Refactor tool and permission foundations

.github/workflows/ci.yml

@@ -39,16 +39,16 @@ jobs:
           components: rustfmt
       - run: cargo fmt --all -- --check
 
-  # clippy:
-  #   name: Clippy
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: dtolnay/rust-toolchain@stable
-  #       with:
-  #         components: clippy
-  #     - uses: Swatinem/rust-cache@v2
-  #     - run: cargo clippy --workspace --all-targets -- -D warnings
+  clippy:
+    name: Clippy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+        with:
+          components: clippy
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo clippy --workspace --all-targets -- -D warnings
 
   doc:
     name: Doc

.gitignore

@@ -1,2 +1,3 @@
 /target
 .DS_Store
+.claude

AGENTS.md

@@ -25,6 +25,7 @@ This repository is a Rust-based coding agent, currently called `devo`.
 - When running Rust-related commands (e.g., `just fix` or `cargo test`), allow them to complete without interruption, do not try to kill them using the PID. Slow execution due to Rust’s locking behavior is expected.
 - Agent can not apply patch to a file more than 800 lines, cause windows patch length limit, agent would failed to apply patch.
 - Do not introduce trivial wrapper functions — call the underlying function directly unless reuse or abstraction is clearly justified.
+- Exclude the target folder when using glob or grep, since it contains a large number of Rust build artifacts.
 
 ## Tests
 

crates/cli/src/agent_command.rs

@@ -1,11 +1,15 @@
 use anyhow::Context;
 use anyhow::Result;
+use devo_core::AppConfigLoader;
+use devo_core::FileSystemAppConfigLoader;
 use devo_core::ModelCatalog;
 use devo_core::PresetModelCatalog;
 use devo_core::ProviderConfigFile;
 use devo_core::ResolvedProviderSettings;
 use devo_core::load_config;
+use devo_core::project_config_key;
 use devo_core::resolve_provider_settings;
+use devo_protocol::PermissionPreset;
 use devo_protocol::ProviderWireApi;
 use devo_tui::InitialTuiSession;
 use devo_tui::InteractiveTuiConfig;
@@ -24,6 +28,13 @@ pub(crate) async fn run_agent(force_onboarding: bool, log_level: Option<&str>) -
     let config_home = find_devo_home().context("could not determine devo home directory")?;
     let model_catalog = PresetModelCatalog::load_from_config(&config_home, Some(&cwd))?;
     let stored_config = load_config().unwrap_or_default();
+    let app_config = FileSystemAppConfigLoader::new(config_home.clone()).load(Some(&cwd))?;
+    let project_key = project_config_key(&cwd);
+    let permission_preset = app_config
+        .projects
+        .get(&project_key)
+        .and_then(|config| config.permission_preset)
+        .unwrap_or(PermissionPreset::Default);
     let (onboarding_mode, resolved) =
         resolve_initial_provider_settings(force_onboarding, &stored_config, &model_catalog)?;
 
@@ -47,6 +58,7 @@ pub(crate) async fn run_agent(force_onboarding: bool, log_level: Option<&str>) -
             model,
             provider: wire_api,
             thinking_selection: model_thinking_selection,
+            permission_preset,
             // TODO: why do we need cwd here, maybe remove it ?
             cwd,
         },

crates/cli/src/prompt_command.rs

@@ -19,7 +19,6 @@ pub(crate) async fn run_prompt(
     use devo_core::SessionConfig;
     use devo_core::SessionState;
     use devo_core::default_base_instructions;
-    use devo_tools::ToolRegistry;
     use devo_tools::ToolRuntime;
 
     let cwd = std::env::current_dir()?;
@@ -48,8 +47,7 @@ pub(crate) async fn run_prompt(
     session_state.push_message(devo_core::Message::user(input.to_string()));
 
     let registry = {
-        let mut reg = ToolRegistry::new();
-        devo_tools::register_builtin_tools(&mut reg);
+        let reg = devo_tools::create_default_tool_registry();
         std::sync::Arc::new(reg)
     };
     let runtime = ToolRuntime::new_without_permissions(std::sync::Arc::clone(&registry));

crates/client/src/stdio.rs

@@ -7,6 +7,7 @@ use std::sync::atomic::Ordering;
 
 use anyhow::Context;
 use anyhow::Result;
+use devo_protocol::ApprovalRespondParams;
 use devo_protocol::ClientNotification;
 use devo_protocol::ClientRequest;
 use devo_protocol::ClientTransportKind;
@@ -28,6 +29,8 @@ use devo_protocol::SessionListParams;
 use devo_protocol::SessionListResult;
 use devo_protocol::SessionMetadataUpdateParams;
 use devo_protocol::SessionMetadataUpdateResult;
+use devo_protocol::SessionPermissionsUpdateParams;
+use devo_protocol::SessionPermissionsUpdateResult;
 use devo_protocol::SessionResumeParams;
 use devo_protocol::SessionResumeResult;
 use devo_protocol::SessionRollbackParams;
@@ -184,6 +187,13 @@ impl StdioServerClient {
         self.request("session/metadata/update", params).await
     }
 
+    pub async fn session_permissions_update(
+        &mut self,
+        params: SessionPermissionsUpdateParams,
+    ) -> Result<SessionPermissionsUpdateResult> {
+        self.request("session/permissions/update", params).await
+    }
+
     pub async fn session_compact(
         &mut self,
         params: SessionCompactParams,
@@ -239,6 +249,11 @@ impl StdioServerClient {
         self.request("turn/steer", params).await
     }
 
+    pub async fn approval_respond(&mut self, params: ApprovalRespondParams) -> Result<()> {
+        let _: serde_json::Value = self.request("approval/respond", params).await?;
+        Ok(())
+    }
+
     pub async fn recv_notification(&mut self) -> Option<ServerNotificationMessage> {
         self.notifications_rx.recv().await
     }

crates/core/src/config/app.rs

@@ -1,10 +1,13 @@
+use std::collections::BTreeMap;
 use std::collections::HashSet;
 use std::fs;
 use std::path::{Path, PathBuf};
 
+use devo_protocol::PermissionPreset;
 use serde::{Deserialize, Serialize};
 
 use devo_utils::FileSystemConfigPathResolver;
+use devo_utils::git_op::get_git_repo_root;
 
 use crate::AgentsMdConfig;
 use crate::SkillsConfig;
@@ -35,6 +38,15 @@ pub struct AppConfig {
     /// TODO: Not sure what's purpose of `project_root_markers`?
     /// Marker names used when discovering a project root.
     pub project_root_markers: Vec<String>,
+    /// User-level settings remembered per project key.
+    pub projects: BTreeMap<String, ProjectConfig>,
+}
+
+/// Settings remembered for one project.
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize, Default)]
+pub struct ProjectConfig {
+    /// Permission preset to use when starting new sessions for this project.
+    pub permission_preset: Option<PermissionPreset>,
 }
 
 /// Controls how the CLI checks for new releases at startup.
@@ -118,6 +130,7 @@ impl Default for AppConfig {
                 check_interval_hours: 24,
             },
             project_root_markers: vec![".git".into()],
+            projects: BTreeMap::new(),
         }
     }
 }
@@ -131,6 +144,28 @@ impl AppConfig {
     }
 }
 
+/// Returns the stable key used to remember project-level permission settings.
+///
+/// Git repositories are keyed by their repository root. Non-git directories fall
+/// back to the canonical current working directory when possible.
+pub fn project_config_key(cwd: &Path) -> String {
+    let root = get_git_repo_root(cwd)
+        .or_else(|| cwd.canonicalize().ok())
+        .unwrap_or_else(|| cwd.to_path_buf());
+    strip_unc_prefix(root).display().to_string()
+}
+
+fn strip_unc_prefix(path: PathBuf) -> PathBuf {
+    #[cfg(windows)]
+    {
+        let value = path.display().to_string();
+        if let Some(stripped) = value.strip_prefix("\\\\?\\") {
+            return PathBuf::from(stripped);
+        }
+    }
+    path
+}
+
 fn read_config_value(path: &Path) -> Result<toml::Value, AppConfigError> {
     let contents = fs::read_to_string(path).map_err(|source| AppConfigError::Io {
         path: path.to_path_buf(),