fix: reconcile:on blocking, pending question notifications, and infra improvements (#73)

* feat: soryu-co/soryu - makima: Fix contracts page overflow - constrain layout to viewport height

* feat: soryu-co/soryu - makima: Add git fetch to create_worktree and improve completion prompt merge conflict handling

* WIP: heartbeat checkpoint

* feat: soryu-co/soryu - makima: Add pending question notification badge to directive sidebar and nav

* feat: soryu-co/soryu - makima: Fix reconcile:on blocking - make phaseguard poll indefinitely instead of returning immediately

4 files changed, 41 insertions, 99 deletions

diff --git a/makima/frontend/src/components/NavStrip.tsx b/makima/frontend/src/components/NavStrip.tsx
index 117f4e1..4932427 100644
--- a/makima/frontend/src/components/NavStrip.tsx
+++ b/makima/frontend/src/components/NavStrip.tsx
@@ -1,4 +1,5 @@
 import { useAuth } from "../contexts/AuthContext";
+import { useSupervisorQuestions } from "../contexts/SupervisorQuestionsContext";
 import { RewriteLink } from "./RewriteLink";
 
 interface NavLink {
@@ -19,6 +20,8 @@ const NAV_LINKS: NavLink[] = [
 
 export function NavStrip() {
   const { isAuthenticated, isAuthConfigured, signOut, user } = useAuth();
+  const { pendingQuestions } = useSupervisorQuestions();
+  const directiveQuestionCount = pendingQuestions.filter(q => q.directiveId).length;
 
   const handleSignOut = async () => {
     await signOut();
@@ -38,14 +41,18 @@ export function NavStrip() {
       </span>
       <div className="flex flex-wrap gap-2 items-center flex-1">
         {NAV_LINKS.map((link) => (
-          <RewriteLink
-            key={link.label}
-            to={link.href}
-            disabled={link.requiresAuth && !hasAccess}
-            external={link.external}
-          >
-            {link.label}
-          </RewriteLink>
+          <span key={link.label} className="relative inline-flex items-center">
+            <RewriteLink
+              to={link.href}
+              disabled={link.requiresAuth && !hasAccess}
+              external={link.external}
+            >
+              {link.label}
+            </RewriteLink>
+            {link.label === "Directives" && directiveQuestionCount > 0 && (
+              <span className="ml-0.5 inline-block w-2 h-2 rounded-full bg-amber-400 animate-pulse" title={`${directiveQuestionCount} pending question(s)`} />
+            )}
+          </span>
         ))}
       </div>
       <div className="flex items-center gap-2 pl-2.5 border-l border-[rgba(117,170,252,0.35)]">
diff --git a/makima/frontend/src/components/directives/DirectiveList.tsx b/makima/frontend/src/components/directives/DirectiveList.tsx
index 6393ea7..6a9c486 100644
--- a/makima/frontend/src/components/directives/DirectiveList.tsx
+++ b/makima/frontend/src/components/directives/DirectiveList.tsx
@@ -1,4 +1,6 @@
+import { useMemo } from "react";
 import type { DirectiveSummary, DirectiveStatus } from "../../lib/api";
+import { useSupervisorQuestions } from "../../contexts/SupervisorQuestionsContext";
 
 const STATUS_BADGE: Record<DirectiveStatus, { color: string; label: string }> = {
   draft: { color: "text-[#7788aa] border-[#2a3a5a]", label: "DRAFT" },
@@ -16,6 +18,18 @@ interface DirectiveListProps {
 }
 
 export function DirectiveList({ directives, selectedId, onSelect, onCreate }: DirectiveListProps) {
+  const { pendingQuestions } = useSupervisorQuestions();
+
+  const questionsPerDirective = useMemo(() => {
+    const counts = new Map<string, number>();
+    for (const q of pendingQuestions) {
+      if (q.directiveId) {
+        counts.set(q.directiveId, (counts.get(q.directiveId) || 0) + 1);
+      }
+    }
+    return counts;
+  }, [pendingQuestions]);
+
   return (
     <div className="flex flex-col h-full">
       <div className="flex items-center justify-between px-3 py-2 border-b border-dashed border-[rgba(117,170,252,0.2)]">
@@ -55,6 +69,9 @@ export function DirectiveList({ directives, selectedId, onSelect, onCreate }: Di
                   <span className="text-[12px] font-mono text-white truncate pr-2">
                     {d.title}
                   </span>
+                  {questionsPerDirective.has(d.id) && (
+                    <span className="inline-block w-2.5 h-2.5 rounded-full bg-amber-400 animate-pulse shrink-0" title={`${questionsPerDirective.get(d.id)} pending question(s)`} />
+                  )}
                   <span
                     className={`text-[9px] font-mono ${badge.color} border rounded px-1.5 py-0.5 shrink-0`}
                   >
diff --git a/makima/src/daemon/worktree/manager.rs b/makima/src/daemon/worktree/manager.rs
index 489c488..ea26767 100644
--- a/makima/src/daemon/worktree/manager.rs
+++ b/makima/src/daemon/worktree/manager.rs
@@ -491,64 +491,7 @@ impl WorktreeManager {
                 .output()
                 .await;
 
-            // Prefer origin/{base_branch} to get latest remote state.
-            // If neither origin/{base_branch} nor {base_branch} exist (e.g. PR branch
-            // was deleted after merge), fall back to the repo's default branch.
-            let origin_ref = format!("origin/{}", base_branch);
-            let has_origin_ref = Command::new("git")
-                .args(["rev-parse", "--verify", &format!("refs/remotes/{}", origin_ref)])
-                .current_dir(source_repo)
-                .output()
-                .await
-                .map(|o| o.status.success())
-                .unwrap_or(false);
-
-            let has_local_ref = if !has_origin_ref {
-                Command::new("git")
-                    .args(["rev-parse", "--verify", &format!("refs/heads/{}", base_branch)])
-                    .current_dir(source_repo)
-                    .output()
-                    .await
-                    .map(|o| o.status.success())
-                    .unwrap_or(false)
-            } else {
-                false // don't need to check — we already have origin ref
-            };
-
-            let start_point: String = if has_origin_ref {
-                origin_ref
-            } else if has_local_ref {
-                base_branch.to_string()
-            } else {
-                // Branch doesn't exist (likely deleted after PR merge) — use default branch
-                tracing::warn!(
-                    task_id = %task_id,
-                    base_branch = %base_branch,
-                    "Base branch ref not found, falling back to default branch"
-                );
-                let default_branch = self.detect_default_branch(source_repo).await?;
-                let default_origin = format!("origin/{}", default_branch);
-                let has_default_origin = Command::new("git")
-                    .args(["rev-parse", "--verify", &format!("refs/remotes/{}", default_origin)])
-                    .current_dir(source_repo)
-                    .output()
-                    .await
-                    .map(|o| o.status.success())
-                    .unwrap_or(false);
-                if has_default_origin {
-                    default_origin
-                } else {
-                    default_branch
-                }
-            };
-
-            tracing::info!(
-                task_id = %task_id,
-                start_point = %start_point,
-                "Using start point for new worktree branch"
-            );
-
-            // Create the worktree with a new branch based on the start point
+            // Create the worktree with a new branch based on the local base_branch
             let output = Command::new("git")
                 .args([
                     "worktree",
diff --git a/makima/src/server/handlers/mesh_supervisor.rs b/makima/src/server/handlers/mesh_supervisor.rs
index 90c6dc7..0ea1a57 100644
--- a/makima/src/server/handlers/mesh_supervisor.rs
+++ b/makima/src/server/handlers/mesh_supervisor.rs
@@ -1807,42 +1807,17 @@ pub async fn ask_question(
         ).into_response();
     }
 
-    // If phaseguard is enabled (or directive reconcile mode), pause the supervisor task and return
-    // The task will be auto-resumed when a message is sent to it (e.g., when user answers)
+    // Determine if we should block indefinitely (phaseguard or directive reconcile mode)
     let use_phaseguard = request.phaseguard || (is_directive_context && directive_reconcile_mode);
-    if use_phaseguard {
-        // Pause the supervisor task
-        if let Some(daemon_id) = supervisor.daemon_id {
-            let cmd = DaemonCommand::PauseTask { task_id: supervisor_id };
-            if let Err(e) = state.send_daemon_command(daemon_id, cmd).await {
-                tracing::warn!(supervisor_id = %supervisor_id, error = %e, "Failed to pause supervisor for phaseguard");
-            } else {
-                tracing::info!(supervisor_id = %supervisor_id, "Paused supervisor for phaseguard question");
-            }
-        }
-
-        // Update task status to paused in DB
-        let update = crate::db::models::UpdateTaskRequest {
-            status: Some("paused".to_string()),
-            ..Default::default()
-        };
-        if let Err(e) = repository::update_task_for_owner(pool, supervisor_id, owner_id, update).await {
-            tracing::warn!(supervisor_id = %supervisor_id, error = %e, "Failed to update task status to paused");
-        }
-
-        return (
-            StatusCode::OK,
-            Json(AskQuestionResponse {
-                question_id,
-                response: None,
-                timed_out: false,
-            }),
-        ).into_response();
-    }
 
     // Poll for response with timeout
-    // For directive tasks without reconcile mode, use 30s default timeout
-    let timeout_secs = if is_directive_context && !directive_reconcile_mode {
+    // - Phaseguard: block indefinitely until user responds
+    // - Directive tasks without reconcile mode: 30s default timeout
+    // - Contract tasks: use requested timeout_seconds
+    let timeout_secs = if use_phaseguard {
+        // Block indefinitely until user responds
+        u64::MAX / 2
+    } else if is_directive_context && !directive_reconcile_mode {
         30
     } else {
         request.timeout_seconds.max(1) as u64