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/papers.rs

@@ -181,13 +181,51 @@ pub fn arxiv_query(topic: &str) -> String {
     format!("all:\"{escaped}\" AND cat:cs.*")
 }
 
+/// The looser form of a topic: every term required, but not adjacent.
+///
+/// A quoted phrase is precise and brittle. "hybrid retrieval BM25 dense" is a
+/// perfectly good topic and appears verbatim in no paper on arXiv — measured, 0
+/// hits — while requiring the same four terms anywhere returns exactly the
+/// hybrid-retrieval evaluations the topic was asking for. Used only when the
+/// phrase finds nothing, so an exact match still wins when one exists.
+pub fn arxiv_query_broad(topic: &str) -> String {
+    let terms: Vec<String> = topic
+        .split_whitespace()
+        .map(|w| w.trim_matches(|c: char| !c.is_alphanumeric() && c != '-'))
+        .filter(|w| !w.is_empty())
+        .map(|w| format!("all:{w}"))
+        .collect();
+    if terms.is_empty() {
+        return arxiv_query(topic);
+    }
+    format!("{} AND cat:cs.*", terms.join(" AND "))
+}
+
 /// Search arXiv. `max_results` is capped to keep one run bounded.
 pub async fn search(query: &str, max_results: usize) -> Result<Vec<Paper>, String> {
+    let found = search_with(&arxiv_query(query), max_results).await?;
+    if !found.is_empty() {
+        return Ok(found);
+    }
+    // The phrase matched nothing. Before reporting a quiet day — which the whole
+    // pipeline treats as a real and legitimate outcome — try the same terms
+    // unquoted. A topic the operator writes as prose often is not a literal
+    // phrase in any title, and silently harvesting zero because of punctuation
+    // would be indistinguishable from a genuinely quiet field.
+    let broad = arxiv_query_broad(query);
+    if broad == arxiv_query(query) {
+        return Ok(found);
+    }
+    eprintln!("papers: no exact phrase match for {query:?} — retrying as {broad}");
+    search_with(&broad, max_results).await
+}
+
+async fn search_with(search_query: &str, max_results: usize) -> Result<Vec<Paper>, String> {
     let max = max_results.clamp(1, 50);
     let url = format!(
         "https://export.arxiv.org/api/query?search_query={}&start=0&max_results={max}\
          &sortBy=submittedDate&sortOrder=descending",
-        urlencoding(&arxiv_query(query))
+        urlencoding(search_query)
     );
     let body = reqwest::Client::new()
         .get(&url)
@@ -314,6 +352,36 @@ mod tests {
         }
     }
 
+    /// The broad form requires every term but not adjacency. Measured: the
+    /// phrase "hybrid retrieval BM25 dense" has 0 hits on arXiv; the same four
+    /// terms unquoted return the hybrid-retrieval evaluations that were asked
+    /// for. Without the fallback that topic silently harvests nothing, which is
+    /// indistinguishable from a genuinely quiet day.
+    #[test]
+    fn the_broad_form_requires_every_term_without_adjacency() {
+        let q = arxiv_query_broad("hybrid retrieval BM25 dense");
+        assert_eq!(
+            q,
+            "all:hybrid AND all:retrieval AND all:BM25 AND all:dense AND cat:cs.*"
+        );
+        assert!(!q.contains('"'), "the broad form must not be a phrase: {q}");
+        assert!(q.contains("cat:cs.*"), "still category-bound: {q}");
+    }
+
+    /// Punctuation must not leak into a term and must not empty the query.
+    #[test]
+    fn the_broad_form_strips_punctuation_and_never_empties() {
+        assert_eq!(
+            arxiv_query_broad("retrieval-augmented, generation!"),
+            "all:retrieval-augmented AND all:generation AND cat:cs.*",
+            "hyphens are part of a term; trailing punctuation is not"
+        );
+        // Nothing usable left: fall back to the phrase form rather than
+        // emitting a bare `cat:cs.*`, which would match all of computer science.
+        let q = arxiv_query_broad("!!!");
+        assert!(q.contains("all:"), "must never degrade to a bare category: {q}");
+    }
+
     /// Quotes in a topic would terminate the phrase early and corrupt the query.
     #[test]
     fn quotes_in_a_topic_cannot_break_out_of_the_phrase() {