feat(skills): support isolated bootstrap directories

crates/aion-agent/src/bootstrap.rs

@@ -63,6 +63,7 @@ pub struct AgentBootstrap {
     config: Config,
     workspace: PathBuf,
     extra_skill_dirs: Vec<PathBuf>,
+    isolate_skill_dirs: bool,
 
     // Output integration.
     output: Arc<dyn OutputSink>,
@@ -104,6 +105,7 @@ impl AgentBootstrap {
             config,
             workspace: PathBuf::from(workspace.into()),
             extra_skill_dirs: Vec::new(),
+            isolate_skill_dirs: false,
             output,
             provider: None,
             resume_session: None,
@@ -142,6 +144,16 @@ impl AgentBootstrap {
         self
     }
 
+    /// Discover skills only from the supplied directories and bundled skills.
+    ///
+    /// Each directory is interpreted as a project root containing
+    /// `.aionrs/skills`.
+    pub fn isolated_skill_dirs(mut self, dirs: Vec<PathBuf>) -> Self {
+        self.extra_skill_dirs = dirs;
+        self.isolate_skill_dirs = true;
+        self
+    }
+
     /// Read-only access to the config (for session management before build).
     pub fn config(&self) -> &Config {
         &self.config
@@ -269,7 +281,7 @@ impl AgentBootstrap {
     }
 
     async fn load_skills(&self, workspace: &Path, mcp_manager: Option<&McpManager>) -> Vec<SkillMetadata> {
-        load_all_skills(workspace, &self.extra_skill_dirs, false, mcp_manager).await
+        load_all_skills(workspace, &self.extra_skill_dirs, self.isolate_skill_dirs, mcp_manager).await
     }
 
     fn configure_system_prompt(&mut self, environment: &BootstrapEnvironment, skills: &[SkillMetadata]) -> PromptUsage {

crates/aion-agent/src/bootstrap_test.rs

@@ -3,6 +3,7 @@ use super::*;
 #[cfg(test)]
 mod tests {
     use std::collections::HashMap;
+    use std::fs;
     use std::sync::Arc;
 
     use aion_config::config::{CliArgs, McpServerConfig, TransportType};
@@ -74,6 +75,34 @@ mod tests {
         .unwrap()
     }
 
+    fn write_skill(project_root: &std::path::Path, name: &str) {
+        let skill_dir = project_root.join(".aionrs").join("skills").join(name);
+        fs::create_dir_all(&skill_dir).unwrap();
+        fs::write(skill_dir.join("SKILL.md"), "---\ndescription: test skill\n---\n").unwrap();
+    }
+
+    #[tokio::test]
+    async fn isolated_skill_dirs_excludes_workspace_skills() {
+        let workspace = tempfile::TempDir::new().unwrap();
+        let isolated_root = tempfile::TempDir::new().unwrap();
+        write_skill(workspace.path(), "workspace-only");
+        write_skill(isolated_root.path(), "isolated-only");
+
+        let output: Arc<dyn OutputSink> = Arc::new(NullSink);
+        let bootstrap = AgentBootstrap::new(test_config(), workspace.path().to_string_lossy(), output)
+            .isolated_skill_dirs(vec![isolated_root.path().to_path_buf()]);
+
+        let names = bootstrap
+            .load_skills(workspace.path(), None)
+            .await
+            .into_iter()
+            .map(|skill| skill.name)
+            .collect::<Vec<_>>();
+
+        assert!(names.iter().any(|name| name == "isolated-only"));
+        assert!(!names.iter().any(|name| name == "workspace-only"));
+    }
+
     #[test]
     fn mcp_servers_with_runtime_env_uses_server_env_as_override() {
         let mut config = test_config();