codex: fix CI failure on PR #24992

codex-rs/app-server-protocol/schema/json/ClientRequest.json

@@ -3011,6 +3011,13 @@
           },
           "type": "array"
         },
+        "environmentId": {
+          "description": "Environment whose filesystem should be used for all requested cwd values.",
+          "type": [
+            "string",
+            "null"
+          ]
+        },
         "forceReload": {
           "description": "When true, bypass the skills cache and re-scan skills from disk.",
           "type": "boolean"

codex-rs/app-server-protocol/schema/json/codex_app_server_protocol.schemas.json

@@ -15201,6 +15201,13 @@
             },
             "type": "array"
           },
+          "environmentId": {
+            "description": "Environment whose filesystem should be used for all requested cwd values.",
+            "type": [
+              "string",
+              "null"
+            ]
+          },
           "forceReload": {
             "description": "When true, bypass the skills cache and re-scan skills from disk.",
             "type": "boolean"

codex-rs/app-server-protocol/schema/json/codex_app_server_protocol.v2.schemas.json

@@ -13025,6 +13025,13 @@
           },
           "type": "array"
         },
+        "environmentId": {
+          "description": "Environment whose filesystem should be used for all requested cwd values.",
+          "type": [
+            "string",
+            "null"
+          ]
+        },
         "forceReload": {
           "description": "When true, bypass the skills cache and re-scan skills from disk.",
           "type": "boolean"

codex-rs/app-server-protocol/schema/json/v2/SkillsListParams.json

@@ -8,6 +8,13 @@
       },
       "type": "array"
     },
+    "environmentId": {
+      "description": "Environment whose filesystem should be used for all requested cwd values.",
+      "type": [
+        "string",
+        "null"
+      ]
+    },
     "forceReload": {
       "description": "When true, bypass the skills cache and re-scan skills from disk.",
       "type": "boolean"

codex-rs/app-server-protocol/schema/typescript/v2/SkillsListParams.ts

@@ -7,6 +7,10 @@ export type SkillsListParams = {
  * When empty, defaults to the current session working directory.
  */
 cwds?: Array<string>,
+/**
+ * Environment whose filesystem should be used for all requested cwd values.
+ */
+environmentId?: string | null,
 /**
  * When true, bypass the skills cache and re-scan skills from disk.
  */

codex-rs/app-server-protocol/src/protocol/common.rs

@@ -1718,6 +1718,7 @@ mod tests {
             request_id: request_id(),
             params: v2::SkillsListParams {
                 cwds: Vec::new(),
+                environment_id: None,
                 force_reload: false,
             },
         };

codex-rs/app-server-protocol/src/protocol/v2/plugin.rs

@@ -23,6 +23,10 @@ pub struct SkillsListParams {
     #[serde(default, skip_serializing_if = "Vec::is_empty")]
     pub cwds: Vec<PathBuf>,
 
+    /// Environment whose filesystem should be used for all requested cwd values.
+    #[ts(optional = nullable)]
+    pub environment_id: Option<String>,
+
     /// When true, bypass the skills cache and re-scan skills from disk.
     #[serde(default, skip_serializing_if = "std::ops::Not::not")]
     pub force_reload: bool,

codex-rs/app-server-protocol/src/protocol/v2/tests.rs

@@ -2607,23 +2607,41 @@ fn skills_list_params_serialization_uses_force_reload() {
     assert_eq!(
         serde_json::to_value(SkillsListParams {
             cwds: Vec::new(),
+            environment_id: None,
             force_reload: false,
         })
         .unwrap(),
-        json!({}),
+        json!({
+            "environmentId": null,
+        }),
     );
 
     assert_eq!(
         serde_json::to_value(SkillsListParams {
             cwds: vec![PathBuf::from("/repo")],
+            environment_id: None,
             force_reload: true,
         })
         .unwrap(),
         json!({
             "cwds": ["/repo"],
+            "environmentId": null,
             "forceReload": true,
         }),
     );
+
+    assert_eq!(
+        serde_json::to_value(SkillsListParams {
+            cwds: vec![PathBuf::from("/repo")],
+            environment_id: Some("devbox".to_string()),
+            force_reload: false,
+        })
+        .unwrap(),
+        json!({
+            "cwds": ["/repo"],
+            "environmentId": "devbox",
+        }),
+    );
 }
 
 #[test]

codex-rs/app-server/README.md

@@ -1504,13 +1504,14 @@ Example:
 $skill-creator Add a new skill for triaging flaky CI and include step-by-step usage.
 ```
 
-Use `skills/list` to fetch the available skills (optionally scoped by `cwds`, with `forceReload`).
+Use `skills/list` to fetch the available skills (optionally scoped by `cwds`, `environmentId`, and `forceReload`).
 `skills/list` might reuse a cached skills result per `cwd`; setting `forceReload` to `true` refreshes the result from disk.
 The server also emits `skills/changed` notifications when watched local skill files change. Treat this as an invalidation signal and re-run `skills/list` with your current params when needed.
 Use `skills/extraRoots/set` to replace additional standalone skill roots for the current app-server process. These roots use the same layout as other standalone skill roots: each root contains skill directories, and each skill directory contains `SKILL.md`. Missing roots are accepted and load no skills until they exist. This setting is lost when app-server exits.
 
 ```json
 { "method": "skills/list", "id": 25, "params": {
+    "environmentId": "local",
     "cwds": ["/Users/me/project", "/Users/me/other-project"],
     "forceReload": true
 } }

codex-rs/app-server/src/request_processors/catalog_processor.rs

@@ -499,7 +499,11 @@ impl CatalogRequestProcessor {
         &self,
         params: SkillsListParams,
     ) -> Result<SkillsListResponse, JSONRPCErrorError> {
-        let SkillsListParams { cwds, force_reload } = params;
+        let SkillsListParams {
+            cwds,
+            environment_id,
+            force_reload,
+        } = params;
         let cwds = if cwds.is_empty() {
             vec![self.config.cwd.to_path_buf()]
         } else {
@@ -513,15 +517,28 @@ impl CatalogRequestProcessor {
             .await;
         let skills_manager = self.thread_manager.skills_manager();
         let plugins_manager = self.thread_manager.plugins_manager();
-        let fs = self
-            .thread_manager
-            .environment_manager()
-            .default_environment()
+        let environment_manager = self.thread_manager.environment_manager();
+        let selected_environment = match environment_id {
+            Some(environment_id) => {
+                let environment = environment_manager
+                    .get_environment(&environment_id)
+                    .ok_or_else(|| {
+                        invalid_request(format!(
+                            "unknown skills/list environment id `{environment_id}`"
+                        ))
+                    })?;
+                Some(environment)
+            }
+            None => environment_manager.try_local_environment(),
+        };
+        let local_file_system = environment_manager
+            .try_local_environment()
             .map(|environment| environment.get_filesystem());
         let mut data = futures::stream::iter(cwds.into_iter().enumerate())
             .map(|(index, cwd)| {
                 let config = &config;
-                let fs = fs.clone();
+                let local_file_system = local_file_system.clone();
+                let selected_environment = selected_environment.clone();
                 let plugins_manager = &plugins_manager;
                 let skills_manager = &skills_manager;
                 async move {
@@ -553,14 +570,31 @@ impl CatalogRequestProcessor {
                     } else {
                         Vec::new()
                     };
+                    let Some(environment) = selected_environment.as_ref() else {
+                        // Omitted `environmentId` uses the legacy implicit local target. When
+                        // local exec is disabled there is no valid implicit target, so return an
+                        // empty catalog rather than silently switching to the default environment.
+                        return (
+                            index,
+                            codex_app_server_protocol::SkillsListEntry {
+                                cwd,
+                                skills: Vec::new(),
+                                errors: Vec::new(),
+                            },
+                        );
+                    };
                     let skills_input = codex_core::skills::SkillsLoadInput::new(
-                        cwd_abs.clone(),
+                        codex_exec_server::EnvironmentPathRef::new(
+                            environment.get_filesystem(),
+                            cwd_abs.clone(),
+                        ),
+                        local_file_system,
                         effective_skill_roots,
                         config_layer_stack,
                         config.bundled_skills_enabled(),
                     );
                     let outcome = skills_manager
-                        .skills_for_cwd(&skills_input, force_reload, fs)
+                        .skills_for_cwd(&skills_input, force_reload)
                         .await;
                     let errors = errors_to_info(&outcome.errors);
                     let skills = skills_to_info(&outcome.skills, &outcome.disabled_paths);

codex-rs/app-server/src/skills_watcher.rs

@@ -9,6 +9,7 @@ use codex_core::ThreadManager;
 use codex_core::config::Config;
 use codex_core::skills::SkillsLoadInput;
 use codex_core::skills::SkillsManager;
+use codex_exec_server::EnvironmentPathRef;
 use codex_file_watcher::FileWatcher;
 use codex_file_watcher::FileWatcherSubscriber;
 use codex_file_watcher::Receiver;
@@ -100,22 +101,29 @@ impl SkillsWatcher {
             return WatchRegistration::default();
         }
 
+        let root_path_ref =
+            EnvironmentPathRef::new(environment.get_filesystem(), config.cwd.clone());
+        let local_file_system = thread_manager
+            .environment_manager()
+            .try_local_environment()
+            .map(|environment| environment.get_filesystem());
         let plugins_input = config.plugins_config_input();
         let plugins_manager = thread_manager.plugins_manager();
         let plugin_outcome = plugins_manager.plugins_for_config(&plugins_input).await;
         let skills_input = SkillsLoadInput::new(
-            config.cwd.clone(),
+            root_path_ref,
+            local_file_system,
             plugin_outcome.effective_plugin_skill_roots(),
             config.config_layer_stack.clone(),
             config.bundled_skills_enabled(),
         );
         let roots = thread_manager
             .skills_manager()
-            .skill_roots_for_config(&skills_input, Some(environment.get_filesystem()))
+            .skill_roots_for_config(&skills_input)
             .await
             .into_iter()
             .map(|root| WatchPath {
-                path: root.path.into_path_buf(),
+                path: root.path.path().to_path_buf(),
                 recursive: true,
             })
             .collect();

codex-rs/app-server/tests/suite/v2/skills_list.rs

@@ -20,6 +20,7 @@ use codex_app_server_protocol::SkillsListResponse;
 use codex_app_server_protocol::ThreadStartParams;
 use codex_config::types::AuthCredentialsStoreMode;
 use codex_exec_server::CODEX_EXEC_SERVER_URL_ENV_VAR;
+use codex_exec_server::LOCAL_ENVIRONMENT_ID;
 use codex_utils_absolute_path::AbsolutePathBuf;
 use pretty_assertions::assert_eq;
 use tempfile::TempDir;
@@ -248,6 +249,7 @@ async fn skills_list_loads_remote_installed_plugin_skills_from_cache() -> Result
     let stale_skills_list_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -298,6 +300,7 @@ async fn skills_list_loads_remote_installed_plugin_skills_from_cache() -> Result
             let skills_list_request_id = mcp
                 .send_skills_list_request(SkillsListParams {
                     cwds: vec![cwd.path().to_path_buf()],
+                    environment_id: None,
                     force_reload: false,
                 })
                 .await?;
@@ -372,6 +375,7 @@ async fn skills_list_excludes_plugin_skills_when_workspace_codex_plugins_disable
     let request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![repo_root.path().to_path_buf()],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -401,7 +405,7 @@ async fn skills_list_excludes_plugin_skills_when_workspace_codex_plugins_disable
 }
 
 #[tokio::test]
-async fn skills_list_skips_cwd_roots_when_environment_disabled() -> Result<()> {
+async fn skills_list_returns_empty_when_implicit_local_environment_is_disabled() -> Result<()> {
     let codex_home = TempDir::new()?;
     let cwd = TempDir::new()?;
     write_skill(&codex_home, "home-skill")?;
@@ -422,6 +426,7 @@ async fn skills_list_skips_cwd_roots_when_environment_disabled() -> Result<()> {
     let request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -435,18 +440,7 @@ async fn skills_list_skips_cwd_roots_when_environment_disabled() -> Result<()> {
     assert_eq!(data.len(), 1);
     assert_eq!(data[0].cwd, cwd.path().to_path_buf());
     assert_eq!(data[0].errors, Vec::new());
-    assert!(
-        data[0]
-            .skills
-            .iter()
-            .any(|skill| skill.name == "home-skill")
-    );
-    assert!(
-        data[0]
-            .skills
-            .iter()
-            .all(|skill| skill.name != "repo-skill")
-    );
+    assert_eq!(data[0].skills, Vec::new());
     Ok(())
 }
 
@@ -462,6 +456,7 @@ async fn skills_list_accepts_relative_cwds() -> Result<()> {
     let request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![relative_cwd.clone()],
+            environment_id: Some(LOCAL_ENVIRONMENT_ID.to_string()),
             force_reload: true,
         })
         .await?;
@@ -493,6 +488,7 @@ async fn skills_list_preserves_requested_cwd_order() -> Result<()> {
                 first_cwd.path().to_path_buf(),
                 second_cwd.path().to_path_buf(),
             ],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -527,6 +523,7 @@ async fn skills_list_uses_cached_result_until_force_reload() -> Result<()> {
     let first_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -554,6 +551,7 @@ async fn skills_list_uses_cached_result_until_force_reload() -> Result<()> {
     let second_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -574,6 +572,7 @@ async fn skills_list_uses_cached_result_until_force_reload() -> Result<()> {
     let third_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -625,6 +624,7 @@ async fn skills_extra_roots_set_updates_process_runtime_roots() -> Result<()> {
     let skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -660,6 +660,7 @@ async fn skills_extra_roots_set_updates_process_runtime_roots() -> Result<()> {
     let skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -693,6 +694,7 @@ async fn skills_extra_roots_set_updates_process_runtime_roots() -> Result<()> {
     let skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -717,6 +719,7 @@ async fn skills_extra_roots_set_updates_process_runtime_roots() -> Result<()> {
     let skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![cwd.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;
@@ -755,6 +758,7 @@ async fn skills_changed_notification_is_emitted_after_skill_change() -> Result<(
     let initial_skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![codex_home.path().to_path_buf()],
+            environment_id: None,
             force_reload: true,
         })
         .await?;
@@ -828,6 +832,7 @@ async fn skills_changed_notification_is_emitted_after_skill_change() -> Result<(
     let updated_skills_request_id = mcp
         .send_skills_list_request(SkillsListParams {
             cwds: vec![codex_home.path().to_path_buf()],
+            environment_id: None,
             force_reload: false,
         })
         .await?;

codex-rs/core-plugins/src/loader.rs

@@ -19,7 +19,7 @@ use codex_core_skills::config_rules::resolve_disabled_skill_paths;
 use codex_core_skills::config_rules::skill_config_rules_from_stack;
 use codex_core_skills::loader::SkillRoot;
 use codex_core_skills::loader::load_skills_from_roots;
-use codex_exec_server::LOCAL_FS;
+use codex_exec_server::EnvironmentPathRef;
 use codex_plugin::AppConnectorId;
 use codex_plugin::LoadedPlugin;
 use codex_plugin::PluginCapabilitySummary;
@@ -40,7 +40,6 @@ use std::collections::HashSet;
 use std::fs;
 use std::path::Path;
 use std::process::Command;
-use std::sync::Arc;
 use tempfile::TempDir;
 use tracing::warn;
 
@@ -564,8 +563,10 @@ async fn load_plugin(
         .or_else(|| Some(manifest.name.clone()));
     loaded_plugin.manifest_description = manifest.description.clone();
     loaded_plugin.skill_roots = plugin_skill_roots(&plugin_root, manifest_paths);
+    // TODO: Support multi-env plugin skill loading. Plugin discovery is local-only today, so bind
+    // plugin skill reads to the local environment instead of the selected turn environment.
     let resolved_skills = load_plugin_skills(
-        &plugin_root,
+        EnvironmentPathRef::local(plugin_root.clone()),
         &loaded_plugin_id,
         manifest_paths,
         restriction_product,
@@ -642,18 +643,17 @@ impl ResolvedPluginSkills {
 }
 
 pub async fn load_plugin_skills(
-    plugin_root: &AbsolutePathBuf,
+    plugin_root: EnvironmentPathRef,
     plugin_id: &PluginId,
     manifest_paths: &PluginManifestPaths,
     restriction_product: Option<Product>,
     skill_config_rules: &SkillConfigRules,
 ) -> ResolvedPluginSkills {
-    let roots = plugin_skill_roots(plugin_root, manifest_paths)
+    let roots = plugin_skill_roots(plugin_root.path(), manifest_paths)
         .into_iter()
         .map(|path| SkillRoot {
-            path,
+            path: plugin_root.with_path(path),
             scope: SkillScope::User,
-            file_system: Arc::clone(&LOCAL_FS),
             plugin_id: Some(plugin_id.as_key()),
             plugin_root: Some(plugin_root.clone()),
         })

codex-rs/core-plugins/src/manager.rs

@@ -1419,8 +1419,10 @@ impl PluginsManager {
             manifest.interface.clone(),
             marketplace_category,
         );
+        // TODO: Support multi-env plugin skill loading. Marketplace plugins are installed and
+        // scanned locally today, so bind plugin skill reads to the local environment.
         let resolved_skills = load_plugin_skills(
-            &source_path,
+            codex_exec_server::EnvironmentPathRef::local(source_path.clone()),
             &plugin_id,
             &manifest.paths,
             self.restriction_product,

codex-rs/core-skills/src/loader.rs

@@ -13,8 +13,8 @@ use codex_config::ConfigLayerStackOrdering;
 use codex_config::default_project_root_markers;
 use codex_config::merge_toml_values;
 use codex_config::project_root_markers_from_config;
+use codex_exec_server::EnvironmentPathRef;
 use codex_exec_server::ExecutorFileSystem;
-use codex_exec_server::LOCAL_FS;
 use codex_protocol::protocol::Product;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBuf;
@@ -151,11 +151,10 @@ impl fmt::Display for SkillParseError {
 impl Error for SkillParseError {}
 
 pub struct SkillRoot {
-    pub path: AbsolutePathBuf,
+    pub path: EnvironmentPathRef,
     pub scope: SkillScope,
-    pub file_system: Arc<dyn ExecutorFileSystem>,
     pub plugin_id: Option<String>,
-    pub plugin_root: Option<AbsolutePathBuf>,
+    pub plugin_root: Option<EnvironmentPathRef>,
 }
 
 pub async fn load_skills_from_roots<I>(roots: I) -> SkillLoadOutcome
@@ -168,12 +167,12 @@ where
     let mut file_systems_by_skill_path: HashMap<AbsolutePathBuf, Arc<dyn ExecutorFileSystem>> =
         HashMap::new();
     for root in roots {
-        let root_path = canonicalize_for_skill_identity(&root.path);
-        let fs = root.file_system;
+        let root_path = canonicalize_for_skill_identity(root.path.path());
+        let root_path_ref = root.path.with_path(root_path.clone());
+        let fs = root_path_ref.file_system();
         let skills_before_root = outcome.skills.len();
         discover_skills_under_root(
-            fs.as_ref(),
-            &root_path,
+            &root_path_ref,
             root.scope,
             root.plugin_id.as_deref(),
             root.plugin_root.as_ref(),
@@ -231,18 +230,21 @@ where
 }
 
 pub(crate) async fn skill_roots(
-    fs: Option<Arc<dyn ExecutorFileSystem>>,
+    env_path: &EnvironmentPathRef,
+    local_file_system: Option<&Arc<dyn ExecutorFileSystem>>,
     config_layer_stack: &ConfigLayerStack,
-    cwd: &AbsolutePathBuf,
     plugin_skill_roots: Vec<PluginSkillRoot>,
     extra_skill_roots: Vec<AbsolutePathBuf>,
 ) -> Vec<SkillRoot> {
+    // `env_path` owns workspace/repo-relative skill discovery for the selected environment.
+    // `local_file_system` owns client-local system/user/plugin roots and is absent when local exec
+    // is disabled, in which case those local roots intentionally do not load.
     let home_dir =
         home_dir().and_then(|path| AbsolutePathBuf::from_absolute_path_checked(path).ok());
     skill_roots_with_home_dir(
-        fs,
+        env_path,
+        local_file_system,
         config_layer_stack,
-        cwd,
         home_dir.as_ref(),
         plugin_skill_roots,
         extra_skill_roots,
@@ -251,38 +253,43 @@ pub(crate) async fn skill_roots(
 }
 
 async fn skill_roots_with_home_dir(
-    fs: Option<Arc<dyn ExecutorFileSystem>>,
+    env_path: &EnvironmentPathRef,
+    local_file_system: Option<&Arc<dyn ExecutorFileSystem>>,
     config_layer_stack: &ConfigLayerStack,
-    cwd: &AbsolutePathBuf,
     home_dir: Option<&AbsolutePathBuf>,
     plugin_skill_roots: Vec<PluginSkillRoot>,
     extra_skill_roots: Vec<AbsolutePathBuf>,
 ) -> Vec<SkillRoot> {
-    let mut roots = skill_roots_from_layer_stack_inner(config_layer_stack, home_dir, fs.clone());
-    roots.extend(plugin_skill_roots.into_iter().map(|root| SkillRoot {
-        path: root.path,
-        scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
-        plugin_id: Some(root.plugin_id),
-        plugin_root: Some(root.plugin_root),
-    }));
-    roots.extend(extra_skill_roots.into_iter().map(|path| SkillRoot {
-        path,
-        scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
-        plugin_id: None,
-        plugin_root: None,
-    }));
-    roots.extend(repo_agents_skill_roots(fs, config_layer_stack, cwd).await);
+    // Assemble one precedence-ordered root list from the two authorities above, then dedupe before
+    // any reads happen so downstream loading stays oblivious to local-vs-selected-env routing.
+    let mut roots = repo_config_skill_roots(env_path, config_layer_stack);
+    roots.extend(local_skill_roots(
+        local_file_system,
+        config_layer_stack,
+        home_dir,
+        plugin_skill_roots,
+        extra_skill_roots,
+    ));
+    roots.extend(repo_agents_skill_roots(env_path, config_layer_stack).await);
     dedupe_skill_roots_by_path(&mut roots);
     roots
 }
 
-fn skill_roots_from_layer_stack_inner(
+fn local_skill_roots(
+    local_file_system: Option<&Arc<dyn ExecutorFileSystem>>,
     config_layer_stack: &ConfigLayerStack,
     home_dir: Option<&AbsolutePathBuf>,
-    repo_fs: Option<Arc<dyn ExecutorFileSystem>>,
+    plugin_skill_roots: Vec<PluginSkillRoot>,
+    extra_skill_roots: Vec<AbsolutePathBuf>,
 ) -> Vec<SkillRoot> {
+    // These roots are absolute paths on the client machine, not paths inside the selected
+    // workspace environment. Bind them to the available local exec filesystem so remote turns
+    // keep loading local installed/bundled/plugin skills without reading those paths remotely.
+    let Some(local_file_system) = local_file_system else {
+        // Local exec can be disabled. In that case, keep repo/env skill loading intact but skip
+        // local absolute roots instead of falling back to the process-global local filesystem.
+        return Vec::new();
+    };
     let mut roots = Vec::new();
 
     for layer in config_layer_stack.get_layers(
@@ -294,24 +301,17 @@ fn skill_roots_from_layer_stack_inner(
         };
 
         match &layer.name {
-            ConfigLayerSource::Project { .. } => {
-                if let Some(repo_fs) = &repo_fs {
-                    roots.push(SkillRoot {
-                        path: config_folder.join(SKILLS_DIR_NAME),
-                        scope: SkillScope::Repo,
-                        file_system: Arc::clone(repo_fs),
-                        plugin_id: None,
-                        plugin_root: None,
-                    });
-                }
-            }
+            ConfigLayerSource::Project { .. } => {}
             ConfigLayerSource::User { .. } => {
                 // Deprecated user skills location (`$CODEX_HOME/skills`), kept for backward
-                // compatibility.
+                // compatibility. These are client-local absolute paths even when the active repo
+                // environment is remote, so bind them to the available local filesystem only.
                 roots.push(SkillRoot {
-                    path: config_folder.join(SKILLS_DIR_NAME),
+                    path: EnvironmentPathRef::new(
+                        Arc::clone(local_file_system),
+                        config_folder.join(SKILLS_DIR_NAME),
+                    ),
                     scope: SkillScope::User,
-                    file_system: Arc::clone(&LOCAL_FS),
                     plugin_id: None,
                     plugin_root: None,
                 });
@@ -319,9 +319,11 @@ fn skill_roots_from_layer_stack_inner(
                 // `$HOME/.agents/skills` (user-installed skills).
                 if let Some(home_dir) = home_dir {
                     roots.push(SkillRoot {
-                        path: home_dir.join(AGENTS_DIR_NAME).join(SKILLS_DIR_NAME),
+                        path: EnvironmentPathRef::new(
+                            Arc::clone(local_file_system),
+                            home_dir.join(AGENTS_DIR_NAME).join(SKILLS_DIR_NAME),
+                        ),
                         scope: SkillScope::User,
-                        file_system: Arc::clone(&LOCAL_FS),
                         plugin_id: None,
                         plugin_root: None,
                     });
@@ -330,9 +332,11 @@ fn skill_roots_from_layer_stack_inner(
                 // Embedded system skills are cached under `$CODEX_HOME/skills/.system` and are a
                 // special case (not a config layer).
                 roots.push(SkillRoot {
-                    path: system_cache_root_dir(&config_folder),
+                    path: EnvironmentPathRef::new(
+                        Arc::clone(local_file_system),
+                        system_cache_root_dir(&config_folder),
+                    ),
                     scope: SkillScope::System,
-                    file_system: Arc::clone(&LOCAL_FS),
                     plugin_id: None,
                     plugin_root: None,
                 });
@@ -341,9 +345,11 @@ fn skill_roots_from_layer_stack_inner(
                 // The system config layer lives under `/etc/codex/` on Unix, so treat
                 // `/etc/codex/skills` as admin-scoped skills.
                 roots.push(SkillRoot {
-                    path: config_folder.join(SKILLS_DIR_NAME),
+                    path: EnvironmentPathRef::new(
+                        Arc::clone(local_file_system),
+                        config_folder.join(SKILLS_DIR_NAME),
+                    ),
                     scope: SkillScope::Admin,
-                    file_system: Arc::clone(&LOCAL_FS),
                     plugin_id: None,
                     plugin_root: None,
                 });
@@ -355,28 +361,77 @@ fn skill_roots_from_layer_stack_inner(
         }
     }
 
+    roots.extend(plugin_skill_roots.into_iter().map(|root| SkillRoot {
+        // Plugin discovery is currently local-only; multi-env plugin skill loading should be an
+        // explicit future change rather than inheriting the selected repo environment here.
+        path: EnvironmentPathRef::new(Arc::clone(local_file_system), root.path),
+        scope: SkillScope::User,
+        plugin_id: Some(root.plugin_id),
+        plugin_root: Some(EnvironmentPathRef::new(
+            Arc::clone(local_file_system),
+            root.plugin_root,
+        )),
+    }));
+    roots.extend(extra_skill_roots.into_iter().map(|path| SkillRoot {
+        path: EnvironmentPathRef::new(Arc::clone(local_file_system), path),
+        scope: SkillScope::User,
+        plugin_id: None,
+        plugin_root: None,
+    }));
+
     roots
 }
 
-async fn repo_agents_skill_roots(
-    fs: Option<Arc<dyn ExecutorFileSystem>>,
+fn repo_config_skill_roots(
+    env_path: &EnvironmentPathRef,
     config_layer_stack: &ConfigLayerStack,
-    cwd: &AbsolutePathBuf,
 ) -> Vec<SkillRoot> {
-    let Some(fs) = fs else {
-        return Vec::new();
-    };
+    // Project config layers describe workspace-local `.codex/skills` directories. Their absolute
+    // paths only make sense inside the selected environment, so keep them bound to `env_path`
+    // rather than the optional local filesystem used for client-local system/user/plugin roots.
+    config_layer_stack
+        .get_layers(
+            ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            /*include_disabled*/ true,
+        )
+        .into_iter()
+        .filter_map(|layer| match &layer.name {
+            ConfigLayerSource::Project { .. } => layer.config_folder().map(|config_folder| {
+                SkillRoot {
+                    // Project and repo `.agents` roots belong to the selected environment because
+                    // their absolute paths are only meaningful within that environment's cwd/repo.
+                    path: env_path.with_path(config_folder.join(SKILLS_DIR_NAME)),
+                    scope: SkillScope::Repo,
+                    plugin_id: None,
+                    plugin_root: None,
+                }
+            }),
+            ConfigLayerSource::User { .. }
+            | ConfigLayerSource::System { .. }
+            | ConfigLayerSource::Mdm { .. }
+            | ConfigLayerSource::SessionFlags
+            | ConfigLayerSource::LegacyManagedConfigTomlFromFile { .. }
+            | ConfigLayerSource::LegacyManagedConfigTomlFromMdm => None,
+        })
+        .collect()
+}
+
+async fn repo_agents_skill_roots(
+    env_path: &EnvironmentPathRef,
+    config_layer_stack: &ConfigLayerStack,
+) -> Vec<SkillRoot> {
+    // Discover repo `.agents/skills` folders by walking from the selected environment's project
+    // root to its cwd; this must never consult the local filesystem for remote workspaces.
     let project_root_markers = project_root_markers_from_stack(config_layer_stack);
-    let project_root = find_project_root(fs.as_ref(), cwd, &project_root_markers).await;
-    let dirs = dirs_between_project_root_and_cwd(cwd, &project_root);
+    let project_root = find_project_root(env_path, &project_root_markers).await;
+    let dirs = dirs_between_project_root_and_cwd(env_path.path(), project_root.path());
     let mut roots = Vec::new();
     for dir in dirs {
-        let agents_skills = dir.join(AGENTS_DIR_NAME).join(SKILLS_DIR_NAME);
-        match fs.get_metadata(&agents_skills, /*sandbox*/ None).await {
+        let agents_skills = env_path.with_path(dir.join(AGENTS_DIR_NAME).join(SKILLS_DIR_NAME));
+        match agents_skills.metadata(/*sandbox*/ None).await {
             Ok(metadata) if metadata.is_directory => roots.push(SkillRoot {
                 path: agents_skills,
                 scope: SkillScope::Repo,
-                file_system: Arc::clone(&fs),
                 plugin_id: None,
                 plugin_root: None,
             }),
@@ -385,7 +440,7 @@ async fn repo_agents_skill_roots(
             Err(err) => {
                 tracing::warn!(
                     "failed to stat repo skills root {}: {err:#}",
-                    agents_skills.display()
+                    agents_skills.path().display()
                 );
             }
         }
@@ -416,24 +471,23 @@ fn project_root_markers_from_stack(config_layer_stack: &ConfigLayerStack) -> Vec
 }
 
 async fn find_project_root(
-    fs: &dyn ExecutorFileSystem,
-    cwd: &AbsolutePathBuf,
+    cwd: &EnvironmentPathRef,
     project_root_markers: &[String],
-) -> AbsolutePathBuf {
+) -> EnvironmentPathRef {
     if project_root_markers.is_empty() {
         return cwd.clone();
     }
 
-    for ancestor in cwd.ancestors() {
+    for ancestor in cwd.path().ancestors() {
         for marker in project_root_markers {
-            let marker_path = ancestor.join(marker);
-            match fs.get_metadata(&marker_path, /*sandbox*/ None).await {
-                Ok(_) => return ancestor,
+            let marker_path = cwd.with_path(ancestor.join(marker));
+            match marker_path.metadata(/*sandbox*/ None).await {
+                Ok(_) => return cwd.with_path(ancestor),
                 Err(err) if err.kind() == io::ErrorKind::NotFound => {}
                 Err(err) => {
                     tracing::warn!(
                         "failed to stat project root marker {}: {err:#}",
-                        marker_path.display()
+                        marker_path.path().display()
                     );
                 }
             }
@@ -465,7 +519,7 @@ fn dirs_between_project_root_and_cwd(
 }
 
 fn dedupe_skill_roots_by_path(roots: &mut Vec<SkillRoot>) {
-    let mut seen: HashSet<AbsolutePathBuf> = HashSet::new();
+    let mut seen: HashSet<EnvironmentPathRef> = HashSet::new();
     roots.retain(|root| seen.insert(root.path.clone()));
 }
 
@@ -474,31 +528,35 @@ fn canonicalize_for_skill_identity(path: &AbsolutePathBuf) -> AbsolutePathBuf {
 }
 
 async fn discover_skills_under_root(
-    fs: &dyn ExecutorFileSystem,
-    root: &AbsolutePathBuf,
+    root: &EnvironmentPathRef,
     scope: SkillScope,
     plugin_id: Option<&str>,
-    plugin_root: Option<&AbsolutePathBuf>,
+    plugin_root: Option<&EnvironmentPathRef>,
     outcome: &mut SkillLoadOutcome,
 ) {
-    let root = canonicalize_for_skill_identity(root);
-    let plugin_root = plugin_root.map(canonicalize_for_skill_identity);
+    let root = root.with_path(canonicalize_for_skill_identity(root.path()));
+    let plugin_root = plugin_root.map(|plugin_root| {
+        plugin_root.with_path(canonicalize_for_skill_identity(plugin_root.path()))
+    });
 
-    match fs.get_metadata(&root, /*sandbox*/ None).await {
+    match root.metadata(/*sandbox*/ None).await {
         Ok(metadata) if metadata.is_directory => {}
         Ok(_) => return,
         Err(err) if err.kind() == io::ErrorKind::NotFound => return,
         Err(err) => {
-            error!("failed to stat skills root {}: {err:#}", root.display());
+            error!(
+                "failed to stat skills root {}: {err:#}",
+                root.path().display()
+            );
             return;
         }
     }
 
     fn enqueue_dir(
-        queue: &mut VecDeque<(AbsolutePathBuf, usize)>,
+        queue: &mut VecDeque<(EnvironmentPathRef, usize)>,
         visited_dirs: &mut HashSet<AbsolutePathBuf>,
         truncated_by_dir_limit: &mut bool,
-        path: AbsolutePathBuf,
+        path: EnvironmentPathRef,
         depth: usize,
     ) {
         if depth > MAX_SCAN_DEPTH {
@@ -508,7 +566,7 @@ async fn discover_skills_under_root(
             *truncated_by_dir_limit = true;
             return;
         }
-        if visited_dirs.insert(path.clone()) {
+        if visited_dirs.insert(path.path().clone()) {
             queue.push_back((path, depth));
         }
     }
@@ -520,16 +578,16 @@ async fn discover_skills_under_root(
     );
 
     let mut visited_dirs: HashSet<AbsolutePathBuf> = HashSet::new();
-    visited_dirs.insert(root.clone());
+    visited_dirs.insert(root.path().clone());
 
-    let mut queue: VecDeque<(AbsolutePathBuf, usize)> = VecDeque::from([(root.clone(), 0)]);
+    let mut queue: VecDeque<(EnvironmentPathRef, usize)> = VecDeque::from([(root.clone(), 0)]);
     let mut truncated_by_dir_limit = false;
 
     while let Some((dir, depth)) = queue.pop_front() {
-        let entries = match fs.read_directory(&dir, /*sandbox*/ None).await {
+        let entries = match dir.read_directory(/*sandbox*/ None).await {
             Ok(entries) => entries,
             Err(e) => {
-                error!("failed to read skills dir {}: {e:#}", dir.display());
+                error!("failed to read skills dir {}: {e:#}", dir.path().display());
                 continue;
             }
         };
@@ -540,11 +598,16 @@ async fn discover_skills_under_root(
                 continue;
             }
 
-            let path = dir.join(&file_name);
-            let metadata = match fs.get_metadata(&path, /*sandbox*/ None).await {
+            let Some(path) = dir.join_relative(Path::new(&file_name)) else {
+                continue;
+            };
+            let metadata = match path.metadata(/*sandbox*/ None).await {
                 Ok(metadata) => metadata,
                 Err(e) => {
-                    error!("failed to stat skills path {}: {e:#}", path.display());
+                    error!(
+                        "failed to stat skills path {}: {e:#}",
+                        path.path().display()
+                    );
                     continue;
                 }
             };
@@ -553,9 +616,10 @@ async fn discover_skills_under_root(
                 if !follow_symlinks {
                     continue;
                 }
-                match fs.read_directory(&path, /*sandbox*/ None).await {
+                match path.read_directory(/*sandbox*/ None).await {
                     Ok(_) => {
-                        let resolved_dir = canonicalize_for_skill_identity(&path);
+                        let resolved_dir =
+                            path.with_path(canonicalize_for_skill_identity(path.path()));
                         enqueue_dir(
                             &mut queue,
                             &mut visited_dirs,
@@ -572,7 +636,7 @@ async fn discover_skills_under_root(
                     Err(err) => {
                         error!(
                             "failed to read skills symlink dir {}: {err:#}",
-                            path.display()
+                            path.path().display()
                         );
                     }
                 }
@@ -580,7 +644,7 @@ async fn discover_skills_under_root(
             }
 
             if metadata.is_directory {
-                let resolved_dir = canonicalize_for_skill_identity(&path);
+                let resolved_dir = path.with_path(canonicalize_for_skill_identity(path.path()));
                 enqueue_dir(
                     &mut queue,
                     &mut visited_dirs,
@@ -592,14 +656,14 @@ async fn discover_skills_under_root(
             }
 
             if metadata.is_file && file_name == SKILLS_FILENAME {
-                match parse_skill_file(fs, &path, scope, plugin_id, plugin_root.as_ref()).await {
+                match parse_skill_file(&path, scope, plugin_id, plugin_root.as_ref()).await {
                     Ok(skill) => {
                         outcome.skills.push(skill);
                     }
                     Err(err) => {
                         if scope != SkillScope::System {
                             outcome.errors.push(SkillError {
-                                path: path.clone(),
+                                path: path.path().clone(),
                                 message: err.to_string(),
                             });
                         }
@@ -613,22 +677,22 @@ async fn discover_skills_under_root(
         tracing::warn!(
             "skills scan truncated after {} directories (root: {})",
             MAX_SKILLS_DIRS_PER_ROOT,
-            root.display()
+            root.path().display()
         );
     }
 }
 
 async fn parse_skill_file(
-    fs: &dyn ExecutorFileSystem,
-    path: &AbsolutePathBuf,
+    skill_path: &EnvironmentPathRef,
     scope: SkillScope,
     plugin_id: Option<&str>,
-    plugin_root: Option<&AbsolutePathBuf>,
+    plugin_root: Option<&EnvironmentPathRef>,
 ) -> Result<SkillMetadata, SkillParseError> {
-    let contents = fs
-        .read_file_text(path, /*sandbox*/ None)
+    let contents = skill_path
+        .read_to_string(/*sandbox*/ None)
         .await
         .map_err(SkillParseError::Read)?;
+    let path = skill_path.path();
 
     let frontmatter = extract_frontmatter(&contents).ok_or(SkillParseError::MissingFrontmatter)?;
 
@@ -641,7 +705,7 @@ async fn parse_skill_file(
         .map(sanitize_single_line)
         .filter(|value| !value.is_empty())
         .unwrap_or_else(|| default_skill_name(path));
-    let name = namespaced_skill_name(fs, path, &base_name).await;
+    let name = namespaced_skill_name(skill_path.file_system().as_ref(), path, &base_name).await;
     let description = parsed
         .description
         .as_deref()
@@ -657,7 +721,7 @@ async fn parse_skill_file(
         interface,
         dependencies,
         policy,
-    } = load_skill_metadata(fs, path, plugin_root).await;
+    } = load_skill_metadata(skill_path, plugin_root).await;
 
     validate_len(&name, MAX_NAME_LEN, "name")?;
     validate_len(&description, MAX_DESCRIPTION_LEN, "description")?;
@@ -708,18 +772,21 @@ async fn namespaced_skill_name(
 }
 
 async fn load_skill_metadata(
-    fs: &dyn ExecutorFileSystem,
-    skill_path: &AbsolutePathBuf,
-    plugin_root: Option<&AbsolutePathBuf>,
+    skill_path: &EnvironmentPathRef,
+    plugin_root: Option<&EnvironmentPathRef>,
 ) -> LoadedSkillMetadata {
     // Fail open: optional metadata should not block loading SKILL.md.
-    let Some(skill_dir) = skill_path.parent() else {
+    let Some(skill_dir) = skill_path.parent_dir() else {
         return LoadedSkillMetadata::default();
     };
-    let metadata_path = skill_dir
-        .join(SKILLS_METADATA_DIR)
-        .join(SKILLS_METADATA_FILENAME);
-    match fs.get_metadata(&metadata_path, /*sandbox*/ None).await {
+    let Some(metadata_path) = skill_dir.join_relative(
+        Path::new(SKILLS_METADATA_DIR)
+            .join(SKILLS_METADATA_FILENAME)
+            .as_path(),
+    ) else {
+        return LoadedSkillMetadata::default();
+    };
+    match metadata_path.metadata(/*sandbox*/ None).await {
         Ok(metadata) if metadata.is_file => {}
         Ok(_) => return LoadedSkillMetadata::default(),
         Err(error) if error.kind() == io::ErrorKind::NotFound => {
@@ -728,19 +795,19 @@ async fn load_skill_metadata(
         Err(error) => {
             tracing::warn!(
                 "ignoring {path}: failed to stat {label}: {error}",
-                path = metadata_path.display(),
+                path = metadata_path.path().display(),
                 label = SKILLS_METADATA_FILENAME
             );
             return LoadedSkillMetadata::default();
         }
     }
 
-    let contents = match fs.read_file_text(&metadata_path, /*sandbox*/ None).await {
+    let contents = match metadata_path.read_to_string(/*sandbox*/ None).await {
         Ok(contents) => contents,
         Err(error) => {
             tracing::warn!(
                 "ignoring {path}: failed to read {label}: {error}",
-                path = metadata_path.display(),
+                path = metadata_path.path().display(),
                 label = SKILLS_METADATA_FILENAME
             );
             return LoadedSkillMetadata::default();
@@ -748,13 +815,13 @@ async fn load_skill_metadata(
     };
 
     let parsed: SkillMetadataFile = {
-        let _guard = AbsolutePathBufGuard::new(skill_dir.as_path());
+        let _guard = AbsolutePathBufGuard::new(skill_dir.path().as_path());
         match serde_yaml::from_str(&contents) {
             Ok(parsed) => parsed,
             Err(error) => {
                 tracing::warn!(
                     "ignoring {path}: invalid {label}: {error}",
-                    path = metadata_path.display(),
+                    path = metadata_path.path().display(),
                     label = SKILLS_METADATA_FILENAME
                 );
                 return LoadedSkillMetadata::default();
@@ -768,7 +835,11 @@ async fn load_skill_metadata(
         policy,
     } = parsed;
     LoadedSkillMetadata {
-        interface: resolve_interface(interface, &skill_dir, plugin_root),
+        interface: resolve_interface(
+            interface,
+            skill_dir.path(),
+            plugin_root.map(EnvironmentPathRef::path),
+        ),
         dependencies: resolve_dependencies(dependencies),
         policy: resolve_policy(policy),
     }
@@ -1061,10 +1132,12 @@ pub(crate) async fn skill_roots_from_layer_stack(
     cwd: &AbsolutePathBuf,
     home_dir: Option<&AbsolutePathBuf>,
 ) -> Vec<SkillRoot> {
+    let path_ref = EnvironmentPathRef::new(fs, cwd.clone());
+    let local_file_system = path_ref.file_system();
     skill_roots_with_home_dir(
-        Some(fs),
+        &path_ref,
+        Some(&local_file_system),
         config_layer_stack,
-        cwd,
         home_dir,
         Vec::new(),
         Vec::new(),

codex-rs/core-skills/src/loader_tests.rs

@@ -4,7 +4,9 @@ use codex_config::ConfigLayerEntry;
 use codex_config::ConfigLayerStack;
 use codex_config::ConfigRequirements;
 use codex_config::ConfigRequirementsToml;
+use codex_exec_server::ExecutorFileSystem;
 use codex_exec_server::LOCAL_FS;
+use codex_exec_server::LocalFileSystem;
 use codex_protocol::protocol::Product;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBuf;
@@ -144,6 +146,19 @@ fn normalized(path: &Path) -> AbsolutePathBuf {
         .abs()
 }
 
+fn local_env_path(path: AbsolutePathBuf) -> EnvironmentPathRef {
+    EnvironmentPathRef::local(path)
+}
+
+fn local_skill_root(path: AbsolutePathBuf, scope: SkillScope) -> SkillRoot {
+    SkillRoot {
+        path: local_env_path(path),
+        scope,
+        plugin_id: None,
+        plugin_root: None,
+    }
+}
+
 #[tokio::test]
 async fn skill_roots_from_layer_stack_maps_user_to_user_and_system_cache_and_system_to_admin()
 -> anyhow::Result<()> {
@@ -187,7 +202,7 @@ async fn skill_roots_from_layer_stack_maps_user_to_user_and_system_cache_and_sys
     )
     .await
     .into_iter()
-    .map(|root| (root.scope, root.path.to_path_buf()))
+    .map(|root| (root.scope, root.path.path().to_path_buf()))
     .collect::<Vec<_>>();
 
     assert_eq!(
@@ -256,7 +271,7 @@ async fn skill_roots_from_layer_stack_includes_disabled_project_layers() -> anyh
     )
     .await
     .into_iter()
-    .map(|root| (root.scope, root.path.to_path_buf()))
+    .map(|root| (root.scope, root.path.path().to_path_buf()))
     .collect::<Vec<_>>();
 
     assert_eq!(
@@ -278,6 +293,57 @@ async fn skill_roots_from_layer_stack_includes_disabled_project_layers() -> anyh
     Ok(())
 }
 
+#[tokio::test]
+async fn skill_roots_bind_repo_and_local_roots_to_their_own_file_systems() -> anyhow::Result<()> {
+    let codex_home = tempfile::tempdir()?;
+    let project_root = codex_home.path().join("workspace");
+    fs::create_dir_all(project_root.join(".git"))?;
+    fs::create_dir_all(project_root.join(REPO_ROOT_CONFIG_DIR_NAME))?;
+    let cfg = make_config_for_cwd(&codex_home, project_root.clone()).await;
+
+    let env_file_system: Arc<dyn ExecutorFileSystem> = Arc::new(LocalFileSystem::unsandboxed());
+    let local_file_system: Arc<dyn ExecutorFileSystem> = Arc::new(LocalFileSystem::unsandboxed());
+    let env_path = EnvironmentPathRef::new(env_file_system.clone(), cfg.cwd.clone());
+    let roots = super::skill_roots(
+        &env_path,
+        Some(&local_file_system),
+        &cfg.config_layer_stack,
+        Vec::new(),
+        Vec::new(),
+    )
+    .await;
+
+    let repo_root = roots
+        .iter()
+        .find(|root| root.scope == SkillScope::Repo)
+        .expect("repo root");
+    let user_root = roots
+        .iter()
+        .find(|root| root.scope == SkillScope::User)
+        .expect("user root");
+    assert!(Arc::ptr_eq(&repo_root.path.file_system(), &env_file_system));
+    assert!(Arc::ptr_eq(
+        &user_root.path.file_system(),
+        &local_file_system
+    ));
+
+    let roots_without_local = super::skill_roots(
+        &env_path,
+        /*local_file_system*/ None,
+        &cfg.config_layer_stack,
+        Vec::new(),
+        Vec::new(),
+    )
+    .await;
+    assert!(
+        roots_without_local
+            .iter()
+            .all(|root| root.scope == SkillScope::Repo)
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn loads_skills_from_home_agents_dir_for_user_scope() -> anyhow::Result<()> {
     let tmp = tempfile::tempdir()?;
@@ -846,11 +912,10 @@ interface:
 
     let plugin_root_abs = plugin_root.abs();
     let outcome = load_skills_from_roots([SkillRoot {
-        path: plugin_root.join("skills").abs(),
+        path: local_env_path(plugin_root.join("skills").abs()),
         scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
         plugin_id: Some("twilio-developer-kit@test".to_string()),
-        plugin_root: Some(plugin_root_abs.clone()),
+        plugin_root: Some(local_env_path(plugin_root_abs.clone())),
     }])
     .await;
 
@@ -903,11 +968,10 @@ interface:
     );
 
     let outcome = load_skills_from_roots([SkillRoot {
-        path: plugin_root.join("skills").abs(),
+        path: local_env_path(plugin_root.join("skills").abs()),
         scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
         plugin_id: Some("twilio-developer-kit@test".to_string()),
-        plugin_root: Some(plugin_root.abs()),
+        plugin_root: Some(local_env_path(plugin_root.abs())),
     }])
     .await;
 
@@ -1048,14 +1112,9 @@ async fn loads_skills_via_symlinked_subdir_for_admin_scope() {
     fs::create_dir_all(admin_root.path()).unwrap();
     symlink_dir(shared.path(), &admin_root.path().join("shared"));
 
-    let outcome = load_skills_from_roots([SkillRoot {
-        path: admin_root.path().abs(),
-        scope: SkillScope::Admin,
-        file_system: Arc::clone(&LOCAL_FS),
-        plugin_id: None,
-        plugin_root: None,
-    }])
-    .await;
+    let outcome =
+        load_skills_from_roots([local_skill_root(admin_root.path().abs(), SkillScope::Admin)])
+            .await;
 
     assert!(
         outcome.errors.is_empty(),
@@ -1130,14 +1189,8 @@ async fn system_scope_ignores_symlinked_subdir() {
     fs::create_dir_all(&system_root).unwrap();
     symlink_dir(shared.path(), &system_root.join("shared"));
 
-    let outcome = load_skills_from_roots([SkillRoot {
-        path: system_root.abs(),
-        scope: SkillScope::System,
-        file_system: Arc::clone(&LOCAL_FS),
-        plugin_id: None,
-        plugin_root: None,
-    }])
-    .await;
+    let outcome =
+        load_skills_from_roots([local_skill_root(system_root.abs(), SkillScope::System)]).await;
     assert!(
         outcome.errors.is_empty(),
         "unexpected errors: {:?}",
@@ -1164,14 +1217,8 @@ async fn respects_max_scan_depth_for_user_scope() {
     );
 
     let skills_root = codex_home.path().join("skills");
-    let outcome = load_skills_from_roots([SkillRoot {
-        path: skills_root.abs(),
-        scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
-        plugin_id: None,
-        plugin_root: None,
-    }])
-    .await;
+    let outcome =
+        load_skills_from_roots([local_skill_root(skills_root.abs(), SkillScope::User)]).await;
 
     assert!(
         outcome.errors.is_empty(),
@@ -1272,11 +1319,10 @@ async fn namespaces_plugin_skills_using_plugin_name() {
     .unwrap();
 
     let outcome = load_skills_from_roots([SkillRoot {
-        path: plugin_root.join("skills").abs(),
+        path: local_env_path(plugin_root.join("skills").abs()),
         scope: SkillScope::User,
-        file_system: Arc::clone(&LOCAL_FS),
         plugin_id: Some("sample@test".to_string()),
-        plugin_root: Some(plugin_root.abs()),
+        plugin_root: Some(local_env_path(plugin_root.abs())),
     }])
     .await;
 
@@ -1595,16 +1641,14 @@ async fn deduplicates_by_path_preferring_first_root() {
 
     let outcome = load_skills_from_roots([
         SkillRoot {
-            path: root.path().abs(),
+            path: local_env_path(root.path().abs()),
             scope: SkillScope::Repo,
-            file_system: Arc::clone(&LOCAL_FS),
             plugin_id: None,
             plugin_root: None,
         },
         SkillRoot {
-            path: root.path().abs(),
+            path: local_env_path(root.path().abs()),
             scope: SkillScope::User,
-            file_system: Arc::clone(&LOCAL_FS),
             plugin_id: None,
             plugin_root: None,
         },
@@ -1895,10 +1939,12 @@ async fn skill_roots_include_admin_with_lowest_priority() {
     let codex_home = tempfile::tempdir().expect("tempdir");
     let cfg = make_config(&codex_home).await;
 
+    let cwd = local_env_path(cfg.cwd.clone());
+    let local_file_system = cwd.file_system();
     let scopes: Vec<SkillScope> = super::skill_roots(
-        Some(Arc::clone(&LOCAL_FS)),
+        &cwd,
+        Some(&local_file_system),
         &cfg.config_layer_stack,
-        &cfg.cwd,
         Vec::new(),
         Vec::new(),
     )

codex-rs/core-skills/src/manager.rs

@@ -4,7 +4,6 @@ use std::sync::Arc;
 use std::sync::RwLock;
 
 use codex_config::ConfigLayerStack;
-use codex_exec_server::ExecutorFileSystem;
 use codex_protocol::protocol::Product;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBuf;
@@ -23,24 +22,42 @@ use crate::loader::skill_roots;
 use crate::system::install_system_skills;
 use crate::system::uninstall_system_skills;
 use codex_config::SkillsConfig;
+use codex_exec_server::EnvironmentPathRef;
+use codex_exec_server::ExecutorFileSystem;
 
-#[derive(Debug, Clone)]
+#[derive(Clone)]
 pub struct SkillsLoadInput {
-    pub cwd: AbsolutePathBuf,
+    pub env_path: EnvironmentPathRef,
+    /// Local user/system/plugin skill roots are read from this filesystem for now.
+    pub local_file_system: Option<Arc<dyn ExecutorFileSystem>>,
     pub effective_skill_roots: Vec<PluginSkillRoot>,
     pub config_layer_stack: ConfigLayerStack,
     pub bundled_skills_enabled: bool,
 }
 
+impl std::fmt::Debug for SkillsLoadInput {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        f.debug_struct("SkillsLoadInput")
+            .field("env_path", &self.env_path)
+            .field("has_local_file_system", &self.local_file_system.is_some())
+            .field("effective_skill_roots", &self.effective_skill_roots)
+            .field("config_layer_stack", &self.config_layer_stack)
+            .field("bundled_skills_enabled", &self.bundled_skills_enabled)
+            .finish()
+    }
+}
+
 impl SkillsLoadInput {
     pub fn new(
-        cwd: AbsolutePathBuf,
+        env_path: EnvironmentPathRef,
+        local_file_system: Option<Arc<dyn ExecutorFileSystem>>,
         effective_skill_roots: Vec<PluginSkillRoot>,
         config_layer_stack: ConfigLayerStack,
         bundled_skills_enabled: bool,
     ) -> Self {
         Self {
-            cwd,
+            env_path,
+            local_file_system,
             effective_skill_roots,
             config_layer_stack,
             bundled_skills_enabled,
@@ -52,7 +69,7 @@ pub struct SkillsManager {
     codex_home: AbsolutePathBuf,
     restriction_product: Option<Product>,
     extra_roots: RwLock<Vec<AbsolutePathBuf>>,
-    cache_by_cwd: RwLock<HashMap<AbsolutePathBuf, SkillLoadOutcome>>,
+    cache_by_path_ref: RwLock<HashMap<SkillsPathCacheKey, SkillLoadOutcome>>,
     cache_by_config: RwLock<HashMap<ConfigSkillsCacheKey, SkillLoadOutcome>>,
 }
 
@@ -70,7 +87,7 @@ impl SkillsManager {
             codex_home,
             restriction_product,
             extra_roots: RwLock::new(Vec::new()),
-            cache_by_cwd: RwLock::new(HashMap::new()),
+            cache_by_path_ref: RwLock::new(HashMap::new()),
             cache_by_config: RwLock::new(HashMap::new()),
         };
         if !bundled_skills_enabled {
@@ -100,12 +117,8 @@ impl SkillsManager {
     /// This path uses a cache keyed by the effective skill-relevant config state rather than just
     /// cwd so role-local and session-local skill overrides cannot bleed across sessions that happen
     /// to share a directory.
-    pub async fn skills_for_config(
-        &self,
-        input: &SkillsLoadInput,
-        fs: Option<Arc<dyn ExecutorFileSystem>>,
-    ) -> SkillLoadOutcome {
-        let roots = self.skill_roots_for_config(input, fs).await;
+    pub async fn skills_for_config(&self, input: &SkillsLoadInput) -> SkillLoadOutcome {
+        let roots = self.skill_roots_for_config(input).await;
         let skill_config_rules = skill_config_rules_from_stack(&input.config_layer_stack);
         let cache_key = config_skills_cache_key(&roots, &skill_config_rules);
         if let Some(outcome) = self.cached_outcome_for_config(&cache_key) {
@@ -121,15 +134,11 @@ impl SkillsManager {
         outcome
     }
 
-    pub async fn skill_roots_for_config(
-        &self,
-        input: &SkillsLoadInput,
-        fs: Option<Arc<dyn ExecutorFileSystem>>,
-    ) -> Vec<SkillRoot> {
+    pub async fn skill_roots_for_config(&self, input: &SkillsLoadInput) -> Vec<SkillRoot> {
         let mut roots = skill_roots(
-            fs,
+            &input.env_path,
+            input.local_file_system.as_ref(),
             &input.config_layer_stack,
-            &input.cwd,
             input.effective_skill_roots.clone(),
             self.extra_roots(),
         )
@@ -144,20 +153,24 @@ impl SkillsManager {
         &self,
         input: &SkillsLoadInput,
         force_reload: bool,
-        fs: Option<Arc<dyn ExecutorFileSystem>>,
     ) -> SkillLoadOutcome {
-        let use_cwd_cache = fs.is_some();
-        if use_cwd_cache
-            && !force_reload
-            && let Some(outcome) = self.cached_outcome_for_cwd(&input.cwd)
+        let path_ref_cache_key = SkillsPathCacheKey {
+            env_path: input.env_path.clone(),
+            local_file_system: input
+                .local_file_system
+                .as_ref()
+                .map(ExecutorFileSystemRef::new),
+        };
+        if !force_reload
+            && let Some(outcome) = self.cached_outcome_for_path_ref(&path_ref_cache_key)
         {
             return outcome;
         }
 
         let mut roots = skill_roots(
-            fs.clone(),
+            &input.env_path,
+            input.local_file_system.as_ref(),
             &input.config_layer_stack,
-            &input.cwd,
             input.effective_skill_roots.clone(),
             self.extra_roots(),
         )
@@ -167,13 +180,11 @@ impl SkillsManager {
         }
         let skill_config_rules = skill_config_rules_from_stack(&input.config_layer_stack);
         let outcome = self.build_skill_outcome(roots, &skill_config_rules).await;
-        if use_cwd_cache {
-            let mut cache = self
-                .cache_by_cwd
-                .write()
-                .unwrap_or_else(std::sync::PoisonError::into_inner);
-            cache.insert(input.cwd.clone(), outcome.clone());
-        }
+        let mut cache = self
+            .cache_by_path_ref
+            .write()
+            .unwrap_or_else(std::sync::PoisonError::into_inner);
+        cache.insert(path_ref_cache_key, outcome.clone());
         outcome
     }
 
@@ -191,9 +202,9 @@ impl SkillsManager {
     }
 
     pub fn clear_cache(&self) {
-        let cleared_cwd = {
+        let cleared_path_refs = {
             let mut cache = self
-                .cache_by_cwd
+                .cache_by_path_ref
                 .write()
                 .unwrap_or_else(std::sync::PoisonError::into_inner);
             let cleared = cache.len();
@@ -209,14 +220,17 @@ impl SkillsManager {
             cache.clear();
             cleared
         };
-        let cleared = cleared_cwd + cleared_config;
+        let cleared = cleared_path_refs + cleared_config;
         info!("skills cache cleared ({cleared} entries)");
     }
 
-    fn cached_outcome_for_cwd(&self, cwd: &AbsolutePathBuf) -> Option<SkillLoadOutcome> {
-        match self.cache_by_cwd.read() {
-            Ok(cache) => cache.get(cwd).cloned(),
-            Err(err) => err.into_inner().get(cwd).cloned(),
+    fn cached_outcome_for_path_ref(
+        &self,
+        cache_key: &SkillsPathCacheKey,
+    ) -> Option<SkillLoadOutcome> {
+        match self.cache_by_path_ref.read() {
+            Ok(cache) => cache.get(cache_key).cloned(),
+            Err(err) => err.into_inner().get(cache_key).cloned(),
         }
     }
 
@@ -238,9 +252,44 @@ impl SkillsManager {
     }
 }
 
+#[derive(Clone, Debug, Eq, Hash, PartialEq)]
+struct SkillsPathCacheKey {
+    env_path: EnvironmentPathRef,
+    local_file_system: Option<ExecutorFileSystemRef>,
+}
+
+#[derive(Clone)]
+struct ExecutorFileSystemRef(Arc<dyn ExecutorFileSystem>);
+
+impl ExecutorFileSystemRef {
+    fn new(file_system: &Arc<dyn ExecutorFileSystem>) -> Self {
+        Self(Arc::clone(file_system))
+    }
+}
+
+impl PartialEq for ExecutorFileSystemRef {
+    fn eq(&self, other: &Self) -> bool {
+        Arc::ptr_eq(&self.0, &other.0)
+    }
+}
+
+impl Eq for ExecutorFileSystemRef {}
+
+impl std::hash::Hash for ExecutorFileSystemRef {
+    fn hash<H: std::hash::Hasher>(&self, state: &mut H) {
+        std::hash::Hash::hash(&(Arc::as_ptr(&self.0) as *const () as usize), state);
+    }
+}
+
+impl std::fmt::Debug for ExecutorFileSystemRef {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        f.debug_struct("ExecutorFileSystemRef").finish()
+    }
+}
+
 #[derive(Debug, Clone, PartialEq, Eq, Hash)]
 struct ConfigSkillsCacheKey {
-    roots: Vec<(AbsolutePathBuf, u8, Option<String>)>,
+    roots: Vec<(EnvironmentPathRef, u8, Option<String>)>,
     skill_config_rules: SkillConfigRules,
 }
 

codex-rs/core-skills/src/manager_tests.rs

@@ -87,6 +87,25 @@ fn test_skill(name: &str, path: PathBuf) -> SkillMetadata {
     }
 }
 
+fn skill_root_path_ref(path: AbsolutePathBuf) -> EnvironmentPathRef {
+    EnvironmentPathRef::local(path)
+}
+
+fn local_skills_input(
+    cwd: AbsolutePathBuf,
+    effective_skill_roots: Vec<PluginSkillRoot>,
+    config_layer_stack: ConfigLayerStack,
+) -> SkillsLoadInput {
+    let path_ref = skill_root_path_ref(cwd);
+    SkillsLoadInput::new(
+        path_ref,
+        Some(Arc::clone(&LOCAL_FS)),
+        effective_skill_roots,
+        config_layer_stack.clone(),
+        bundled_skills_enabled_from_stack(&config_layer_stack),
+    )
+}
+
 fn write_demo_skill(tempdir: &TempDir) -> PathBuf {
     let skill_path = tempdir.path().join("skills").join("demo").join("SKILL.md");
     fs::create_dir_all(skill_path.parent().expect("skill path should have parent"))
@@ -164,15 +183,12 @@ async fn skills_for_config_with_stack(
     config_layer_stack: &ConfigLayerStack,
     effective_skill_roots: &[PluginSkillRoot],
 ) -> SkillLoadOutcome {
-    let skills_input = SkillsLoadInput::new(
+    let skills_input = local_skills_input(
         cwd.path().abs(),
         effective_skill_roots.to_vec(),
         config_layer_stack.clone(),
-        bundled_skills_enabled_from_stack(config_layer_stack),
     );
-    skills_manager
-        .skills_for_config(&skills_input, Some(Arc::clone(&LOCAL_FS)))
-        .await
+    skills_manager.skills_for_config(&skills_input).await
 }
 
 #[test]
@@ -232,18 +248,9 @@ async fn set_extra_roots_replaces_runtime_roots_and_clears_cache() {
         /*bundled_skills_enabled*/ true,
     );
 
-    let skills_input = SkillsLoadInput::new(
-        cwd.path().abs(),
-        Vec::new(),
-        config_layer_stack.clone(),
-        bundled_skills_enabled_from_stack(&config_layer_stack),
-    );
+    let skills_input = local_skills_input(cwd.path().abs(), Vec::new(), config_layer_stack.clone());
     let empty_outcome = skills_manager
-        .skills_for_cwd(
-            &skills_input,
-            /*force_reload*/ false,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&skills_input, /*force_reload*/ false)
         .await;
     assert!(
         empty_outcome
@@ -263,11 +270,7 @@ async fn set_extra_roots_replaces_runtime_roots_and_clears_cache() {
     skills_manager.set_extra_roots(vec![extra_skills_root.abs()]);
 
     let runtime_outcome = skills_manager
-        .skills_for_cwd(
-            &skills_input,
-            /*force_reload*/ false,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&skills_input, /*force_reload*/ false)
         .await;
     assert!(
         runtime_outcome
@@ -278,11 +281,7 @@ async fn set_extra_roots_replaces_runtime_roots_and_clears_cache() {
 
     skills_manager.set_extra_roots(vec![extra_root.path().join("missing-skills").abs()]);
     let replaced_outcome = skills_manager
-        .skills_for_cwd(
-            &skills_input,
-            /*force_reload*/ false,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&skills_input, /*force_reload*/ false)
         .await;
     assert_eq!(replaced_outcome.errors, Vec::new());
     assert!(
@@ -421,23 +420,14 @@ async fn skills_for_cwd_loads_repo_and_user_roots_with_local_fs() {
         ConfigRequirementsToml::default(),
     )
     .expect("valid config layer stack");
-    let skills_input = SkillsLoadInput::new(
-        cwd.path().abs(),
-        Vec::new(),
-        config_layer_stack.clone(),
-        bundled_skills_enabled_from_stack(&config_layer_stack),
-    );
+    let skills_input = local_skills_input(cwd.path().abs(), Vec::new(), config_layer_stack.clone());
     let skills_manager = SkillsManager::new(
         codex_home.path().abs(),
         /*bundled_skills_enabled*/ true,
     );
 
     let outcome = skills_manager
-        .skills_for_cwd(
-            &skills_input,
-            /*force_reload*/ true,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&skills_input, /*force_reload*/ true)
         .await;
 
     assert!(
@@ -455,7 +445,7 @@ async fn skills_for_cwd_loads_repo_and_user_roots_with_local_fs() {
 }
 
 #[tokio::test]
-async fn skills_for_cwd_without_fs_skips_repo_roots() {
+async fn skills_for_cwd_without_local_fs_skips_local_roots() {
     let codex_home = tempfile::tempdir().expect("tempdir");
     let cwd = tempfile::tempdir().expect("tempdir");
     let repo_dot_codex = cwd.path().join(".codex");
@@ -485,7 +475,8 @@ async fn skills_for_cwd_without_fs_skips_repo_roots() {
     )
     .expect("valid config layer stack");
     let skills_input = SkillsLoadInput::new(
-        cwd.path().abs(),
+        skill_root_path_ref(cwd.path().abs()),
+        /*local_file_system*/ None,
         Vec::new(),
         config_layer_stack.clone(),
         bundled_skills_enabled_from_stack(&config_layer_stack),
@@ -496,7 +487,7 @@ async fn skills_for_cwd_without_fs_skips_repo_roots() {
     );
 
     let outcome = skills_manager
-        .skills_for_cwd(&skills_input, /*force_reload*/ true, /*fs*/ None)
+        .skills_for_cwd(&skills_input, /*force_reload*/ true)
         .await;
 
     assert!(
@@ -509,8 +500,8 @@ async fn skills_for_cwd_without_fs_skips_repo_roots() {
         .iter()
         .map(|skill| skill.name.as_str())
         .collect::<HashSet<_>>();
-    assert!(loaded_names.contains("user-skill"));
-    assert!(!loaded_names.contains("repo-skill"));
+    assert!(!loaded_names.contains("user-skill"));
+    assert!(loaded_names.contains("repo-skill"));
 }
 
 #[tokio::test]
@@ -565,18 +556,9 @@ async fn skills_for_cwd_uses_cached_result_until_force_reload() {
         /*bundled_skills_enabled*/ true,
     );
     let _ = skills_for_config_with_stack(&skills_manager, &cwd, &config_layer_stack, &[]).await;
-    let base_input = SkillsLoadInput::new(
-        cwd.path().abs(),
-        Vec::new(),
-        config_layer_stack.clone(),
-        bundled_skills_enabled_from_stack(&config_layer_stack),
-    );
+    let base_input = local_skills_input(cwd.path().abs(), Vec::new(), config_layer_stack.clone());
     let outcome_a = skills_manager
-        .skills_for_cwd(
-            &base_input,
-            /*force_reload*/ false,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&base_input, /*force_reload*/ false)
         .await;
     assert!(
         outcome_a
@@ -588,11 +570,7 @@ async fn skills_for_cwd_uses_cached_result_until_force_reload() {
     write_user_skill(&codex_home, "late", "late-skill", "added after cache");
 
     let outcome_b = skills_manager
-        .skills_for_cwd(
-            &base_input,
-            /*force_reload*/ false,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&base_input, /*force_reload*/ false)
         .await;
     assert!(
         outcome_b
@@ -602,11 +580,7 @@ async fn skills_for_cwd_uses_cached_result_until_force_reload() {
     );
 
     let outcome_reloaded = skills_manager
-        .skills_for_cwd(
-            &base_input,
-            /*force_reload*/ true,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&base_input, /*force_reload*/ true)
         .await;
     assert!(
         outcome_reloaded
@@ -779,19 +753,10 @@ async fn skills_for_config_ignores_cwd_cache_when_session_flags_reenable_skill()
         codex_home.path().abs(),
         /*bundled_skills_enabled*/ true,
     );
-    let parent_input = SkillsLoadInput::new(
-        cwd.path().abs(),
-        Vec::new(),
-        parent_stack.clone(),
-        bundled_skills_enabled_from_stack(&parent_stack),
-    );
+    let parent_input = local_skills_input(cwd.path().abs(), Vec::new(), parent_stack.clone());
 
     let parent_outcome = skills_manager
-        .skills_for_cwd(
-            &parent_input,
-            /*force_reload*/ true,
-            Some(Arc::clone(&LOCAL_FS)),
-        )
+        .skills_for_cwd(&parent_input, /*force_reload*/ true)
         .await;
     let parent_skill = parent_outcome
         .skills

codex-rs/core-skills/src/model.rs

@@ -1,12 +1,11 @@
-use std::collections::HashMap;
-use std::collections::HashSet;
-use std::fmt;
-use std::sync::Arc;
-
 use codex_exec_server::ExecutorFileSystem;
 use codex_protocol::protocol::Product;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBuf;
+use std::collections::HashMap;
+use std::collections::HashSet;
+use std::fmt;
+use std::sync::Arc;
 
 #[derive(Debug, Clone, PartialEq)]
 pub struct SkillMetadata {
@@ -210,3 +209,30 @@ pub fn filter_skill_load_outcome_for_product(
     );
     outcome
 }
+
+#[cfg(test)]
+mod tests {
+    use std::path::Path;
+
+    use codex_exec_server::EnvironmentPathRef;
+    use codex_utils_absolute_path::test_support::PathBufExt;
+    use pretty_assertions::assert_eq;
+
+    #[test]
+    fn environment_path_ref_joins_only_relative_paths() {
+        let root_path = std::env::temp_dir().join("skills");
+        let path_ref = EnvironmentPathRef::local(root_path.abs());
+
+        assert_eq!(
+            path_ref
+                .join_relative(Path::new("demo/SKILL.md"))
+                .map(|path_ref| path_ref.path().clone()),
+            Some(root_path.join("demo/SKILL.md").abs())
+        );
+        assert!(
+            path_ref
+                .join_relative(std::env::temp_dir().join("SKILL.md").as_path())
+                .is_none()
+        );
+    }
+}

codex-rs/core/src/agent/role_tests.rs

@@ -421,13 +421,17 @@ enabled = false
     let plugins_input = config.plugins_config_input();
     let plugin_outcome = plugins_manager.plugins_for_config(&plugins_input).await;
     let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
-    let skills_input = skills_load_input_from_config(&config, effective_skill_roots);
-    let outcome = skills_manager
-        .skills_for_config(
-            &skills_input,
-            Some(Arc::clone(&codex_exec_server::LOCAL_FS)),
-        )
-        .await;
+    let cwd = crate::skills::EnvironmentPathRef::new(
+        Arc::clone(&codex_exec_server::LOCAL_FS),
+        config.cwd.clone(),
+    );
+    let skills_input = skills_load_input_from_config(
+        &config,
+        cwd,
+        Some(Arc::clone(&codex_exec_server::LOCAL_FS)),
+        effective_skill_roots,
+    );
+    let outcome = skills_manager.skills_for_config(&skills_input).await;
     let skill = outcome
         .skills
         .iter()

codex-rs/core/src/environment_selection.rs

@@ -2,7 +2,6 @@ use std::collections::HashSet;
 use std::sync::Arc;
 
 use codex_exec_server::EnvironmentManager;
-use codex_exec_server::ExecutorFileSystem;
 use codex_protocol::error::CodexErr;
 use codex_protocol::error::Result as CodexResult;
 use codex_protocol::protocol::TurnEnvironmentSelection;
@@ -45,11 +44,6 @@ impl ResolvedTurnEnvironments {
         self.primary()
             .map(|environment| Arc::clone(&environment.environment))
     }
-
-    pub(crate) fn primary_filesystem(&self) -> Option<Arc<dyn ExecutorFileSystem>> {
-        self.primary()
-            .map(|environment| environment.environment.get_filesystem())
-    }
 }
 
 pub(crate) fn resolve_environment_selections(

codex-rs/core/src/session/session.rs

@@ -447,20 +447,36 @@ async fn warm_plugins_and_skills_for_session_init(
     skills_manager: Arc<SkillsManager>,
     environments: Vec<TurnEnvironmentSelection>,
 ) -> Vec<SkillError> {
-    let fs = crate::environment_selection::resolve_environment_selections(
+    let resolved_environments = crate::environment_selection::resolve_environment_selections(
         environment_manager.as_ref(),
         &environments,
     )
-    .ok()
-    .and_then(|resolved| resolved.primary_filesystem());
+    .ok();
+    let path_ref = resolved_environments
+        .as_ref()
+        .and_then(crate::environment_selection::ResolvedTurnEnvironments::primary)
+        .map(|environment| {
+            crate::skills::EnvironmentPathRef::new(
+                environment.environment.get_filesystem(),
+                environment.cwd.clone(),
+            )
+        });
+    let Some(path_ref) = path_ref else {
+        return Vec::new();
+    };
+    let local_file_system = environment_manager
+        .try_local_environment()
+        .map(|environment| environment.get_filesystem());
     let plugins_input = config.plugins_config_input();
     let plugin_outcome = plugins_manager.plugins_for_config(&plugins_input).await;
     let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
-    let skills_input = skills_load_input_from_config(config.as_ref(), effective_skill_roots);
-    skills_manager
-        .skills_for_config(&skills_input, fs)
-        .await
-        .errors
+    let skills_input = skills_load_input_from_config(
+        config.as_ref(),
+        path_ref,
+        local_file_system,
+        effective_skill_roots,
+    );
+    skills_manager.skills_for_config(&skills_input).await.errors
 }
 
 impl Session {

codex-rs/core/src/session/tests.rs

@@ -4127,9 +4127,20 @@ async fn new_default_turn_uses_config_aware_skills_for_role_overrides() {
         .services
         .skills_manager
         .skills_for_cwd(
-            &crate::skills_load_input_from_config(&parent_config, Vec::new()),
+            &crate::skills_load_input_from_config(
+                &parent_config,
+                crate::skills::EnvironmentPathRef::new(
+                    Arc::clone(&skill_fs),
+                    parent_config.cwd.clone(),
+                ),
+                session
+                    .services
+                    .environment_manager
+                    .try_local_environment()
+                    .map(|environment| environment.get_filesystem()),
+                Vec::new(),
+            ),
             /*force_reload*/ true,
-            Some(Arc::clone(&skill_fs)),
         )
         .await;
     let parent_skill = parent_outcome
@@ -4692,13 +4703,23 @@ pub(crate) async fn make_session_and_context() -> (Session, TurnContext) {
         .plugins_for_config(&per_turn_config.plugins_config_input())
         .await;
     let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
-    let skills_input =
-        crate::skills_load_input_from_config(&per_turn_config, effective_skill_roots);
-    let skill_fs = environment.get_filesystem();
+    let cwd = crate::skills::EnvironmentPathRef::new(
+        environment.get_filesystem(),
+        per_turn_config.cwd.clone(),
+    );
+    let skills_input = crate::skills_load_input_from_config(
+        &per_turn_config,
+        cwd,
+        services
+            .environment_manager
+            .try_local_environment()
+            .map(|environment| environment.get_filesystem()),
+        effective_skill_roots,
+    );
     let skills_outcome = Arc::new(
         services
             .skills_manager
-            .skills_for_config(&skills_input, Some(Arc::clone(&skill_fs)))
+            .skills_for_config(&skills_input)
             .await,
     );
     let turn_environments = turn_environments_for_tests(&environment, &session_configuration.cwd);
@@ -6535,13 +6556,23 @@ where
         .plugins_for_config(&per_turn_config.plugins_config_input())
         .await;
     let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
-    let skills_input =
-        crate::skills_load_input_from_config(&per_turn_config, effective_skill_roots);
-    let skill_fs = environment.get_filesystem();
+    let cwd = crate::skills::EnvironmentPathRef::new(
+        environment.get_filesystem(),
+        per_turn_config.cwd.clone(),
+    );
+    let skills_input = crate::skills_load_input_from_config(
+        &per_turn_config,
+        cwd,
+        services
+            .environment_manager
+            .try_local_environment()
+            .map(|environment| environment.get_filesystem()),
+        effective_skill_roots,
+    );
     let skills_outcome = Arc::new(
         services
             .skills_manager
-            .skills_for_config(&skills_input, Some(Arc::clone(&skill_fs)))
+            .skills_for_config(&skills_input)
             .await,
     );
     let turn_environments = turn_environments_for_tests(&environment, &session_configuration.cwd);

codex-rs/core/src/session/turn_context.rs

@@ -678,21 +678,42 @@ impl Session {
                 &per_turn_config.to_models_manager_config(),
             )
             .await;
-        let plugin_outcome = self
-            .services
-            .plugins_manager
-            .plugins_for_config(&per_turn_config.plugins_config_input())
-            .await;
-        let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
-        let skills_input = skills_load_input_from_config(&per_turn_config, effective_skill_roots);
-        let fs = primary_turn_environment
-            .map(|turn_environment| turn_environment.environment.get_filesystem());
-        let skills_outcome = Arc::new(
-            self.services
-                .skills_manager
-                .skills_for_config(&skills_input, fs)
-                .await,
-        );
+        let path_ref = primary_turn_environment.map(|turn_environment| {
+            crate::skills::EnvironmentPathRef::new(
+                turn_environment.environment.get_filesystem(),
+                turn_environment.cwd.clone(),
+            )
+        });
+        let skills_outcome = if let Some(path_ref) = path_ref {
+            // Workspace/repo skill roots use the selected turn environment path above, while
+            // user/system/plugin skill roots still read from the available local filesystem.
+            let local_file_system = self
+                .services
+                .environment_manager
+                .try_local_environment()
+                .map(|environment| environment.get_filesystem());
+            let plugins_input = per_turn_config.plugins_config_input();
+            let plugin_outcome = self
+                .services
+                .plugins_manager
+                .plugins_for_config(&plugins_input)
+                .await;
+            let effective_skill_roots = plugin_outcome.effective_plugin_skill_roots();
+            let skills_input = skills_load_input_from_config(
+                &per_turn_config,
+                path_ref,
+                local_file_system,
+                effective_skill_roots,
+            );
+            Arc::new(
+                self.services
+                    .skills_manager
+                    .skills_for_config(&skills_input)
+                    .await,
+            )
+        } else {
+            Arc::new(SkillLoadOutcome::default())
+        };
         let goal_tools_supported = !per_turn_config.ephemeral && self.state_db().is_some();
         let mut turn_context: TurnContext = Self::make_turn_context(
             self.thread_id(),

codex-rs/core/src/skills.rs

@@ -4,9 +4,12 @@ use crate::session::turn_context::TurnContext;
 use codex_analytics::InvocationType;
 use codex_analytics::SkillInvocation;
 use codex_analytics::build_track_events_context;
+pub use codex_exec_server::EnvironmentPathRef;
+use codex_exec_server::ExecutorFileSystem;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBuf;
 use codex_utils_plugins::PluginSkillRoot;
+use std::sync::Arc;
 
 pub use codex_core_skills::SkillError;
 pub use codex_core_skills::SkillLoadOutcome;
@@ -35,10 +38,13 @@ pub use codex_core_skills::system;
 
 pub(crate) fn skills_load_input_from_config(
     config: &Config,
+    env_path: EnvironmentPathRef,
+    local_file_system: Option<Arc<dyn ExecutorFileSystem>>,
     effective_skill_roots: Vec<PluginSkillRoot>,
 ) -> SkillsLoadInput {
     SkillsLoadInput::new(
-        config.cwd.clone(),
+        env_path,
+        local_file_system,
         effective_skill_roots,
         config.config_layer_stack.clone(),
         config.bundled_skills_enabled(),

codex-rs/exec-server/src/environment_path.rs

@@ -0,0 +1,325 @@
+use std::fmt;
+use std::hash::Hash;
+use std::hash::Hasher;
+use std::io;
+use std::path::Path;
+use std::sync::Arc;
+
+use codex_utils_absolute_path::AbsolutePathBuf;
+
+use crate::ExecutorFileSystem;
+use crate::FileMetadata;
+use crate::FileSystemSandboxContext;
+use crate::LOCAL_FS;
+use crate::ReadDirectoryEntry;
+
+/// Binds an absolute path to the executor filesystem that owns it.
+#[derive(Clone)]
+pub struct EnvironmentPathRef {
+    file_system: Arc<dyn ExecutorFileSystem>,
+    path: AbsolutePathBuf,
+}
+
+impl EnvironmentPathRef {
+    pub fn new(file_system: Arc<dyn ExecutorFileSystem>, path: AbsolutePathBuf) -> Self {
+        Self { file_system, path }
+    }
+
+    pub fn local(path: AbsolutePathBuf) -> Self {
+        Self::new(Arc::clone(&LOCAL_FS), path)
+    }
+
+    pub fn path(&self) -> &AbsolutePathBuf {
+        &self.path
+    }
+
+    pub fn file_system(&self) -> Arc<dyn ExecutorFileSystem> {
+        Arc::clone(&self.file_system)
+    }
+
+    pub async fn read_to_string(
+        &self,
+        sandbox: Option<&FileSystemSandboxContext>,
+    ) -> io::Result<String> {
+        self.file_system.read_file_text(&self.path, sandbox).await
+    }
+
+    pub async fn metadata(
+        &self,
+        sandbox: Option<&FileSystemSandboxContext>,
+    ) -> io::Result<FileMetadata> {
+        self.file_system.get_metadata(&self.path, sandbox).await
+    }
+
+    pub async fn read_directory(
+        &self,
+        sandbox: Option<&FileSystemSandboxContext>,
+    ) -> io::Result<Vec<ReadDirectoryEntry>> {
+        self.file_system.read_directory(&self.path, sandbox).await
+    }
+
+    pub fn join_relative(&self, relative: &Path) -> Option<Self> {
+        relative
+            .is_relative()
+            .then(|| self.with_path(self.path.join(relative)))
+    }
+
+    pub fn parent_dir(&self) -> Option<Self> {
+        self.path.parent().map(|path| self.with_path(path))
+    }
+
+    pub fn with_path(&self, path: AbsolutePathBuf) -> Self {
+        Self::new(Arc::clone(&self.file_system), path)
+    }
+}
+
+impl PartialEq for EnvironmentPathRef {
+    fn eq(&self, other: &Self) -> bool {
+        Arc::ptr_eq(&self.file_system, &other.file_system) && self.path == other.path
+    }
+}
+
+impl Eq for EnvironmentPathRef {}
+
+impl Hash for EnvironmentPathRef {
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        (Arc::as_ptr(&self.file_system) as *const () as usize).hash(state);
+        self.path.hash(state);
+    }
+}
+
+impl fmt::Debug for EnvironmentPathRef {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        f.debug_struct("EnvironmentPathRef")
+            .field("path", &self.path)
+            .finish()
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    use async_trait::async_trait;
+    use codex_protocol::models::PermissionProfile;
+    use codex_protocol::permissions::FileSystemSandboxPolicy;
+    use codex_protocol::permissions::NetworkSandboxPolicy;
+    use codex_utils_absolute_path::test_support::PathBufExt;
+    use pretty_assertions::assert_eq;
+    use std::collections::HashSet;
+    use std::sync::Mutex;
+
+    #[derive(Clone, Debug, Eq, PartialEq)]
+    enum RecordedMethod {
+        ReadFileText,
+        Metadata,
+        ReadDirectory,
+    }
+
+    #[derive(Clone, Debug, Eq, PartialEq)]
+    struct RecordedCall {
+        method: RecordedMethod,
+        path: AbsolutePathBuf,
+        sandbox: Option<FileSystemSandboxContext>,
+    }
+
+    #[derive(Default)]
+    struct RecordingFileSystem {
+        calls: Mutex<Vec<RecordedCall>>,
+    }
+
+    impl RecordingFileSystem {
+        fn recorded_calls(&self) -> Vec<RecordedCall> {
+            match self.calls.lock() {
+                Ok(calls) => calls.clone(),
+                Err(err) => err.into_inner().clone(),
+            }
+        }
+
+        fn push_call(&self, call: RecordedCall) {
+            match self.calls.lock() {
+                Ok(mut calls) => calls.push(call),
+                Err(err) => err.into_inner().push(call),
+            }
+        }
+    }
+
+    #[async_trait]
+    impl ExecutorFileSystem for RecordingFileSystem {
+        async fn read_file(
+            &self,
+            path: &AbsolutePathBuf,
+            sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<Vec<u8>> {
+            self.push_call(RecordedCall {
+                method: RecordedMethod::ReadFileText,
+                path: path.clone(),
+                sandbox: sandbox.cloned(),
+            });
+            Ok(b"skill contents".to_vec())
+        }
+
+        async fn write_file(
+            &self,
+            _path: &AbsolutePathBuf,
+            _contents: Vec<u8>,
+            _sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<()> {
+            unreachable!("write_file should not be called")
+        }
+
+        async fn create_directory(
+            &self,
+            _path: &AbsolutePathBuf,
+            _create_directory_options: crate::CreateDirectoryOptions,
+            _sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<()> {
+            unreachable!("create_directory should not be called")
+        }
+
+        async fn get_metadata(
+            &self,
+            path: &AbsolutePathBuf,
+            sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<FileMetadata> {
+            self.push_call(RecordedCall {
+                method: RecordedMethod::Metadata,
+                path: path.clone(),
+                sandbox: sandbox.cloned(),
+            });
+            Ok(FileMetadata {
+                is_directory: true,
+                is_file: false,
+                is_symlink: false,
+                created_at_ms: 1,
+                modified_at_ms: 2,
+            })
+        }
+
+        async fn read_directory(
+            &self,
+            path: &AbsolutePathBuf,
+            sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<Vec<ReadDirectoryEntry>> {
+            self.push_call(RecordedCall {
+                method: RecordedMethod::ReadDirectory,
+                path: path.clone(),
+                sandbox: sandbox.cloned(),
+            });
+            Ok(vec![ReadDirectoryEntry {
+                file_name: "SKILL.md".to_string(),
+                is_directory: false,
+                is_file: true,
+            }])
+        }
+
+        async fn remove(
+            &self,
+            _path: &AbsolutePathBuf,
+            _remove_options: crate::RemoveOptions,
+            _sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<()> {
+            unreachable!("remove should not be called")
+        }
+
+        async fn copy(
+            &self,
+            _source_path: &AbsolutePathBuf,
+            _destination_path: &AbsolutePathBuf,
+            _copy_options: crate::CopyOptions,
+            _sandbox: Option<&FileSystemSandboxContext>,
+        ) -> io::Result<()> {
+            unreachable!("copy should not be called")
+        }
+    }
+
+    fn restricted_sandbox() -> FileSystemSandboxContext {
+        FileSystemSandboxContext::from_permission_profile(
+            PermissionProfile::from_runtime_permissions(
+                &FileSystemSandboxPolicy::restricted(Vec::new()),
+                NetworkSandboxPolicy::Restricted,
+            ),
+        )
+    }
+
+    #[tokio::test]
+    async fn environment_path_ref_forwards_sandbox_to_file_system_methods() {
+        let path = std::env::temp_dir().join("skills/demo").abs();
+        let file_system = Arc::new(RecordingFileSystem::default());
+        let path_ref = EnvironmentPathRef::new(file_system.clone(), path.clone());
+        let sandbox = restricted_sandbox();
+
+        assert_eq!(
+            path_ref
+                .read_to_string(Some(&sandbox))
+                .await
+                .expect("read skill contents"),
+            "skill contents".to_string()
+        );
+        assert_eq!(
+            path_ref
+                .metadata(Some(&sandbox))
+                .await
+                .expect("read metadata"),
+            FileMetadata {
+                is_directory: true,
+                is_file: false,
+                is_symlink: false,
+                created_at_ms: 1,
+                modified_at_ms: 2,
+            }
+        );
+        assert_eq!(
+            path_ref
+                .read_directory(Some(&sandbox))
+                .await
+                .expect("read directory"),
+            vec![ReadDirectoryEntry {
+                file_name: "SKILL.md".to_string(),
+                is_directory: false,
+                is_file: true,
+            }]
+        );
+        assert_eq!(
+            file_system.recorded_calls(),
+            vec![
+                RecordedCall {
+                    method: RecordedMethod::ReadFileText,
+                    path: path.clone(),
+                    sandbox: Some(sandbox.clone()),
+                },
+                RecordedCall {
+                    method: RecordedMethod::Metadata,
+                    path: path.clone(),
+                    sandbox: Some(sandbox.clone()),
+                },
+                RecordedCall {
+                    method: RecordedMethod::ReadDirectory,
+                    path,
+                    sandbox: Some(sandbox),
+                },
+            ]
+        );
+    }
+
+    #[test]
+    fn environment_path_ref_equality_and_hash_include_file_system_identity() {
+        let path = std::env::temp_dir().join("skills/demo").abs();
+        let file_system = Arc::new(RecordingFileSystem::default());
+        let same_file_system: Arc<dyn ExecutorFileSystem> = file_system.clone();
+        let different_file_system: Arc<dyn ExecutorFileSystem> =
+            Arc::new(RecordingFileSystem::default());
+
+        let left = EnvironmentPathRef::new(same_file_system.clone(), path.clone());
+        let same = EnvironmentPathRef::new(same_file_system, path.clone());
+        let different_path = EnvironmentPathRef::new(file_system, path.parent().unwrap());
+        let different_fs = EnvironmentPathRef::new(different_file_system, path);
+
+        assert_eq!(left, same);
+        assert_ne!(left, different_path);
+        assert_ne!(left, different_fs);
+
+        let set = HashSet::from([left, same, different_path, different_fs]);
+        assert_eq!(set.len(), 3);
+    }
+}

codex-rs/exec-server/src/lib.rs

@@ -3,6 +3,7 @@ mod client_api;
 mod client_transport;
 mod connection;
 mod environment;
+mod environment_path;
 mod environment_provider;
 mod environment_toml;
 mod fs_helper;
@@ -43,6 +44,7 @@ pub use environment::Environment;
 pub use environment::EnvironmentManager;
 pub use environment::LOCAL_ENVIRONMENT_ID;
 pub use environment::REMOTE_ENVIRONMENT_ID;
+pub use environment_path::EnvironmentPathRef;
 pub use environment_provider::DefaultEnvironmentProvider;
 pub use environment_provider::EnvironmentProvider;
 pub use fs_helper::CODEX_FS_HELPER_ARG1;

codex-rs/tui/src/app/background_requests.rs

@@ -674,6 +674,7 @@ pub(super) async fn fetch_skills_list(
             request_id,
             params: SkillsListParams {
                 cwds: vec![cwd],
+                environment_id: None,
                 force_reload: true,
             },
         })

codex-rs/tui/src/app/thread_routing.rs

@@ -621,6 +621,7 @@ impl App {
                     app_server
                         .skills_list(codex_app_server_protocol::SkillsListParams {
                             cwds: cwds.clone(),
+                            environment_id: None,
                             force_reload: *force_reload,
                         })
                         .await,