huskies: merge 626_refactor_introduce_services_bundle_and_migrate_appcontext_matrix_transport

server/src/http/agents.rs

@@ -215,12 +215,13 @@ impl AgentsApi {
     ) -> OpenApiResult<Json<AgentInfoResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
 
         let info = svc::start_agent(
-            &self.ctx.agents,
+            &self.ctx.services.agents,
             &project_root,
             &payload.0.story_id,
             payload.0.agent_name.as_deref(),
@@ -244,12 +245,13 @@ impl AgentsApi {
     async fn stop_agent(&self, payload: Json<StopAgentPayload>) -> OpenApiResult<Json<bool>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
 
         svc::stop_agent(
-            &self.ctx.agents,
+            &self.ctx.services.agents,
             &project_root,
             &payload.0.story_id,
             &payload.0.agent_name,
@@ -267,9 +269,14 @@ impl AgentsApi {
     /// on frontend startup.
     #[oai(path = "/agents", method = "get")]
     async fn list_agents(&self) -> OpenApiResult<Json<Vec<AgentInfoResponse>>> {
-        let project_root = self.ctx.agents.get_project_root(&self.ctx.state).ok();
-        let agents =
-            svc::list_agents(&self.ctx.agents, project_root.as_deref()).map_err(map_svc_error)?;
+        let project_root = self
+            .ctx
+            .services
+            .agents
+            .get_project_root(&self.ctx.state)
+            .ok();
+        let agents = svc::list_agents(&self.ctx.services.agents, project_root.as_deref())
+            .map_err(map_svc_error)?;
 
         Ok(Json(
             agents
@@ -290,6 +297,7 @@ impl AgentsApi {
     async fn get_agent_config(&self) -> OpenApiResult<Json<Vec<AgentConfigInfoResponse>>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -308,6 +316,7 @@ impl AgentsApi {
     async fn reload_config(&self) -> OpenApiResult<Json<Vec<AgentConfigInfoResponse>>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -329,13 +338,18 @@ impl AgentsApi {
     ) -> OpenApiResult<Json<WorktreeInfoResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
 
-        let info = svc::create_worktree(&self.ctx.agents, &project_root, &payload.0.story_id)
-            .await
-            .map_err(map_svc_error)?;
+        let info = svc::create_worktree(
+            &self.ctx.services.agents,
+            &project_root,
+            &payload.0.story_id,
+        )
+        .await
+        .map_err(map_svc_error)?;
 
         Ok(Json(WorktreeInfoResponse {
             story_id: payload.0.story_id,
@@ -350,6 +364,7 @@ impl AgentsApi {
     async fn list_worktrees(&self) -> OpenApiResult<Json<Vec<WorktreeListEntry>>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -378,6 +393,7 @@ impl AgentsApi {
     ) -> OpenApiResult<Json<WorkItemContentResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -417,6 +433,7 @@ impl AgentsApi {
         // Slow path: fall back to results persisted in the story file.
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -446,6 +463,7 @@ impl AgentsApi {
     ) -> OpenApiResult<Json<AgentOutputResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -461,6 +479,7 @@ impl AgentsApi {
     async fn remove_worktree(&self, story_id: Path<String>) -> OpenApiResult<Json<bool>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -483,6 +502,7 @@ impl AgentsApi {
     ) -> OpenApiResult<Json<TokenCostResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -517,6 +537,7 @@ impl AgentsApi {
     async fn get_all_token_usage(&self) -> OpenApiResult<Json<AllTokenUsageResponse>> {
         let project_root = self
             .ctx
+            .services
             .agents
             .get_project_root(&self.ctx.state)
             .map_err(bad_request)?;
@@ -604,9 +625,13 @@ mod tests {
 
         let ctx = AppContext::new_test(root);
         // Inject an agent for the archived story (completed) and one for an active story
-        ctx.agents
-            .inject_test_agent("79_story_archived", "coder-1", AgentStatus::Completed);
-        ctx.agents
+        ctx.services.agents.inject_test_agent(
+            "79_story_archived",
+            "coder-1",
+            AgentStatus::Completed,
+        );
+        ctx.services
+            .agents
             .inject_test_agent("80_story_active", "coder-1", AgentStatus::Running);
 
         let api = AgentsApi { ctx: Arc::new(ctx) };
@@ -631,8 +656,11 @@ mod tests {
         let ctx = AppContext::new_test(tmp.path().to_path_buf());
         // Clear the project_root so get_project_root returns Err
         *ctx.state.project_root.lock().unwrap() = None;
-        ctx.agents
-            .inject_test_agent("42_story_whatever", "coder-1", AgentStatus::Completed);
+        ctx.services.agents.inject_test_agent(
+            "42_story_whatever",
+            "coder-1",
+            AgentStatus::Completed,
+        );
 
         let api = AgentsApi { ctx: Arc::new(ctx) };
         let result = api.list_agents().await.unwrap().0;
@@ -821,7 +849,8 @@ allowed_tools = ["Read", "Bash"]
     async fn stop_agent_succeeds_with_running_agent() {
         let tmp = TempDir::new().unwrap();
         let ctx = AppContext::new_test(tmp.path().to_path_buf());
-        ctx.agents
+        ctx.services
+            .agents
             .inject_test_agent("42_story_foo", "coder-1", AgentStatus::Running);
         let api = AgentsApi { ctx: Arc::new(ctx) };
         let result = api

server/src/http/agents_sse.rs

@@ -18,7 +18,7 @@ pub async fn agent_stream(
     Path((story_id, agent_name)): Path<(String, String)>,
     ctx: Data<&Arc<AppContext>>,
 ) -> impl IntoResponse {
-    let mut rx = match ctx.agents.subscribe(&story_id, &agent_name) {
+    let mut rx = match ctx.services.agents.subscribe(&story_id, &agent_name) {
         Ok(rx) => rx,
         Err(e) => {
             return Response::builder()
@@ -89,6 +89,7 @@ mod tests {
 
         // Inject a running agent and get its broadcast sender.
         let tx = ctx
+            .services
             .agents
             .inject_test_agent("1_story", "coder-1", AgentStatus::Running);
 
@@ -152,6 +153,7 @@ mod tests {
         let ctx = Arc::new(AppContext::new_test(tmp.path().to_path_buf()));
 
         let tx = ctx
+            .services
             .agents
             .inject_test_agent("2_story", "coder-1", AgentStatus::Running);
 

server/src/http/bot_command.rs

@@ -66,7 +66,7 @@ impl BotCommandApi {
         let cmd = body.command.trim().to_ascii_lowercase();
         let args = body.args.trim();
 
-        let response = svc::execute(&cmd, args, &project_root, &self.ctx.agents)
+        let response = svc::execute(&cmd, args, &project_root, &self.ctx.services.agents)
             .await
             .map_err(|e| match e {
                 svc::Error::UnknownCommand(msg) => {

server/src/http/context.rs

@@ -1,8 +1,9 @@
 //! Application context — shared state (`AppContext`) threaded through all HTTP handlers.
-use crate::agents::{AgentPool, ReconciliationEvent};
+use crate::agents::ReconciliationEvent;
 use crate::io::watcher::WatcherEvent;
 use crate::rebuild::{BotShutdownNotifier, ShutdownReason};
 use crate::service::timer::TimerStore;
+use crate::services::Services;
 use crate::state::SessionState;
 use crate::store::JsonFileStore;
 use crate::workflow::WorkflowState;
@@ -64,7 +65,8 @@ pub struct AppContext {
     pub state: Arc<SessionState>,
     pub store: Arc<JsonFileStore>,
     pub workflow: Arc<std::sync::Mutex<WorkflowState>>,
-    pub agents: Arc<AgentPool>,
+    /// Shared services bundle (agent pool, bot identity, permissions, etc.).
+    pub services: Arc<Services>,
     /// Broadcast channel for filesystem watcher events. WebSocket handlers
     /// subscribe to this to push lifecycle notifications to connected clients.
     pub watcher_tx: broadcast::Sender<WatcherEvent>,
@@ -76,9 +78,6 @@ pub struct AppContext {
     /// `prompt_permission` tool. The MCP handler sends a [`PermissionForward`]
     /// and awaits the oneshot response.
     pub perm_tx: mpsc::UnboundedSender<PermissionForward>,
-    /// Receiver for permission requests. The active WebSocket handler locks
-    /// this and polls for incoming permission forwards.
-    pub perm_rx: Arc<tokio::sync::Mutex<mpsc::UnboundedReceiver<PermissionForward>>>,
     /// Child process of the QA app launched for manual testing.
     /// Only one instance runs at a time.
     pub qa_app_process: Arc<std::sync::Mutex<Option<std::process::Child>>>,
@@ -110,6 +109,7 @@ pub struct AppContext {
 #[cfg(test)]
 impl AppContext {
     pub fn new_test(project_root: std::path::PathBuf) -> Self {
+        use crate::agents::AgentPool;
         let state = SessionState::default();
         *state.project_root.lock().unwrap() = Some(project_root.clone());
         let store_path = project_root.join(".huskies_store.json");
@@ -119,15 +119,24 @@ impl AppContext {
         let timer_store = Arc::new(TimerStore::load(
             project_root.join(".huskies").join("timers.json"),
         ));
+        let services = Arc::new(Services {
+            project_root: project_root.clone(),
+            agents: Arc::new(AgentPool::new(3001, watcher_tx.clone())),
+            bot_name: "Assistant".to_string(),
+            bot_user_id: String::new(),
+            ambient_rooms: Arc::new(std::sync::Mutex::new(std::collections::HashSet::new())),
+            perm_rx: Arc::new(tokio::sync::Mutex::new(perm_rx)),
+            pending_perm_replies: Arc::new(tokio::sync::Mutex::new(HashMap::new())),
+            permission_timeout_secs: 120,
+        });
         Self {
             state: Arc::new(state),
             store: Arc::new(JsonFileStore::new(store_path).unwrap()),
             workflow: Arc::new(std::sync::Mutex::new(WorkflowState::default())),
-            agents: Arc::new(AgentPool::new(3001, watcher_tx.clone())),
+            services,
             watcher_tx,
             reconciliation_tx,
             perm_tx,
-            perm_rx: Arc::new(tokio::sync::Mutex::new(perm_rx)),
             qa_app_process: Arc::new(std::sync::Mutex::new(None)),
             bot_shutdown: None,
             matrix_shutdown_tx: None,

server/src/http/mcp/agent_tools.rs

@@ -14,8 +14,9 @@ pub(super) async fn tool_start_agent(args: &Value, ctx: &AppContext) -> Result<S
         .ok_or("Missing required argument: story_id")?;
     let agent_name = args.get("agent_name").and_then(|v| v.as_str());
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let info = ctx
+        .services
         .agents
         .start_agent(&project_root, story_id, agent_name, None, None)
         .await?;
@@ -67,8 +68,9 @@ pub(super) async fn tool_stop_agent(args: &Value, ctx: &AppContext) -> Result<St
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: agent_name")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
-    ctx.agents
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
+    ctx.services
+        .agents
         .stop_agent(&project_root, story_id, agent_name)
         .await?;
 
@@ -78,8 +80,8 @@ pub(super) async fn tool_stop_agent(args: &Value, ctx: &AppContext) -> Result<St
 }
 
 pub(super) fn tool_list_agents(ctx: &AppContext) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state).ok();
-    let agents = ctx.agents.list_agents()?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state).ok();
+    let agents = ctx.services.agents.list_agents()?;
     serde_json::to_string_pretty(&json!(
         agents
             .iter()
@@ -125,7 +127,7 @@ pub(super) async fn tool_get_agent_output(
         .map(|n| n as usize);
     let filter = args.get("filter").and_then(|v| v.as_str());
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Collect all matching log files, oldest first.
     let log_files = agent_log::list_story_log_files(&project_root, story_id, agent_name_filter);
@@ -149,7 +151,7 @@ pub(super) async fn tool_get_agent_output(
     // writer failed and nothing was persisted to disk.
     if log_files.is_empty()
         && let Some(agent_name) = agent_name_filter
-        && let Ok(live_events) = ctx.agents.drain_events(story_id, agent_name)
+        && let Ok(live_events) = ctx.services.agents.drain_events(story_id, agent_name)
         && !live_events.is_empty()
     {
         all_lines.push(format!("=== {agent_name} (live) ==="));
@@ -195,7 +197,7 @@ pub(super) async fn tool_get_agent_output(
 }
 
 pub(super) fn tool_get_agent_config(ctx: &AppContext) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let config = ProjectConfig::load(&project_root)?;
 
     // Collect available (idle) agent names across all stages so the caller can
@@ -207,7 +209,11 @@ pub(super) fn tool_get_agent_config(ctx: &AppContext) -> Result<String, String>
         PipelineStage::Mergemaster,
         PipelineStage::Other,
     ] {
-        if let Ok(names) = ctx.agents.available_agents_for_stage(&config, stage) {
+        if let Ok(names) = ctx
+            .services
+            .agents
+            .available_agents_for_stage(&config, stage)
+        {
             available_names.extend(names);
         }
     }
@@ -249,7 +255,7 @@ pub(super) fn tool_get_agent_remaining_turns_and_budget(
         .ok_or("Missing required argument: agent_name")?;
 
     // Verify the agent exists and is running/pending.
-    let agents = ctx.agents.list_agents()?;
+    let agents = ctx.services.agents.list_agents()?;
     let agent_info = agents
         .iter()
         .find(|a| a.story_id == story_id && a.agent_name == agent_name)
@@ -275,7 +281,7 @@ pub(super) fn tool_get_agent_remaining_turns_and_budget(
         ));
     }
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let config = ProjectConfig::load(&project_root)?;
 
     // Find the agent config (max_turns, max_budget_usd).
@@ -341,6 +347,7 @@ pub(super) async fn tool_wait_for_agent(args: &Value, ctx: &AppContext) -> Resul
         .unwrap_or(300_000); // default: 5 minutes
 
     let info = ctx
+        .services
         .agents
         .wait_for_agent(story_id, agent_name, timeout_ms)
         .await?;
@@ -377,8 +384,12 @@ pub(super) async fn tool_create_worktree(args: &Value, ctx: &AppContext) -> Resu
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
-    let info = ctx.agents.create_worktree(&project_root, story_id).await?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
+    let info = ctx
+        .services
+        .agents
+        .create_worktree(&project_root, story_id)
+        .await?;
 
     serde_json::to_string_pretty(&json!({
         "story_id": story_id,
@@ -390,7 +401,7 @@ pub(super) async fn tool_create_worktree(args: &Value, ctx: &AppContext) -> Resu
 }
 
 pub(super) fn tool_list_worktrees(ctx: &AppContext) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let entries = worktree::list_worktrees(&project_root)?;
 
     serde_json::to_string_pretty(&json!(
@@ -411,7 +422,7 @@ pub(super) async fn tool_remove_worktree(args: &Value, ctx: &AppContext) -> Resu
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let config = ProjectConfig::load(&project_root)?;
     worktree::remove_worktree_by_story_id(&project_root, story_id, &config).await?;
 
@@ -876,7 +887,8 @@ stage = "coder"
         use crate::agents::AgentStatus;
         let tmp = tempfile::tempdir().unwrap();
         let ctx = test_ctx(tmp.path());
-        ctx.agents
+        ctx.services
+            .agents
             .inject_test_agent("41_story", "worker", AgentStatus::Completed);
 
         let result = tool_wait_for_agent(
@@ -980,7 +992,8 @@ stage = "coder"
         use crate::agents::AgentStatus;
         let tmp = tempfile::tempdir().unwrap();
         let ctx = test_ctx(tmp.path());
-        ctx.agents
+        ctx.services
+            .agents
             .inject_test_agent("42_story", "coder-1", AgentStatus::Completed);
 
         let result = tool_get_agent_remaining_turns_and_budget(
@@ -1004,7 +1017,8 @@ stage = "coder"
         let ctx = test_ctx(tmp.path());
         ctx.store
             .set("project_root", json!(tmp.path().to_string_lossy().as_ref()));
-        ctx.agents
+        ctx.services
+            .agents
             .inject_test_agent("42_story", "coder-1", AgentStatus::Running);
 
         let result = tool_get_agent_remaining_turns_and_budget(

server/src/http/mcp/diagnostics.rs

@@ -46,7 +46,7 @@ pub(super) async fn tool_rebuild_and_restart(ctx: &AppContext) -> Result<String,
 
     let project_root = ctx.state.get_project_root().unwrap_or_default();
     let notifier = ctx.bot_shutdown.as_deref();
-    crate::rebuild::rebuild_and_restart(&ctx.agents, &project_root, notifier).await
+    crate::rebuild::rebuild_and_restart(&ctx.services.agents, &project_root, notifier).await
 }
 
 /// MCP tool called by Claude Code via `--permission-prompt-tool`.
@@ -84,7 +84,7 @@ pub(super) async fn tool_prompt_permission(
     // Without this check, agent permission requests queue in the channel and
     // get forwarded to Matrix/Slack/etc. at the start of the next user session,
     // flooding chat with stale agent prompts.
-    if ctx.perm_rx.try_lock().is_ok() {
+    if ctx.services.perm_rx.try_lock().is_ok() {
         crate::slog!(
             "[permission] Auto-denied '{tool_name}' (no interactive session — agent mode)"
         );
@@ -212,7 +212,7 @@ pub(super) fn tool_move_story(args: &Value, ctx: &AppContext) -> Result<String,
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: target_stage")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     let (from_stage, to_stage) = move_story_to_stage(&project_root, story_id, target_stage)?;
 
@@ -273,7 +273,7 @@ pub(super) fn tool_get_version(ctx: &AppContext) -> Result<String, String> {
     serde_json::to_string_pretty(&json!({
         "version": env!("CARGO_PKG_VERSION"),
         "build_hash": build_hash.trim(),
-        "port": ctx.agents.port(),
+        "port": ctx.services.agents.port(),
     }))
     .map_err(|e| format!("Serialization error: {e}"))
 }
@@ -420,7 +420,7 @@ mod tests {
         // then respond with approval. The try_lock() inside tool_prompt_permission
         // must fail (lock held) so the request is forwarded rather than auto-denied.
         let (ready_tx, ready_rx) = tokio::sync::oneshot::channel::<()>();
-        let perm_rx = ctx.perm_rx.clone();
+        let perm_rx = ctx.services.perm_rx.clone();
         tokio::spawn(async move {
             let mut rx = perm_rx.lock().await;
             let _ = ready_tx.send(()); // signal: lock is held
@@ -459,7 +459,7 @@ mod tests {
 
         // Simulate an interactive session: lock perm_rx first, then deny.
         let (ready_tx, ready_rx) = tokio::sync::oneshot::channel::<()>();
-        let perm_rx = ctx.perm_rx.clone();
+        let perm_rx = ctx.services.perm_rx.clone();
         tokio::spawn(async move {
             let mut rx = perm_rx.lock().await;
             let _ = ready_tx.send(()); // signal: lock is held
@@ -637,8 +637,8 @@ mod tests {
         // then exec() will be called — which would replace our test process.
         // So we only test that the function *runs* without panicking up to
         // the agent-kill step. We do this by checking the pool is empty.
-        assert_eq!(ctx.agents.list_agents().unwrap().len(), 0);
-        ctx.agents.kill_all_children(); // should not panic on empty pool
+        assert_eq!(ctx.services.agents.list_agents().unwrap().len(), 0);
+        ctx.services.agents.kill_all_children(); // should not panic on empty pool
     }
 
     #[test]

server/src/http/mcp/git_tools.rs

@@ -12,7 +12,7 @@ use std::path::PathBuf;
 /// Thin wrapper that obtains the project root from `ctx` and delegates to
 /// `service::git_ops::io::validate_worktree_path`.
 fn validate_worktree_path(worktree_path: &str, ctx: &AppContext) -> Result<PathBuf, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     crate::service::git_ops::io::validate_worktree_path(worktree_path, &project_root)
         .map_err(|e| e.to_string())
 }

server/src/http/mcp/merge_tools.rs

@@ -32,15 +32,17 @@ pub(super) async fn tool_merge_agent_work(
         .map_err(|e| format!("Serialization error: {e}"));
     }
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
-    ctx.agents.start_merge_agent_work(&project_root, story_id)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
+    ctx.services
+        .agents
+        .start_merge_agent_work(&project_root, story_id)?;
 
     // Block until the merge completes instead of returning immediately.
     // Uses tokio::time::sleep so the async executor is not blocked.
     // This prevents the mergemaster from burning all its turns polling
     // get_merge_status in a tight loop.
     let sid = story_id.to_string();
-    let agents = ctx.agents.clone();
+    let agents = ctx.services.agents.clone();
     loop {
         tokio::time::sleep(std::time::Duration::from_secs(10)).await;
         if let Some(job) = agents.get_merge_status(&sid) {
@@ -64,9 +66,13 @@ pub(super) fn tool_get_merge_status(args: &Value, ctx: &AppContext) -> Result<St
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let job = ctx.agents.get_merge_status(story_id).ok_or_else(|| {
-        format!("No merge job found for story '{story_id}'. Call merge_agent_work first.")
-    })?;
+    let job = ctx
+        .services
+        .agents
+        .get_merge_status(story_id)
+        .ok_or_else(|| {
+            format!("No merge job found for story '{story_id}'. Call merge_agent_work first.")
+        })?;
 
     match &job.status {
         crate::agents::merge::MergeJobStatus::Running => {
@@ -130,13 +136,14 @@ pub(super) async fn tool_move_story_to_merge(
         .and_then(|v| v.as_str())
         .unwrap_or("mergemaster");
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Move story from work/2_current/ to work/4_merge/
     move_story_to_merge(&project_root, story_id)?;
 
     // Start the mergemaster agent on the story worktree
     let info = ctx
+        .services
         .agents
         .start_agent(&project_root, story_id, Some(agent_name), None, None)
         .await?;
@@ -165,7 +172,7 @@ pub(super) fn tool_report_merge_failure(args: &Value, ctx: &AppContext) -> Resul
         .ok_or("Missing required argument: reason")?;
 
     slog!("[mergemaster] Merge failure reported for '{story_id}': {reason}");
-    ctx.agents.set_merge_failure_reported(story_id);
+    ctx.services.agents.set_merge_failure_reported(story_id);
 
     // Broadcast the failure so the Matrix notification listener can post an
     // error message to configured rooms without coupling this tool to the bot.

server/src/http/mcp/qa_tools.rs

@@ -21,13 +21,14 @@ pub(super) async fn tool_request_qa(args: &Value, ctx: &AppContext) -> Result<St
         .and_then(|v| v.as_str())
         .unwrap_or("qa");
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Move story from work/2_current/ to work/3_qa/
     move_story_to_qa(&project_root, story_id)?;
 
     // Start the QA agent on the story worktree
     let info = ctx
+        .services
         .agents
         .start_agent(&project_root, story_id, Some(agent_name), None, None)
         .await?;
@@ -51,7 +52,7 @@ pub(super) async fn tool_approve_qa(args: &Value, ctx: &AppContext) -> Result<St
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Clear review_hold before moving
     let qa_path = project_root
@@ -76,7 +77,7 @@ pub(super) async fn tool_approve_qa(args: &Value, ctx: &AppContext) -> Result<St
 
         move_story_to_done(&project_root, story_id)?;
 
-        let pool = std::sync::Arc::clone(&ctx.agents);
+        let pool = std::sync::Arc::clone(&ctx.services.agents);
         pool.remove_agents_for_story(story_id);
 
         let wt_path = crate::worktree::worktree_path(&project_root, story_id);
@@ -102,6 +103,7 @@ pub(super) async fn tool_approve_qa(args: &Value, ctx: &AppContext) -> Result<St
 
         // Start the mergemaster agent
         let info = ctx
+            .services
             .agents
             .start_agent(&project_root, story_id, Some("mergemaster"), None, None)
             .await?;
@@ -129,7 +131,7 @@ pub(super) async fn tool_reject_qa(args: &Value, ctx: &AppContext) -> Result<Str
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: notes")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Move story from work/3_qa/ back to work/2_current/ with rejection notes
     reject_story_from_qa(&project_root, story_id, notes)?;
@@ -155,6 +157,7 @@ pub(super) async fn tool_reject_qa(args: &Value, ctx: &AppContext) -> Result<Str
          Please fix the issues described above and try again."
     );
     if let Err(e) = ctx
+        .services
         .agents
         .start_agent(
             &project_root,
@@ -179,7 +182,7 @@ pub(super) async fn tool_launch_qa_app(args: &Value, ctx: &AppContext) -> Result
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Find the worktree path for this story
     let worktrees = crate::worktree::list_worktrees(&project_root)?;

server/src/http/mcp/shell_tools.rs

@@ -22,7 +22,7 @@ const MAX_OUTPUT_LINES: usize = 100;
 /// Thin wrapper that obtains the project root from `ctx` and delegates to
 /// `service::shell::io::validate_working_dir`.
 fn validate_working_dir(working_dir: &str, ctx: &AppContext) -> Result<PathBuf, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     crate::service::shell::io::validate_working_dir(working_dir, &project_root)
         .map_err(|e| e.to_string())
 }
@@ -264,7 +264,7 @@ pub(super) fn handle_run_command_sse(
 ///
 /// The child process is properly killed on timeout (no zombies).
 pub(super) async fn tool_run_tests(args: &Value, ctx: &AppContext) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     let working_dir = match args.get("worktree_path").and_then(|v| v.as_str()) {
         Some(wt) => validate_working_dir(wt, ctx)?,
@@ -423,7 +423,7 @@ const TEST_POLL_BLOCK_SECS: u64 = 20;
 /// when the test finishes, or after 15s with `{"status": "running"}`.
 /// This server-side blocking prevents agents from wasting turns polling.
 pub(super) async fn tool_get_test_result(args: &Value, ctx: &AppContext) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     let working_dir = match args.get("worktree_path").and_then(|v| v.as_str()) {
         Some(wt) => validate_working_dir(wt, ctx)?,
@@ -563,7 +563,7 @@ async fn run_script_tool(
     args: &Value,
     ctx: &AppContext,
 ) -> Result<String, String> {
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     let working_dir = match args.get("worktree_path").and_then(|v| v.as_str()) {
         Some(wt) => validate_working_dir(wt, ctx)?,

server/src/http/mcp/story_tools.rs

@@ -300,7 +300,7 @@ pub(super) fn tool_accept_story(args: &Value, ctx: &AppContext) -> Result<String
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
 
     // Bug 226: Refuse to accept if the feature branch has unmerged code.
     // The code must be squash-merged via merge_agent_work first.
@@ -313,7 +313,7 @@ pub(super) fn tool_accept_story(args: &Value, ctx: &AppContext) -> Result<String
     }
 
     move_story_to_done(&project_root, story_id)?;
-    ctx.agents.remove_agents_for_story(story_id);
+    ctx.services.agents.remove_agents_for_story(story_id);
 
     Ok(format!(
         "Story '{story_id}' accepted, moved to done/, and committed to master."
@@ -521,9 +521,9 @@ pub(super) fn tool_close_bug(args: &Value, ctx: &AppContext) -> Result<String, S
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: bug_id")?;
 
-    let root = ctx.agents.get_project_root(&ctx.state)?;
+    let root = ctx.services.agents.get_project_root(&ctx.state)?;
     close_bug_to_archive(&root, bug_id)?;
-    ctx.agents.remove_agents_for_story(bug_id);
+    ctx.services.agents.remove_agents_for_story(bug_id);
 
     Ok(format!(
         "Bug '{bug_id}' closed, moved to bugs/archive/, and committed to master."
@@ -557,7 +557,7 @@ pub(super) async fn tool_delete_story(args: &Value, ctx: &AppContext) -> Result<
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
 
-    let project_root = ctx.agents.get_project_root(&ctx.state)?;
+    let project_root = ctx.services.agents.get_project_root(&ctx.state)?;
     let mut failed_steps: Vec<String> = Vec::new();
 
     // 0. Cancel any pending rate-limit retry timers for this story (bug 514).
@@ -571,9 +571,10 @@ pub(super) async fn tool_delete_story(args: &Value, ctx: &AppContext) -> Result<
     }
 
     // 1. Stop any running agents for this story (best-effort).
-    if let Ok(agents) = ctx.agents.list_agents() {
+    if let Ok(agents) = ctx.services.agents.list_agents() {
         for agent in agents.iter().filter(|a| a.story_id == story_id) {
             match ctx
+                .services
                 .agents
                 .stop_agent(&project_root, story_id, &agent.agent_name)
                 .await
@@ -596,7 +597,7 @@ pub(super) async fn tool_delete_story(args: &Value, ctx: &AppContext) -> Result<
     }
 
     // 2. Remove agent pool entries.
-    let removed_count = ctx.agents.remove_agents_for_story(story_id);
+    let removed_count = ctx.services.agents.remove_agents_for_story(story_id);
     slog_warn!("[delete_story] Removed {removed_count} agent pool entries for '{story_id}'");
 
     // 3. Remove worktree (best-effort).
@@ -903,7 +904,7 @@ mod tests {
         );
 
         let ctx = test_ctx(tmp.path());
-        ctx.agents.inject_test_agent(
+        ctx.services.agents.inject_test_agent(
             "9921_story_active",
             "coder-1",
             crate::agents::AgentStatus::Running,

server/src/http/project.rs

@@ -52,7 +52,7 @@ impl ProjectApi {
             payload.0.path,
             &self.ctx.state,
             self.ctx.store.as_ref(),
-            self.ctx.agents.port(),
+            self.ctx.services.agents.port(),
         )
         .await
         .map_err(map_project_error)?;

server/src/http/workflow/mod.rs

@@ -164,7 +164,7 @@ pub fn load_pipeline_state(ctx: &AppContext) -> Result<PipelineState, String> {
 
 /// Build a map from story_id → AgentAssignment for all pending/running agents.
 fn build_active_agent_map(ctx: &AppContext) -> HashMap<String, AgentAssignment> {
-    let agents = match ctx.agents.list_agents() {
+    let agents = match ctx.services.agents.list_agents() {
         Ok(a) => a,
         Err(_) => return HashMap::new(),
     };
@@ -569,7 +569,7 @@ mod tests {
         );
 
         let ctx = crate::http::context::AppContext::new_test(root);
-        ctx.agents.inject_test_agent(
+        ctx.services.agents.inject_test_agent(
             "9860_story_test",
             "coder-1",
             crate::agents::AgentStatus::Running,
@@ -604,7 +604,7 @@ mod tests {
         );
 
         let ctx = crate::http::context::AppContext::new_test(root);
-        ctx.agents.inject_test_agent(
+        ctx.services.agents.inject_test_agent(
             "9861_story_done",
             "coder-1",
             crate::agents::AgentStatus::Completed,
@@ -636,7 +636,7 @@ mod tests {
         );
 
         let ctx = crate::http::context::AppContext::new_test(root);
-        ctx.agents.inject_test_agent(
+        ctx.services.agents.inject_test_agent(
             "9862_story_pending",
             "coder-1",
             crate::agents::AgentStatus::Pending,

server/src/http/ws.rs

@@ -102,7 +102,7 @@ pub async fn ws_handler(ws: WebSocket, ctx: Data<&Arc<AppContext>>) -> impl poem
                     );
                     tokio::pin!(chat_fut);
 
-                    let mut perm_rx = ctx.perm_rx.lock().await;
+                    let mut perm_rx = ctx.services.perm_rx.lock().await;
 
                     let chat_result = loop {
                         tokio::select! {