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, 63 insertions, 0 deletions

diff --git a/makima/src/orchestration/directive.rs b/makima/src/orchestration/directive.rs
index df44ee4..420b3e1 100644
--- a/makima/src/orchestration/directive.rs
+++ b/makima/src/orchestration/directive.rs
@@ -339,6 +339,27 @@ impl DirectiveOrchestrator {
                     "Directive goal updated — spawning re-planning task"
                 );
 
+                // If directive already has a PR, remove completed steps that were included in it
+                if directive.pr_url.is_some() || directive.pr_branch.is_some() {
+                    match remove_already_merged_steps(&self.pool, directive.id).await {
+                        Ok(count) if count > 0 => {
+                            tracing::info!(
+                                directive_id = %directive.id,
+                                removed = count,
+                                "Auto-removed completed steps already included in PR before replanning"
+                            );
+                        }
+                        Err(e) => {
+                            tracing::warn!(
+                                directive_id = %directive.id,
+                                error = %e,
+                                "Failed to auto-remove merged steps before replanning"
+                            );
+                        }
+                        _ => {}
+                    }
+                }
+
                 let existing_steps =
                     repository::list_directive_steps(&self.pool, directive.id).await?;
                 let generation =
@@ -758,6 +779,25 @@ impl DirectiveOrchestrator {
                         }
 
                         repository::clear_completion_task(&self.pool, check.directive_id).await?;
+
+                        // Auto-remove completed steps that were just included in the PR
+                        match remove_already_merged_steps(&self.pool, check.directive_id).await {
+                            Ok(count) if count > 0 => {
+                                tracing::info!(
+                                    directive_id = %check.directive_id,
+                                    removed = count,
+                                    "Auto-removed completed steps after PR completion"
+                                );
+                            }
+                            Err(e) => {
+                                tracing::warn!(
+                                    directive_id = %check.directive_id,
+                                    error = %e,
+                                    "Failed to auto-remove merged steps after completion"
+                                );
+                            }
+                            _ => {}
+                        }
                     }
                     "failed" | "interrupted" => {
                         tracing::warn!(
@@ -915,6 +955,29 @@ impl DirectiveOrchestrator {
     }
 }
 
+/// Remove completed directive steps whose branches have already been included
+/// in a PR (i.e., the directive has a pr_url or pr_branch set).
+/// This prevents duplicate branch merges in subsequent PRs.
+pub async fn remove_already_merged_steps(
+    pool: &PgPool,
+    directive_id: Uuid,
+) -> Result<usize, anyhow::Error> {
+    let step_tasks = repository::get_completed_step_tasks(pool, directive_id).await?;
+    let mut removed = 0;
+    for st in &step_tasks {
+        if repository::delete_directive_step(pool, st.step_id).await? {
+            tracing::info!(
+                step_id = %st.step_id,
+                step_name = %st.step_name,
+                directive_id = %directive_id,
+                "Auto-removed completed step (already included in PR)"
+            );
+            removed += 1;
+        }
+    }
+    Ok(removed)
+}
+
 /// Trigger a completion task (PR creation/update) for a directive.
 ///
 /// This is the public entry point used by both the orchestrator tick and the