|(idx, table)| {
+                table
+                    .get("path")
+                    .and_then(|item| item.as_str())
+                    .map(Path::new)
+                    .map(normalize_skill_config_path)
+                    .filter(|value| *value == normalized_path)
+                    .map(|_| idx)
+            });
+
+            if enabled {
+                if let Some(index) = existing_index {
+                    overrides.remove(index);
+                    mutated = true;
+                    if overrides.is_empty() {
+                        skills_table.remove("config");
+                        if skills_table.is_empty() {
+                            remove_skills_table = true;
+                        }
+                    }
+                }
+            } else if let Some(index) = existing_index {
+                for (idx, table) in overrides.iter_mut().enumerate() {
+                    if idx == index {
+                        table["path"] = value(normalized_path);
+                        table["enabled"] = value(false);
+                        mutated = true;
+                        break;
+                    }
+                }
+            } else {
+                let mut entry = TomlTable::new();
+                entry.set_implicit(false);
+                entry["path"] = value(normalized_path);
+                entry["enabled"] = value(false);
+                overrides.push(entry);
+                mutated = true;
+            }
+        }
+
+        if remove_skills_table {
+            let root = self.doc.as_table_mut();
+            root.remove("skills");
+        }
+
+        mutated
+    }
+
     fn scoped_segments(&self, scope: Scope, segments: &[&str]) -> Vec<String> {
         let resolved: Vec<String> = segments
             .iter()
@@ -494,6 +607,13 @@ impl ConfigDocument {
     }
 }
 
+fn normalize_skill_config_path(path: &Path) -> String {
+    dunce::canonicalize(path)
+        .unwrap_or_else(|_| path.to_path_buf())
+        .to_string_lossy()
+        .to_string()
+}
+
 /// Persist edits using a blocking strategy.
 pub fn apply_blocking(
     codex_home: &Path,
@@ -737,6 +857,54 @@ model_reasoning_effort = "high"
         assert_eq!(contents, "enabled = true\n");
     }
 
+    #[test]
+    fn set_skill_config_writes_disabled_entry() {
+        let tmp = tempdir().expect("tmpdir");
+        let codex_home = tmp.path();
+
+        ConfigEditsBuilder::new(codex_home)
+            .with_edits([ConfigEdit::SetSkillConfig {
+                path: PathBuf::from("/tmp/skills/demo/SKILL.md"),
+                enabled: false,
+            }])
+            .apply_blocking()
+            .expect("persist");
+
+        let contents =
+            std::fs::read_to_string(codex_home.join(CONFIG_TOML_FILE)).expect("read config");
+        let expected = r#"[[skills.config]]
+path = "/tmp/skills/demo/SKILL.md"
+enabled = false
+"#;
+        assert_eq!(contents, expected);
+    }
+
+    #[test]
+    fn set_skill_config_removes_entry_when_enabled() {
+        let tmp = tempdir().expect("tmpdir");
+        let codex_home = tmp.path();
+        std::fs::write(
+            codex_home.join(CONFIG_TOML_FILE),
+            r#"[[skills.config]]
+path = "/tmp/skills/demo/SKILL.md"
+enabled = false
+"#,
+        )
+        .expect("seed config");
+
+        ConfigEditsBuilder::new(codex_home)
+            .with_edits([ConfigEdit::SetSkillConfig {
+                path: PathBuf::from("/tmp/skills/demo/SKILL.md"),
+                enabled: true,
+            }])
+            .apply_blocking()
+            .expect("persist");
+
+        let contents =
+            std::fs::read_to_string(codex_home.join(CONFIG_TOML_FILE)).expect("read config");
+        assert_eq!(contents, "");
+    }
+
     #[test]
     fn blocking_set_model_preserves_inline_table_contents() {
         let tmp = tempdir().expect("tmpdir");

codex-rs/core/src/config/mod.rs

@@ -13,6 +13,7 @@ use crate::config::types::SandboxWorkspaceWrite;
 use crate::config::types::ScrollInputMode;
 use crate::config::types::ShellEnvironmentPolicy;
 use crate::config::types::ShellEnvironmentPolicyToml;
+use crate::config::types::SkillsConfig;
 use crate::config::types::Tui;
 use crate::config::types::UriBasedFileOpener;
 use crate::config_loader::ConfigLayerStack;
@@ -911,6 +912,9 @@ pub struct ConfigToml {
     /// Nested tools section for feature toggles
     pub tools: Option<ToolsToml>,
 
+    /// User-level skill config entries keyed by SKILL.md path.
+    pub skills: Option<SkillsConfig>,
+
     /// Centralized feature flags (new). Prefer this over individual toggles.
     #[serde(default)]
     // Injects known feature keys into the schema and forbids unknown keys.

codex-rs/core/src/config/types.rs

@@ -600,6 +600,20 @@ impl Notice {
     pub(crate) const TABLE_KEY: &'static str = "notice";
 }
 
+#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq, JsonSchema)]
+#[schemars(deny_unknown_fields)]
+pub struct SkillConfig {
+    pub path: AbsolutePathBuf,
+    pub enabled: bool,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone, Default, PartialEq, Eq, JsonSchema)]
+#[schemars(deny_unknown_fields)]
+pub struct SkillsConfig {
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub config: Vec<SkillConfig>,
+}
+
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Default, JsonSchema)]
 #[schemars(deny_unknown_fields)]
 pub struct SandboxWorkspaceWrite {