feat: auto-remove merged steps, fix UI overflow, and improve worktree handling (#74)

* 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

* feat: soryu-co/soryu - makima: Auto-remove merged steps before planning runs

1 files changed, 38 insertions, 1 deletions

diff --git a/makima/src/server/handlers/directives.rs b/makima/src/server/handlers/directives.rs
index 56278a8..992affe 100644
--- a/makima/src/server/handlers/directives.rs
+++ b/makima/src/server/handlers/directives.rs
@@ -931,6 +931,19 @@ pub async fn cleanup_directive(
             .into_response();
     }
 
+    // Auto-remove completed steps that were already included in a merged PR
+    if directive.pr_url.is_some() || directive.pr_branch.is_some() {
+        match crate::orchestration::directive::remove_already_merged_steps(pool, id).await {
+            Ok(count) if count > 0 => {
+                tracing::info!("Auto-removed {} completed steps already in PR for directive {} during cleanup", count, id);
+            }
+            Err(e) => {
+                tracing::warn!("Failed to auto-remove merged steps during cleanup for directive {}: {}", id, e);
+            }
+            _ => {}
+        }
+    }
+
     // Get completed step tasks for branch name computation
     let step_tasks = match repository::get_completed_step_tasks(pool, id).await {
         Ok(tasks) => tasks,
@@ -1155,7 +1168,7 @@ pub async fn pick_up_orders(
     };
 
     // Verify directive ownership and get directive with steps
-    let (directive, steps) =
+    let (directive, mut steps) =
         match repository::get_directive_with_steps_for_owner(pool, auth.owner_id, id).await {
             Ok(Some((d, s))) => (d, s),
             Ok(None) => {
@@ -1175,6 +1188,30 @@ pub async fn pick_up_orders(
             }
         };
 
+    // Auto-remove completed steps that were already included in a PR
+    if directive.pr_url.is_some() || directive.pr_branch.is_some() {
+        match crate::orchestration::directive::remove_already_merged_steps(pool, id).await {
+            Ok(count) if count > 0 => {
+                tracing::info!("Auto-removed {} completed steps already in PR for directive {}", count, id);
+                // Re-fetch steps since some were removed
+                steps = match repository::list_directive_steps(pool, id).await {
+                    Ok(s) => s,
+                    Err(e) => {
+                        tracing::error!("Failed to re-fetch steps after cleanup: {}", e);
+                        return (
+                            StatusCode::INTERNAL_SERVER_ERROR,
+                            Json(ApiError::new("REFETCH_STEPS_FAILED", &e.to_string())),
+                        ).into_response();
+                    }
+                };
+            }
+            Err(e) => {
+                tracing::warn!("Failed to auto-remove merged steps for directive {}: {}", id, e);
+            }
+            _ => {}
+        }
+    }
+
     // Reconcile existing orders: mark done if step completed, under_review if step in progress
     match repository::reconcile_directive_orders(pool, auth.owner_id, id).await {
         Ok(count) => {