research: fix wizard loops never firing + missing clone/spawn (regression)

Two bugs surfaced by the first end-to-end wizard run — the pipeline
diagnostic showed "0 run(s)", "Repo bound but never cloned", and
"Container not spawned" for a topic that had been created with a
nightly research loop.

Bug 1: materialize_topic_loops bypassed initial_burst firing.
The wizard-materialized loops path calls cm_db::repo::loops::create
directly (a plain INSERT). The initial_burst-fires-first-iteration
logic lived inside the create_loop HTTP handler, so wizard loops
landed in the DB but never fired their initial iteration.

Fix: extract routes::loops::fire_initial_burst_if_set as a pub helper
that read triggers, ensures the loop container, and calls the
kind-aware compose_and_enqueue_iteration. Both create_loop and
materialize_topic_loops now call it.

Bug 2: research-kind loop iterations skipped clone/spawn.
compose_research_iteration_task only built the coordinator prompt;
the repo clone and topic container spawn lived only in start_topic.
So the first research iteration ran against a nonexistent clone
directory and a stale gateway, and every run failed.

Fix: extract routes::research::prepare_topic_runtime as a pub helper
that runs ensure_repo_workspace + research_container::spawn.
Idempotent — second iteration reattaches. Called from
compose_and_enqueue_iteration before enqueuing a research iteration.
Topics without a repo bound are a no-op.

Both fixes ship as one commit because they surface together on the
same user path (wizard → research loop → first iteration) — you
can't hit one without the other manifesting.

Follow-up: start_topic still runs its own inline clone/spawn code
(now duplicated with prepare_topic_runtime). Next commit collapses
start_topic to just call prepare_topic_runtime + build_task like
the loop path does, so the one-shot and loop paths agree on setup.

crates/cm-api/src/routes/loops.rs

@@ -86,6 +86,11 @@ pub async fn compose_and_enqueue_iteration(
         let Some(topic_id) = source_topic else {
             return Err(cm_db::DbError::NotFound);
         };
+        // Clone + spawn container BEFORE enqueuing so the run has real
+        // repo files + an isolated daemon to hit. Idempotent — the
+        // second iteration reattaches to the existing container. Runs
+        // even when the topic has no repo (harmless no-op).
+        crate::routes::research::prepare_topic_runtime(pool, workspace_id, topic_id).await;
         let task = compose_research_iteration_task(pool, topic_id, template_ref).await;
         cm_db::repo::loops::enqueue_iteration_with_topic(
             pool,
@@ -400,47 +405,21 @@ pub async fn create_loop(
         }
     }
 
-    // initial_burst — fire the first iteration inline, so every loop
-    // runs at least once when the trigger requests it (D1). The burst
-    // continues via the on_completion trigger up to `initial_burst`
-    // (tracked in loops.initial_burst_remaining, decremented on each
-    // completion). Best-effort: a docker/DB failure on the FIRST fire
-    // logs but the loop still lives with next_fire_at set for its
-    // cron.
-    let parsed = parse_triggers(&body.triggers);
-    let initial_burst = parsed.as_ref().map(|t| t.initial_burst).unwrap_or(0);
-    let chain_on_completion = parsed.as_ref().map(|t| t.on_completion).unwrap_or(false);
-    if initial_burst > 0 {
-        ensure_loop_container(&state.pool, user.workspace_id.as_uuid(), id).await;
-        // Kind-aware compose + enqueue — research-kind loops get a
-        // research prompt and research_topic_id set on the run.
-        let template = body.task_template.trim();
-        match compose_and_enqueue_iteration(
-            &state.pool,
-            id,
-            user.workspace_id.as_uuid(),
-            &body.graph,
-            None,
-            Some(template),
-        )
-        .await
-        {
-            Ok(run_id) => {
-                let _ = cm_db::repo::loops::mark_fired(&state.pool, id, run_id, next_fire_at).await;
-                // Log the burst remaining so on_completion can advance it.
-                // Stored on loops.initial_burst_remaining (added by the
-                // same migration as loops.kind). Falls back silently on
-                // schema absence so we don't break dev DBs mid-rollout.
-                let remaining = initial_burst.saturating_sub(1) as i32;
-                if remaining > 0 || chain_on_completion {
-                    let _ =
-                        cm_db::repo::loops::set_initial_burst_remaining(&state.pool, id, remaining)
-                            .await;
-                }
-            }
-            Err(e) => eprintln!("loops::create: initial_burst enqueue failed: {e:?}"),
-        }
-    }
+    // Fire the initial burst if the triggers request it. Extracted so
+    // materialize_topic_loops (the wizard-materialized loops path) can
+    // reuse the same logic — previously the burst logic lived only in
+    // this handler and wizard-created loops never fired their first
+    // iteration.
+    fire_initial_burst_if_set(
+        &state.pool,
+        user.workspace_id.as_uuid(),
+        id,
+        &body.triggers,
+        body.task_template.trim(),
+        &body.graph,
+        next_fire_at,
+    )
+    .await;
 
     Ok((
         StatusCode::CREATED,
@@ -452,6 +431,52 @@ pub async fn create_loop(
     ))
 }
 
+/// Fire the initial_burst if the loop's triggers request one. On the
+/// first fire, ensures the per-loop container is spawned and
+/// (for kind='research' loops) that the topic's repo is cloned and
+/// the topic container is up. Sets `initial_burst_remaining = burst
+/// - 1` so the completion hook can continue the chain. Best-effort:
+/// a docker or DB hiccup on the FIRST fire logs but the loop row
+/// still lives — cron / on_artifact_update / webhook can still fire
+/// it later.
+pub async fn fire_initial_burst_if_set(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    loop_id: Uuid,
+    triggers: &Value,
+    task_template: &str,
+    graph: &Value,
+    next_fire_at: Option<OffsetDateTime>,
+) {
+    let parsed = parse_triggers(triggers);
+    let initial_burst = parsed.as_ref().map(|t| t.initial_burst).unwrap_or(0);
+    let chain_on_completion = parsed.as_ref().map(|t| t.on_completion).unwrap_or(false);
+    if initial_burst == 0 {
+        return;
+    }
+    ensure_loop_container(pool, workspace_id, loop_id).await;
+    match compose_and_enqueue_iteration(
+        pool,
+        loop_id,
+        workspace_id,
+        graph,
+        None,
+        Some(task_template),
+    )
+    .await
+    {
+        Ok(run_id) => {
+            let _ = cm_db::repo::loops::mark_fired(pool, loop_id, run_id, next_fire_at).await;
+            let remaining = initial_burst.saturating_sub(1) as i32;
+            if remaining > 0 || chain_on_completion {
+                let _ =
+                    cm_db::repo::loops::set_initial_burst_remaining(pool, loop_id, remaining).await;
+            }
+        }
+        Err(e) => eprintln!("fire_initial_burst_if_set({loop_id}): enqueue failed: {e:?}"),
+    }
+}
+
 async fn apply_staffing(
     pool: &sqlx::PgPool,
     loop_id: Uuid,

crates/cm-api/src/routes/research.rs

@@ -329,6 +329,68 @@ fn research_workspace_root() -> std::path::PathBuf {
     std::env::temp_dir().join("clawmates-research")
 }
 
+/// Set up the on-disk workspace + container for a research topic —
+/// clone repo (idempotent) + spawn ZeroClaw team container (idempotent).
+/// Callable from both the one-shot `start_topic` handler and the
+/// kind='research' loop iteration path in routes::loops. Fully
+/// best-effort: any failure (docker unreachable, no clone_url) logs
+/// and returns, letting the caller enqueue the run against the
+/// workspace-wide gateway instead.
+pub async fn prepare_topic_runtime(pool: &sqlx::PgPool, workspace_id: Uuid, topic_id: Uuid) {
+    let topic = match cm_db::repo::research_topics::get_any_workspace(pool, topic_id).await {
+        Ok(Some(t)) => t,
+        _ => return,
+    };
+    // Repo binding is optional; without it we just skip clone + spawn.
+    let Some(repo_id) = topic.repo_id else {
+        return;
+    };
+    let repo =
+        match cm_db::repo::repos::get(pool, repo_id, cm_domain::WorkspaceId::from(workspace_id))
+            .await
+        {
+            Ok(r) => r,
+            Err(e) => {
+                eprintln!("prepare_topic_runtime({topic_id}): repo fetch failed: {e:?}");
+                return;
+            }
+        };
+    let ctx = match ensure_repo_workspace(pool, topic_id, workspace_id, &repo, &topic).await {
+        Ok(c) => c,
+        Err(e) => {
+            eprintln!("prepare_topic_runtime({topic_id}): clone failed: {e}");
+            return;
+        }
+    };
+    let repo_path = std::path::PathBuf::from(&ctx.path);
+    let state_root = research_workspace_root()
+        .join(topic_id.to_string())
+        .join("state");
+    let docker = match crate::research_container::connect() {
+        Ok(d) => d,
+        Err(e) => {
+            eprintln!("prepare_topic_runtime({topic_id}): docker connect failed: {e}");
+            return;
+        }
+    };
+    match crate::research_container::spawn(&docker, topic_id, &repo_path, &state_root).await {
+        Ok(spawned) => {
+            if let Err(e) = cm_db::repo::research_topics::set_zeroclaw_container(
+                pool,
+                topic_id,
+                workspace_id,
+                Some(&spawned.name),
+                Some(&spawned.gateway_url),
+            )
+            .await
+            {
+                eprintln!("prepare_topic_runtime({topic_id}): persist container failed: {e}");
+            }
+        }
+        Err(e) => eprintln!("prepare_topic_runtime({topic_id}): spawn failed: {e}"),
+    }
+}
+
 /// Clone the bound repo (shallow, single branch) into a per-topic
 /// workspace and gather a tree preview for the coordinator prompt.
 /// Persists the clone path on the topic so a re-start reuses it instead
@@ -583,6 +645,21 @@ async fn materialize_topic_loops(
             )
             .await;
             let _ = cm_db::repo::loops::set_kind(pool, loop_id, "research").await;
+            // Fire the initial burst NOW (this is what create_loop's
+            // handler does after inserting the row; materialize_topic_loops
+            // bypasses that handler). Without this call the loop lands
+            // in the DB but its initial_burst=1 never fires and the
+            // diagnostic shows "0 runs".
+            crate::routes::loops::fire_initial_burst_if_set(
+                pool,
+                workspace_id,
+                loop_id,
+                &r_triggers,
+                "Refresh the topic's research per the outcome kind.",
+                &graph,
+                next_fire_at,
+            )
+            .await;
         }
         Err(e) => {
             eprintln!("materialize_topic_loops: research loop create failed: {e:?}");
@@ -621,6 +698,20 @@ async fn materialize_topic_loops(
                     Some(topic_id),
                 )
                 .await;
+                // Fire the coding loop's initial burst too. It's
+                // typically 1 (single wake to consume the first
+                // artifact) and on_artifact_update handles subsequent
+                // waves via the fan-out hook.
+                crate::routes::loops::fire_initial_burst_if_set(
+                    pool,
+                    workspace_id,
+                    loop_id,
+                    &c_triggers,
+                    "Execute the next unconsumed INT-XX from the artifact.",
+                    &graph,
+                    None,
+                )
+                .await;
             }
             Err(e) => {
                 eprintln!("materialize_topic_loops: coding loop create failed: {e:?}");