Makima system improvements: Orders, directive questions, PR creation fix, bug fixes (#62)

* feat: soryu-co/soryu - makima: Fix directive goal update bug - stale closure issue

* WIP: heartbeat checkpoint

* WIP: heartbeat checkpoint

* feat: soryu-co/soryu - makima: Create Orders database schema and backend API

* feat: soryu-co/soryu - makima: Fix task Claude instance not receiving user inputs from input box

* WIP: heartbeat checkpoint

* feat: soryu-co/soryu - makima: Build Orders frontend page replacing the Board page

* WIP: heartbeat checkpoint

* WIP: heartbeat checkpoint

* feat: soryu-co/soryu - makima: Fix directive PR creation system

1 files changed, 86 insertions, 2 deletions

diff --git a/makima/src/orchestration/directive.rs b/makima/src/orchestration/directive.rs
index ea8009d..0deacca 100644
--- a/makima/src/orchestration/directive.rs
+++ b/makima/src/orchestration/directive.rs
@@ -248,6 +248,16 @@ impl DirectiveOrchestrator {
                         .await?;
                     repository::check_directive_idle(&self.pool, step.directive_id).await?;
                 }
+                "paused" => {
+                    // Task is paused (e.g., waiting for user answer in reconcile mode)
+                    // Keep step in running status — task will auto-resume when answered
+                    tracing::debug!(
+                        step_id = %step.step_id,
+                        directive_id = %step.directive_id,
+                        task_id = %step.task_id,
+                        "Step task paused (waiting for user response) — keeping step running"
+                    );
+                }
                 _ => {
                     // Still running — do nothing
                 }
@@ -627,6 +637,45 @@ impl DirectiveOrchestrator {
                         task_id = %check.completion_task_id,
                         "Completion task finished"
                     );
+
+                    // If directive has no pr_url yet, try to extract from task output
+                    if check.pr_url.is_none() {
+                        match self.extract_pr_url_from_task(check.completion_task_id).await {
+                            Ok(Some(url)) => {
+                                tracing::info!(
+                                    directive_id = %check.directive_id,
+                                    pr_url = %url,
+                                    "Extracted PR URL from completion task output"
+                                );
+                                let update = crate::db::models::UpdateDirectiveRequest {
+                                    pr_url: Some(url),
+                                    ..Default::default()
+                                };
+                                let _ = repository::update_directive_for_owner(
+                                    &self.pool,
+                                    check.owner_id,
+                                    check.directive_id,
+                                    update,
+                                )
+                                .await;
+                            }
+                            Ok(None) => {
+                                tracing::warn!(
+                                    directive_id = %check.directive_id,
+                                    task_id = %check.completion_task_id,
+                                    "Completion task finished but no PR URL found in output"
+                                );
+                            }
+                            Err(e) => {
+                                tracing::warn!(
+                                    directive_id = %check.directive_id,
+                                    error = %e,
+                                    "Failed to extract PR URL from completion task output"
+                                );
+                            }
+                        }
+                    }
+
                     repository::clear_completion_task(&self.pool, check.directive_id).await?;
                 }
                 "failed" | "interrupted" => {
@@ -688,6 +737,36 @@ impl DirectiveOrchestrator {
 
         Ok(task.id)
     }
+
+    /// Extract a GitHub PR URL from a completion task's output events.
+    /// Searches task output for patterns like `https://github.com/.../pull/123`.
+    async fn extract_pr_url_from_task(
+        &self,
+        task_id: Uuid,
+    ) -> Result<Option<String>, anyhow::Error> {
+        let events = repository::get_task_output(&self.pool, task_id, Some(500)).await?;
+
+        let pr_url_re = regex::Regex::new(r"https://github\.com/[^/\s]+/[^/\s]+/pull/\d+")?;
+
+        // Search from most recent events backwards for the PR URL
+        for event in events.iter().rev() {
+            if let Some(ref data) = event.event_data {
+                // Check the content field inside event_data JSON
+                if let Some(content) = data.get("content").and_then(|c| c.as_str()) {
+                    if let Some(m) = pr_url_re.find(content) {
+                        return Ok(Some(m.as_str().to_string()));
+                    }
+                }
+                // Also check the raw JSON string representation as fallback
+                let data_str = data.to_string();
+                if let Some(m) = pr_url_re.find(&data_str) {
+                    return Ok(Some(m.as_str().to_string()));
+                }
+            }
+        }
+
+        Ok(None)
+    }
 }
 
 /// Build the planning prompt for a directive.
@@ -952,10 +1031,15 @@ Then create the PR:
 gh pr create --title "{title}" --body "{pr_body}" --head {directive_branch} --base {base_branch}
 ```
 
-After creating the PR, store the URL:
+IMPORTANT: After creating the PR, you MUST store the PR URL so the directive system can track it.
+
+1. Run `gh pr create` as shown above and capture its output
+2. The output will contain the PR URL (e.g., https://github.com/owner/repo/pull/123)
+3. Then run this command to store the URL:
 ```
-makima directive update --pr-url "<the PR URL from gh pr create output>"
+makima directive update --pr-url "https://github.com/..."
 ```
+Replace the URL with the actual PR URL from the `gh pr create` output. This step is CRITICAL — the PR will not be tracked by the directive system without it.
 
 If there are merge conflicts, resolve them sensibly before pushing.
 "#,