fix(research): the manifest belongs to the mission, and a brittle phrase must not mean silence

Two defects from the first on-topic run.

**1. The manifest could never be updated twice in a day.** It was written into
the VAULT at a per-DATE path, but it is per-RUN data. A second mission the same
day rewrites a file that already exists, and `auto_merge` correctly refused the
whole branch:

    diff is not additive (1 non-add change(s), first:
    M ContinuousResearch/2026-08-18/harvest.jsonl); left for a human

So `main` kept the FIRST run's manifest, the next mission cloned it, and the
agents analysed yesterday's papers while every log line reported a successful
harvest. The merge policy was right; the placement was wrong. The manifest now
goes into the mission's own checkout after `ensure_checkout`, which keeps the
vault additive and gives each mission exactly its own papers. The agents commit
it alongside their analysis through the normal delivery path.

**2. A quoted phrase that matches nothing looked like a quiet day.** Phrase
search is precise and brittle: "hybrid retrieval BM25 dense" is a reasonable
topic and appears verbatim in no paper on arXiv — measured, 0 hits — while the
same four terms unquoted return exactly the hybrid-retrieval evaluations the
topic asked for. Harvesting zero because of adjacency is indistinguishable from
a genuinely quiet field, which is the distinction `Harvest::healthy()` vs
`added_anything()` exists to preserve. `search` now retries unquoted when the
phrase finds nothing, and says so in the log.

Proven in one run, all three behaviours at once:

    "approximate nearest neighbor search" -> 5 candidates, 5 already held, 0 shelved
    "hybrid retrieval BM25 dense"         -> no exact phrase match, retrying broad
                                          -> 5 candidates, 0 already held, 5 shelved
    "LLM as a judge evaluation"           -> 5 candidates, 5 already held, 0 shelved
    wrote 5 paper(s) to .../ContinuousResearch/2026-08-18/harvest.jsonl

The seen-set suppressing 10 of 15 is the whole point of a recurring mission, and
the 5 that landed are on topic for the first time: RAG architecture evaluation,
agent-controlled search over chat logs, compute-aware retrieval and reranking,
hybrid retrieval in hyperbolic space, sparse-dense fusion limits.

353 tests pass.

Co-Authored-By: Claude Opus 5 <[email protected]>

crates/cm-api/src/mission_orchestrator.rs

@@ -75,6 +75,7 @@ pub async fn on_launch(
     // because the phase is what reports whether today was quiet or broken, and
     // those must stay distinguishable. What is never acceptable is silence, so
     // both outcomes are logged with their counts.
+    let mut harvested: Vec<crate::papers::Paper> = Vec::new();
     if mission.template_kind == crate::continuous_research::TEMPLATE_KIND {
         match blobs.as_ref() {
             Some(b) => {
@@ -89,9 +90,13 @@ pub async fn on_launch(
                 )
                 .await
                 {
-                    Ok(n) => eprintln!(
-                        "mission_orchestrator: continuous research harvest shelved {n} paper(s)                          for mission {mission_id}"
-                    ),
+                    Ok(papers) => {
+                        eprintln!(
+                            "mission_orchestrator: continuous research harvest shelved {} paper(s) for mission {mission_id}",
+                            papers.len()
+                        );
+                        harvested = papers;
+                    }
                     Err(e) => eprintln!(
                         "mission_orchestrator: continuous research harvest FAILED for                          {mission_id} (phases still start, and will report an empty day): {e}"
                     ),
@@ -113,10 +118,33 @@ pub async fn on_launch(
     // repo checkout even though its team was minted on the first
     // launch. Non-fatal — logs and continues on failure.
     match crate::mission_workspace::ensure_checkout(pool, workspace_id, mission_id).await {
-        Ok(Some(path)) => eprintln!(
-            "mission_orchestrator: repo checked out at {} for mission {mission_id}",
-            path.display()
-        ),
+        Ok(Some(path)) => {
+            eprintln!(
+                "mission_orchestrator: repo checked out at {} for mission {mission_id}",
+                path.display()
+            );
+            // The manifest goes in the CHECKOUT, not the vault: it is this run's
+            // input, and the vault path is per-date and shared, so a second run
+            // the same day rewrites a file that already exists and auto_merge
+            // rightly refuses the branch. See `write_manifest`.
+            if mission.template_kind == crate::continuous_research::TEMPLATE_KIND {
+                let date = crate::continuous_research::today();
+                match crate::continuous_research::write_manifest(&path, &harvested, &date) {
+                    Ok(at) => eprintln!(
+                        "mission_orchestrator: wrote {} paper(s) to {}",
+                        harvested.len(),
+                        at.display()
+                    ),
+                    // Loud: the reader phase would find no manifest and, being
+                    // resourceful, go and search arXiv itself — which corrupts
+                    // the seen-set. Better to see why here.
+                    Err(e) => eprintln!(
+                        "mission_orchestrator: could NOT write the harvest manifest for \
+                         {mission_id} — the reader phase will see no papers: {e}"
+                    ),
+                }
+            }
+        }
         Ok(None) => eprintln!(
             "mission_orchestrator: mission {mission_id} has no repo bound, skipping checkout"
         ),