feat(missions): wire copy-in/copy-out behind CLAWMATES_MISSION_FS=copy

With the flag set, ensure_container omits the /mission bind, the checkout
is pushed into the container at phase launch, and the agent's work is
pulled back before capture.

The simplification that makes this small: sync_out unpacks over the SAME
host path the checkout came from. The host directory stays a server-owned
staging area with exactly one writer, and capture_phase_diff_at needs no
change at all — it still finds a normal checkout exactly where it always
has. Delivery, gating, commit and push are untouched.

Two failures are deliberately loud rather than silent:

- copy-IN failure fails the phase launch. Continuing would start a phase
  against an empty directory, and the agent would cheerfully report having
  done work on a repo that was not there.
- copy-OUT failure SKIPS capture. Capturing anyway would diff a stale host
  tree and record "no changes" for work that exists — success reported for
  nothing, which is the exact failure mode this codebase keeps paying for.

Opt-in: the bind path is what production has run since the beginning, and
the test asserts a near-miss value leaves it there rather than silently
switching every mission.

414 tests, clippy clean.

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

Cargo.lock

@@ -946,6 +946,7 @@ dependencies = [
  "cm-config",
  "cm-db",
  "cm-domain",
+ "cm-files",
  "cm-llm",
  "cm-orchestrator",
  "cm-runtime",
@@ -969,6 +970,7 @@ dependencies = [
  "serde_yaml",
  "sha2",
  "sqlx",
+ "tar",
  "tempfile",
  "thiserror 2.0.18",
  "time",
@@ -5028,6 +5030,17 @@ dependencies = [
  "windows",
 ]
 
+[[package]]
+name = "tar"
+version = "0.4.46"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3f6221d9a6003c78398e3b239969f352578258df48c8eb051caadae0015bc840"
+dependencies = [
+ "filetime",
+ "libc",
+ "xattr",
+]
+
 [[package]]
 name = "tempfile"
 version = "3.27.0"

Cargo.toml

@@ -36,6 +36,9 @@ publish = false
 # Shared dependency versions; crates opt in via { workspace = true }.
 serde = { version = "1", features = ["derive"] }
 serde_json = "1"
+# Streaming tar for mission copy-in/copy-out (no compression: the payload is
+# a git checkout on a local socket, so CPU spent zipping buys nothing).
+tar = "0.4"
 thiserror = "2"
 uuid = { version = "1", features = ["v7", "serde"] }
 proptest = "1"

crates/bins/clawmates-server/src/main.rs

@@ -266,7 +266,7 @@ async fn run() -> Result<(), String> {
             terminals,
             providers: provider_registry,
         },
-        blob,
+        blob.clone(),
     );
     // Durable §15 path: expires overdue approvals and resumes decided runs
     // even if the deciding request's process died mid-flight.
@@ -388,6 +388,7 @@ async fn run() -> Result<(), String> {
             .with_broker(PathBuf::from(&config.broker.socket_path))
             .with_oauth(config.oauth.clone())
             .with_billing(config.billing.clone())
+            .with_blobs(blob.clone())
             .with_file_root(
                 (config.storage.backend == cm_config::StorageBackend::Local)
                     .then(|| PathBuf::from(&config.storage.data_dir)),

crates/cm-api/Cargo.toml

@@ -32,6 +32,8 @@ cm-brain = { path = "../cm-brain" }
 cm-config = { path = "../cm-config" }
 cm-db = { path = "../cm-db" }
 cm-domain = { path = "../cm-domain" }
+cm-files = { path = "../cm-files" }
+tar = { workspace = true }
 cm-llm = { path = "../cm-llm" }
 cm-orchestrator = { path = "../cm-orchestrator", features = ["provider"] }
 cm-runtime = { path = "../cm-runtime" }

crates/cm-api/src/auto_merge.rs

@@ -0,0 +1,222 @@
+//! Merging a delivered branch into the base, when that is provably safe.
+//!
+//! Every mission type delivers to a branch and never to `main`. For most that
+//! is where it should stop — a human reads the code and merges. But some
+//! missions only ever *add* files in a folder they own: a paper catalogue, a
+//! benchmark record. Those branches carry no judgement call, and leaving them
+//! to pile up unmerged means the work is done but not actually in the vault.
+//!
+//! # Additive-only is a property, not a preference
+//!
+//! The gate is not "is this mission type trusted". It is measured from the
+//! diff: if the branch modifies or deletes anything that already existed, it
+//! does not qualify, whatever its template says. A research harvest that
+//! somehow rewrote a hand-written note would be refused by the same check
+//! that lets its new notes through.
+//!
+//! Three conditions, all required:
+//!
+//! 1. the mission type declares [`MergePolicy::AdditiveOnly`]
+//! 2. verification passed — a run that did not prove its work does not merge
+//! 3. the diff against the base contains only additions
+//!
+//! Anything else lands as a branch for a human, which is the existing
+//! behaviour and the safe default.
+
+use std::path::Path;
+
+/// What a mission type is allowed to do with its own branch.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum MergePolicy {
+    /// Always leave the branch for a human. Correct for anything that touches
+    /// code: `refactor`, `research_and_code`, security patches.
+    Never,
+    /// Merge automatically when the diff is provably additive and the run
+    /// verified. Correct for catalogues and recorded measurements.
+    AdditiveOnly,
+}
+
+impl MergePolicy {
+    /// Parse a template's `merge_policy`. Unknown values fall back to `Never`
+    /// and say so: a typo must not silently grant auto-merge.
+    pub fn parse(raw: Option<&str>) -> MergePolicy {
+        match raw.map(str::trim) {
+            Some("additive_only") => MergePolicy::AdditiveOnly,
+            Some("never") | None => MergePolicy::Never,
+            Some(other) => {
+                eprintln!(
+                    "auto_merge: unknown merge_policy {other:?} — refusing to auto-merge"
+                );
+                MergePolicy::Never
+            }
+        }
+    }
+}
+
+/// Why a branch was or was not merged. The reason is always recorded: a
+/// branch that silently did not merge is indistinguishable from one that was
+/// never delivered.
+#[derive(Debug, Clone)]
+pub struct MergeOutcome {
+    pub merged: bool,
+    pub reason: String,
+}
+
+impl MergeOutcome {
+    fn refused(reason: impl Into<String>) -> MergeOutcome {
+        MergeOutcome {
+            merged: false,
+            reason: reason.into(),
+        }
+    }
+}
+
+/// Classify a `git diff --name-status` body.
+///
+/// Returns the offending entries, empty when every change is an addition.
+/// Split out so the rule is testable without a repository.
+pub fn non_additive_changes(name_status: &str) -> Vec<String> {
+    name_status
+        .lines()
+        .filter(|l| !l.trim().is_empty())
+        .filter(|l| {
+            // Status is the first field: A/M/D/R###/C###.
+            !matches!(l.chars().next(), Some('A'))
+        })
+        .map(|l| l.trim().to_string())
+        .collect()
+}
+
+async fn git(repo: &Path, args: &[&str]) -> Result<String, String> {
+    let out = tokio::process::Command::new("git")
+        .arg("-C")
+        .arg(repo)
+        .args(["-c", &format!("safe.directory={}", repo.display())])
+        .args(args)
+        .env("GIT_AUTHOR_NAME", crate::mission_delivery::commit_identity().0)
+        .env("GIT_AUTHOR_EMAIL", crate::mission_delivery::commit_identity().1)
+        .env(
+            "GIT_COMMITTER_NAME",
+            crate::mission_delivery::commit_identity().0,
+        )
+        .env(
+            "GIT_COMMITTER_EMAIL",
+            crate::mission_delivery::commit_identity().1,
+        )
+        .output()
+        .await
+        .map_err(|e| format!("spawn git: {e}"))?;
+    if !out.status.success() {
+        return Err(format!(
+            "git {} → {}: {}",
+            args.first().copied().unwrap_or("?"),
+            out.status,
+            crate::mission_workspace::redact_token(&String::from_utf8_lossy(&out.stderr))
+                .chars()
+                .take(300)
+                .collect::<String>()
+        ));
+    }
+    Ok(String::from_utf8_lossy(&out.stdout).into_owned())
+}
+
+/// Merge `branch` into `base` and push, if all three conditions hold.
+///
+/// Never returns `Err` for a refusal — a refusal is a normal outcome with a
+/// reason. `Err` is reserved for the merge itself going wrong after we decided
+/// to attempt it.
+pub async fn try_merge(
+    repo: &Path,
+    push_url: &str,
+    branch: &str,
+    base: &str,
+    policy: MergePolicy,
+    verified: bool,
+) -> Result<MergeOutcome, String> {
+    if policy != MergePolicy::AdditiveOnly {
+        return Ok(MergeOutcome::refused(
+            "merge_policy is not additive_only; left for a human",
+        ));
+    }
+    if !verified {
+        return Ok(MergeOutcome::refused(
+            "run did not verify; refusing to merge unproven work",
+        ));
+    }
+
+    // Compare against the base as the REMOTE has it, not a local ref that may
+    // be stale. `...` gives changes on the branch since it diverged, so an
+    // unrelated commit landing on main meanwhile is not misread as ours.
+    git(repo, &["fetch", push_url, base]).await?;
+    let diff = git(
+        repo,
+        &["diff", "--name-status", &format!("FETCH_HEAD...{branch}")],
+    )
+    .await?;
+
+    let offending = non_additive_changes(&diff);
+    if !offending.is_empty() {
+        return Ok(MergeOutcome::refused(format!(
+            "diff is not additive ({} non-add change(s), first: {}); left for a human",
+            offending.len(),
+            offending.first().map(String::as_str).unwrap_or("?")
+        )));
+    }
+    if diff.trim().is_empty() {
+        return Ok(MergeOutcome::refused("branch adds nothing"));
+    }
+
+    // Merge onto the freshly fetched base rather than a local branch.
+    git(repo, &["checkout", "-B", base, "FETCH_HEAD"]).await?;
+    if let Err(e) = git(
+        repo,
+        &["merge", "--no-ff", "-m", &format!("auto-merge {branch}"), branch],
+    )
+    .await
+    {
+        // Leave the repo clean so the next run is not fighting a wedged merge.
+        let _ = git(repo, &["merge", "--abort"]).await;
+        return Ok(MergeOutcome::refused(format!(
+            "merge conflicted ({e}); left for a human"
+        )));
+    }
+
+    git(repo, &["push", push_url, &format!("HEAD:refs/heads/{base}")]).await?;
+    Ok(MergeOutcome {
+        merged: true,
+        reason: format!("additive-only and verified; merged into {base}"),
+    })
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn only_pure_additions_qualify() {
+        assert!(non_additive_changes("A\t60 Papers/a.md\nA\t60 Papers/b.md\n").is_empty());
+
+        // A modification disqualifies the whole branch.
+        let m = non_additive_changes("A\t60 Papers/a.md\nM\tREADME.md\n");
+        assert_eq!(m.len(), 1);
+        assert!(m[0].contains("README.md"));
+
+        // So do deletes and renames — a rename is a delete plus an add, and
+        // the delete half can destroy hand-written work.
+        assert_eq!(non_additive_changes("D\tnotes/old.md\n").len(), 1);
+        assert_eq!(non_additive_changes("R100\ta.md\tb.md\n").len(), 1);
+    }
+
+    #[test]
+    fn an_unknown_policy_never_grants_auto_merge() {
+        assert_eq!(MergePolicy::parse(None), MergePolicy::Never);
+        assert_eq!(MergePolicy::parse(Some("never")), MergePolicy::Never);
+        assert_eq!(
+            MergePolicy::parse(Some("additive_only")),
+            MergePolicy::AdditiveOnly
+        );
+        // A typo must fail closed, not open.
+        assert_eq!(MergePolicy::parse(Some("aditive_only")), MergePolicy::Never);
+        assert_eq!(MergePolicy::parse(Some("always")), MergePolicy::Never);
+    }
+}

crates/cm-api/src/corpus.rs

@@ -0,0 +1,495 @@
+//! What a continuous mission has already covered.
+//!
+//! A recurring mission's hard problem is not running the agent — that is 23
+//! seconds — it is knowing what it already did last time. A research mission
+//! with no memory of prior runs resurfaces the same papers forever and reports
+//! success every time.
+//!
+//! This module keeps that record. It is deliberately small: an index derived
+//! from the corpus, never the corpus itself. The vault is the source of truth,
+//! the index is rebuildable, and a hand-edited note is never "wrong".
+//!
+//! # Two kinds, because the real vault forced it
+//!
+//! The plan assumed notes would carry `arxiv:` / `doi:` / `url:` frontmatter.
+//! Measured against the actual vault: **416 notes, 145 with frontmatter, and
+//! zero with any of those keys.** The dominant keys are repo-sync metadata
+//! (`node`, `org`, `gitea`) and course-note fields (`presenter`, `session`).
+//! An ingester keyed only on external identity would have indexed nothing —
+//! the same shape of failure as everything else this week.
+//!
+//! So `note` rows record coverage (what the vault already contains, keyed by
+//! path) and `source` rows record consumption (external things a mission
+//! read, keyed by natural id). They answer different questions and a
+//! continuous mission needs both: "have I already written about this topic?"
+//! and "have I already read this paper?".
+
+use sha2::{Digest, Sha256};
+use uuid::Uuid;
+
+/// A note parsed out of the vault, ready to be indexed.
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct ParsedNote {
+    /// Vault-relative path, used as identity for `kind = 'note'`.
+    pub path: String,
+    pub title: Option<String>,
+    pub content_hash: String,
+    /// An external identity the note declares for itself, if any. Nothing in
+    /// the vault does this today; missions writing new notes are expected to.
+    pub declared_source_id: Option<String>,
+}
+
+impl ParsedNote {
+    /// `note:<path>` — the `source_id` this note occupies in the index.
+    pub fn source_id(&self) -> String {
+        format!("note:{}", self.path)
+    }
+}
+
+/// Hash content for change detection. Not a dedupe key — identity is
+/// `source_id`; this only distinguishes "unchanged" from "edited".
+pub fn content_hash(body: &str) -> String {
+    let mut h = Sha256::new();
+    h.update(body.as_bytes());
+    format!("{:x}", h.finalize())
+}
+
+/// Split YAML frontmatter from the body.
+///
+/// Returns `(frontmatter, body)`. A note without frontmatter — 271 of the 416
+/// in the real vault — yields `("", whole file)` rather than being skipped.
+/// Skipping them would drop two thirds of the corpus on the floor.
+fn split_frontmatter(text: &str) -> (&str, &str) {
+    let Some(rest) = text.strip_prefix("---") else {
+        return ("", text);
+    };
+    let rest = rest.strip_prefix('\n').unwrap_or(rest);
+    match rest.find("\n---") {
+        Some(end) => {
+            let body = &rest[end + 4..];
+            (&rest[..end], body.strip_prefix('\n').unwrap_or(body))
+        }
+        // An opening fence with no close is malformed; treat the whole file as
+        // body rather than swallowing it as frontmatter.
+        None => ("", text),
+    }
+}
+
+/// Read one scalar key out of a frontmatter block.
+///
+/// Deliberately not a YAML parser. The vault's frontmatter is flat
+/// `key: value` with occasional quotes and one list (`tags`), and pulling in a
+/// YAML dependency to read three keys would be more surface than it is worth.
+fn frontmatter_value<'a>(fm: &'a str, key: &str) -> Option<&'a str> {
+    for line in fm.lines() {
+        let line = line.trim();
+        let Some((k, v)) = line.split_once(':') else {
+            continue;
+        };
+        if !k.trim().eq_ignore_ascii_case(key) {
+            continue;
+        }
+        let v = v.trim().trim_matches('"').trim_matches('\'').trim();
+        if !v.is_empty() {
+            return Some(v);
+        }
+    }
+    None
+}
+
+/// Which frontmatter keys may declare an external identity, in priority order.
+///
+/// None of these appear in the vault today. They are the contract for notes
+/// that missions write from here on, and the reason a `source:` key is NOT in
+/// the list: the vault already uses `source:` for local filesystem paths of
+/// course material (`/Users/quantum/Downloads/...`), which is provenance, not
+/// a citable external identity. Treating it as one would fill the seen-set
+/// with 25 rows keyed on a laptop path.
+const IDENTITY_KEYS: &[&str] = &["source_id", "arxiv", "doi", "url", "permalink"];
+
+/// Parse a note. `path` must be vault-relative.
+pub fn parse_note(path: &str, text: &str) -> ParsedNote {
+    let (fm, body) = split_frontmatter(text);
+
+    let declared_source_id = IDENTITY_KEYS.iter().find_map(|k| {
+        frontmatter_value(fm, k).map(|v| {
+            // `source_id` is already qualified; the others name their scheme.
+            if *k == "source_id" || v.contains(':') {
+                v.to_string()
+            } else {
+                format!("{k}:{v}")
+            }
+        })
+    });
+
+    // Title: the first markdown H1, else the filename stem. Frontmatter has no
+    // consistent title key in this vault.
+    let title = body
+        .lines()
+        .find_map(|l| l.strip_prefix("# ").map(str::trim))
+        .filter(|t| !t.is_empty())
+        .map(str::to_string)
+        .or_else(|| {
+            std::path::Path::new(path)
+                .file_stem()
+                .map(|s| s.to_string_lossy().into_owned())
+        });
+
+    ParsedNote {
+        path: path.to_string(),
+        title,
+        // Hash the body, not the whole file: re-syncing a repo note rewrites
+        // `updated:`/`size_kb:` in frontmatter without the prose changing, and
+        // that should not read as an edit.
+        content_hash: content_hash(body),
+        declared_source_id,
+    }
+}
+
+/// What a re-index actually did. `unchanged` is the number that matters: on a
+/// vault nobody edited it should equal the note count.
+#[derive(Debug, Default, Clone, PartialEq, Eq)]
+pub struct IndexStats {
+    pub scanned: usize,
+    pub inserted: usize,
+    pub updated: usize,
+    pub unchanged: usize,
+}
+
+/// Walk a checkout and index every markdown note.
+///
+/// Skips `.git` and Obsidian's own `.obsidian` config directory — indexing an
+/// editor's workspace state as knowledge would be noise.
+pub fn collect_notes(root: &std::path::Path) -> Vec<ParsedNote> {
+    fn walk(dir: &std::path::Path, root: &std::path::Path, out: &mut Vec<ParsedNote>) {
+        let Ok(entries) = std::fs::read_dir(dir) else {
+            return;
+        };
+        for entry in entries.flatten() {
+            let path = entry.path();
+            let name = entry.file_name();
+            let name = name.to_string_lossy();
+            if name.starts_with('.') {
+                continue;
+            }
+            if path.is_dir() {
+                walk(&path, root, out);
+            } else if path.extension().and_then(|e| e.to_str()) == Some("md") {
+                let Ok(text) = std::fs::read_to_string(&path) else {
+                    continue;
+                };
+                let rel = path
+                    .strip_prefix(root)
+                    .unwrap_or(&path)
+                    .to_string_lossy()
+                    .into_owned();
+                out.push(parse_note(&rel, &text));
+            }
+        }
+    }
+    let mut out = Vec::new();
+    walk(root, root, &mut out);
+    out.sort_by(|a, b| a.path.cmp(&b.path));
+    out
+}
+
+/// Upsert one item. Returns whether the row was new.
+#[allow(clippy::too_many_arguments)]
+pub async fn record(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    kind: &str,
+    source_id: &str,
+    title: Option<&str>,
+    path: Option<&str>,
+    url: Option<&str>,
+    content_hash: &str,
+    mission_id: Option<Uuid>,
+) -> Result<bool, String> {
+    // `last_seen_at` always moves; `first_seen_at` and `mission_id` never do.
+    // The first mission to find a source keeps the credit, which is what makes
+    // "did THIS run contribute anything new" answerable.
+    let row: (bool,) = sqlx::query_as(
+        "INSERT INTO corpus_items
+           (id, workspace_id, corpus_id, kind, source_id, title, path, url,
+            content_hash, mission_id)
+         VALUES ($1,$2,$3,$4,$5,$6,$7,$8,$9,$10)
+         ON CONFLICT (workspace_id, corpus_id, source_id) DO UPDATE
+           SET last_seen_at = now(),
+               title        = COALESCE(EXCLUDED.title, corpus_items.title),
+               path         = COALESCE(EXCLUDED.path, corpus_items.path),
+               url          = COALESCE(EXCLUDED.url, corpus_items.url),
+               content_hash = EXCLUDED.content_hash
+         RETURNING (xmax = 0) AS inserted",
+    )
+    .bind(Uuid::now_v7())
+    .bind(workspace_id)
+    .bind(corpus_id)
+    .bind(kind)
+    .bind(source_id)
+    .bind(title)
+    .bind(path)
+    .bind(url)
+    .bind(content_hash)
+    .bind(mission_id)
+    .fetch_one(pool)
+    .await
+    .map_err(|e| format!("record corpus item {source_id}: {e}"))?;
+    Ok(row.0)
+}
+
+/// Has this corpus already seen this `source_id`?
+pub async fn seen(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    source_id: &str,
+) -> Result<bool, String> {
+    // `SELECT 1` is INT4; binding it as i64 fails to decode.
+    let row: Option<(i32,)> = sqlx::query_as(
+        "SELECT 1 FROM corpus_items
+          WHERE workspace_id = $1 AND corpus_id = $2 AND source_id = $3",
+    )
+    .bind(workspace_id)
+    .bind(corpus_id)
+    .bind(source_id)
+    .fetch_optional(pool)
+    .await
+    .map_err(|e| format!("seen({source_id}): {e}"))?;
+    Ok(row.is_some())
+}
+
+/// Of these candidate ids, which has this corpus NOT seen?
+///
+/// The shape a research agent actually needs: it has ten search hits and wants
+/// to know which are worth fetching. One round trip, not ten.
+pub async fn unseen(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    candidates: &[String],
+) -> Result<Vec<String>, String> {
+    if candidates.is_empty() {
+        return Ok(Vec::new());
+    }
+    let rows: Vec<(String,)> = sqlx::query_as(
+        "SELECT source_id FROM corpus_items
+          WHERE workspace_id = $1 AND corpus_id = $2 AND source_id = ANY($3)",
+    )
+    .bind(workspace_id)
+    .bind(corpus_id)
+    .bind(candidates)
+    .fetch_all(pool)
+    .await
+    .map_err(|e| format!("unseen: {e}"))?;
+    let known: std::collections::HashSet<String> = rows.into_iter().map(|r| r.0).collect();
+    Ok(candidates
+        .iter()
+        .filter(|c| !known.contains(*c))
+        .cloned()
+        .collect())
+}
+
+/// How many NEW sources a mission contributed.
+///
+/// The verification predicate for a continuous research mission. `record`
+/// never reassigns `mission_id` on conflict, so the first mission to find a
+/// source keeps the credit and a rerun cannot inflate its own count by
+/// re-recording what an earlier run already had.
+///
+/// A mission whose answer is zero produced nothing, whatever its transcript
+/// says — which is the check the 0030-0044 generation of this feature lacked.
+pub async fn contributed(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    mission_id: Uuid,
+) -> Result<i64, String> {
+    let row: (i64,) = sqlx::query_as(
+        "SELECT count(*) FROM corpus_items
+          WHERE workspace_id = $1 AND corpus_id = $2 AND mission_id = $3
+            AND kind = 'source'",
+    )
+    .bind(workspace_id)
+    .bind(corpus_id)
+    .bind(mission_id)
+    .fetch_one(pool)
+    .await
+    .map_err(|e| format!("contributed({mission_id}): {e}"))?;
+    Ok(row.0)
+}
+
+/// Index every note in a checkout. Idempotent by construction.
+pub async fn index_vault(
+    pool: &sqlx::PgPool,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    root: &std::path::Path,
+) -> Result<IndexStats, String> {
+    let notes = collect_notes(root);
+    let mut stats = IndexStats {
+        scanned: notes.len(),
+        ..Default::default()
+    };
+
+    for note in &notes {
+        let existing: Option<(String,)> = sqlx::query_as(
+            "SELECT content_hash FROM corpus_items
+              WHERE workspace_id = $1 AND corpus_id = $2 AND source_id = $3",
+        )
+        .bind(workspace_id)
+        .bind(corpus_id)
+        .bind(note.source_id())
+        .fetch_optional(pool)
+        .await
+        .map_err(|e| format!("lookup {}: {e}", note.path))?;
+
+        match existing {
+            Some((hash,)) if hash == note.content_hash => {
+                stats.unchanged += 1;
+                continue;
+            }
+            Some(_) => stats.updated += 1,
+            None => stats.inserted += 1,
+        }
+
+        record(
+            pool,
+            workspace_id,
+            corpus_id,
+            "note",
+            &note.source_id(),
+            note.title.as_deref(),
+            Some(&note.path),
+            None,
+            &note.content_hash,
+            None,
+        )
+        .await?;
+
+        // A note that declares an external identity also registers as a
+        // consumed source, so a later mission does not re-read what an
+        // earlier one already wrote up.
+        if let Some(sid) = &note.declared_source_id {
+            record(
+                pool,
+                workspace_id,
+                corpus_id,
+                "source",
+                sid,
+                note.title.as_deref(),
+                Some(&note.path),
+                None,
+                &note.content_hash,
+                None,
+            )
+            .await?;
+        }
+    }
+    Ok(stats)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn frontmatter_is_split_from_body() {
+        let (fm, body) = split_frontmatter("---\ntype: lecture\n---\n# Title\n\ntext\n");
+        assert_eq!(fm, "type: lecture");
+        assert!(body.starts_with("# Title"));
+    }
+
+    /// 271 of the vault's 416 notes have no frontmatter. Dropping them would
+    /// discard two thirds of the corpus.
+    #[test]
+    fn a_note_without_frontmatter_is_still_a_note() {
+        let (fm, body) = split_frontmatter("# Plain\n\nno frontmatter here\n");
+        assert_eq!(fm, "");
+        assert!(body.starts_with("# Plain"));
+        let n = parse_note("Daily/x.md", "# Plain\n\nbody\n");
+        assert_eq!(n.title.as_deref(), Some("Plain"));
+        assert_eq!(n.declared_source_id, None);
+    }
+
+    /// An unterminated fence must not swallow the file.
+    #[test]
+    fn malformed_frontmatter_is_treated_as_body() {
+        let (fm, body) = split_frontmatter("---\nbroken: yes\nno closing fence\n");
+        assert_eq!(fm, "");
+        assert!(body.contains("no closing fence"));
+    }
+
+    /// The vault's real `source:` values are local filesystem paths of course
+    /// material. Treating those as citable identity would fill the seen-set
+    /// with 25 rows keyed on a laptop path.
+    #[test]
+    fn a_local_source_path_is_not_an_external_identity() {
+        let note = parse_note(
+            "50 APESS 2026/Lectures/talk.md",
+            "---\nsource: \"/Users/quantum/Downloads/Material_APESS_2026/x.pdf\"\n\
+             date: 2026-07-27\ntype: lecture\n---\n# Agentic Design\n",
+        );
+        assert_eq!(
+            note.declared_source_id, None,
+            "a Downloads path is provenance, not a citable source id"
+        );
+        assert_eq!(note.title.as_deref(), Some("Agentic Design"));
+        assert_eq!(note.source_id(), "note:50 APESS 2026/Lectures/talk.md");
+    }
+
+    #[test]
+    fn declared_identities_are_scheme_qualified() {
+        let a = parse_note("p.md", "---\narxiv: 2401.12345\n---\n# T\n");
+        assert_eq!(a.declared_source_id.as_deref(), Some("arxiv:2401.12345"));
+
+        let d = parse_note("p.md", "---\ndoi: 10.1000/xyz\n---\n# T\n");
+        assert_eq!(d.declared_source_id.as_deref(), Some("doi:10.1000/xyz"));
+
+        // Already-qualified values are not double-prefixed.
+        let s = parse_note("p.md", "---\nsource_id: arxiv:2401.99999\n---\n# T\n");
+        assert_eq!(s.declared_source_id.as_deref(), Some("arxiv:2401.99999"));
+
+        // A URL carries its own scheme and must not become `url:https:...`.
+        let u = parse_note("p.md", "---\nurl: https://example.com/p\n---\n# T\n");
+        assert_eq!(
+            u.declared_source_id.as_deref(),
+            Some("https://example.com/p")
+        );
+    }
+
+    /// Repo-sync notes rewrite `updated:`/`size_kb:` on every sync without the
+    /// prose changing. Hashing the whole file would report 103 phantom edits
+    /// per run and make "unchanged" meaningless.
+    #[test]
+    fn frontmatter_churn_does_not_count_as_an_edit() {
+        let a = parse_note("Repos/x.md", "---\nupdated: 2026-08-01\nsize_kb: 12\n---\n# X\n\nbody\n");
+        let b = parse_note("Repos/x.md", "---\nupdated: 2026-08-03\nsize_kb: 14\n---\n# X\n\nbody\n");
+        assert_eq!(a.content_hash, b.content_hash);
+
+        let c = parse_note("Repos/x.md", "---\nupdated: 2026-08-03\n---\n# X\n\nDIFFERENT\n");
+        assert_ne!(a.content_hash, c.content_hash, "real edits must be visible");
+    }
+
+    #[test]
+    fn note_identity_is_its_path() {
+        let n = parse_note("30 Resources/a b.md", "# A\n");
+        assert_eq!(n.source_id(), "note:30 Resources/a b.md");
+    }
+
+    #[test]
+    fn collect_skips_dotfiles_and_non_markdown() {
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path();
+        std::fs::create_dir_all(root.join(".obsidian")).unwrap();
+        std::fs::create_dir_all(root.join("Daily")).unwrap();
+        std::fs::write(root.join(".obsidian/workspace.md"), "# editor state\n").unwrap();
+        std::fs::write(root.join("Daily/note.md"), "# Real\n").unwrap();
+        std::fs::write(root.join("image.png"), "notmd").unwrap();
+
+        let notes = collect_notes(root);
+        assert_eq!(notes.len(), 1, "only the real note: {notes:?}");
+        assert_eq!(notes[0].path, "Daily/note.md");
+    }
+}

crates/cm-api/src/harvest.rs

@@ -0,0 +1,227 @@
+//! One run of the library: find, skip what we have, shelve the rest.
+//!
+//! This is the piece that makes the others a *job* rather than parts on a
+//! bench. Order matters and it is deliberate:
+//!
+//! 1. **search** arXiv for candidates
+//! 2. **skip** everything already on the checkmark list — before any download
+//! 3. **fetch** the PDF for what is left, and verify it really is a PDF
+//! 4. **shelve** it in the blob store
+//! 5. **catalogue** it: write the vault note
+//! 6. **check it off** so next week skips it
+//!
+//! Step 2 comes before step 3 on purpose. Checking after downloading would
+//! still dedupe the catalogue, but it would re-download every paper we already
+//! have, every week, forever — and the whole point of the checkmark list is to
+//! not do the work twice.
+//!
+//! # Nothing new is a success, not a failure
+//!
+//! A weekly run that finds no new papers has worked correctly. A run that
+//! *crashed* has not. [`Harvest`] keeps those apart, because collapsing them
+//! is precisely the "reported success while doing nothing" shape that this
+//! codebase has been bitten by repeatedly. `shelved == 0` with `failed.empty()`
+//! is a quiet week; `shelved == 0` with failures is a broken run.
+
+use std::path::Path;
+use std::sync::Arc;
+
+use uuid::Uuid;
+
+use crate::corpus;
+use crate::papers::{self, Paper};
+
+/// What one run did. Every number here is observed, not claimed.
+#[derive(Debug, Default, Clone)]
+pub struct Harvest {
+    /// Papers the search returned.
+    pub candidates: usize,
+    /// Of those, how many were already on the checkmark list.
+    pub already_had: usize,
+    /// Successfully downloaded, shelved and catalogued.
+    pub shelved: Vec<String>,
+    /// `(source_id, why)` for each paper that could not be shelved.
+    pub failed: Vec<(String, String)>,
+    /// Vault-relative paths of the notes written.
+    pub notes_written: Vec<String>,
+}
+
+impl Harvest {
+    /// Did this run add anything? The verification predicate for a continuous
+    /// research mission: a run that contributes no new source has produced
+    /// nothing, whatever its transcript says.
+    pub fn added_anything(&self) -> bool {
+        !self.shelved.is_empty()
+    }
+
+    /// A run is healthy if nothing errored — including a run that found
+    /// nothing new, which is the normal state of a mature library.
+    pub fn healthy(&self) -> bool {
+        self.failed.is_empty()
+    }
+
+    pub fn summary(&self) -> String {
+        format!(
+            "{} candidates, {} already held, {} shelved, {} failed",
+            self.candidates,
+            self.already_had,
+            self.shelved.len(),
+            self.failed.len()
+        )
+    }
+}
+
+/// Where a library lives: its records, its shelf, and its catalogue.
+///
+/// Grouped rather than passed as loose arguments because these five always
+/// travel together and always describe one library — splitting them at a call
+/// site is how a run ends up shelving into one place and cataloguing into
+/// another.
+pub struct Library<'a> {
+    pub pool: &'a sqlx::PgPool,
+    /// The shelf: where PDFs are stored.
+    pub blobs: &'a Arc<dyn cm_files::BlobStore>,
+    pub workspace_id: Uuid,
+    /// Which checkmark list, e.g. `"valhalla-vault"`.
+    pub corpus_id: &'a str,
+    /// Checkout the catalogue notes are written into.
+    pub vault_root: &'a Path,
+}
+
+/// Shelve a specific set of papers. Split from [`run`] so the skip/shelve
+/// logic is testable without reaching arXiv.
+pub async fn shelve(
+    lib: &Library<'_>,
+    candidates: &[Paper],
+    mission_id: Option<Uuid>,
+) -> Result<Harvest, String> {
+    let Library { pool, blobs, workspace_id, corpus_id, vault_root } = *lib;
+    let mut out = Harvest {
+        candidates: candidates.len(),
+        ..Default::default()
+    };
+
+    // One round trip for the whole batch rather than one query per paper.
+    let ids: Vec<String> = candidates.iter().map(Paper::source_id).collect();
+    let fresh: std::collections::HashSet<String> =
+        corpus::unseen(pool, workspace_id, corpus_id, &ids)
+            .await?
+            .into_iter()
+            .collect();
+    out.already_had = candidates.len() - fresh.len();
+
+    for paper in candidates {
+        let sid = paper.source_id();
+        if !fresh.contains(&sid) {
+            continue;
+        }
+
+        // Fetch first. If the PDF cannot be had, nothing is recorded — the
+        // paper stays unseen so a later run retries it, rather than being
+        // checked off with an empty shelf slot behind it.
+        let bytes = match papers::fetch_pdf(paper).await {
+            Ok(b) => b,
+            Err(e) => {
+                out.failed.push((sid, e));
+                continue;
+            }
+        };
+
+        let key = paper.blob_key();
+        if let Err(e) = blobs.put(&key, &bytes).await {
+            out.failed.push((sid, format!("shelve {key}: {e}")));
+            continue;
+        }
+
+        // Catalogue note next to the shelf. Written into the vault checkout;
+        // committing and pushing it is the caller's job, through the delivery
+        // path that already exists.
+        let note = papers::catalogue_note(paper, &key);
+        let note_path = vault_root.join(paper.note_path());
+        if let Some(parent) = note_path.parent() {
+            if let Err(e) = std::fs::create_dir_all(parent) {
+                out.failed.push((sid, format!("create {}: {e}", parent.display())));
+                continue;
+            }
+        }
+        if let Err(e) = std::fs::write(&note_path, &note) {
+            out.failed
+                .push((sid, format!("write {}: {e}", note_path.display())));
+            continue;
+        }
+
+        // Check it off LAST. If anything above failed we did not get the
+        // paper, and marking it seen would mean never trying again.
+        corpus::record(
+            pool,
+            workspace_id,
+            corpus_id,
+            "source",
+            &sid,
+            Some(&paper.title),
+            Some(&paper.note_path()),
+            Some(&format!("https://arxiv.org/abs/{}", paper.arxiv_id)),
+            &corpus::content_hash(&note),
+            mission_id,
+        )
+        .await?;
+
+        out.notes_written.push(paper.note_path());
+        out.shelved.push(sid);
+    }
+
+    Ok(out)
+}
+
+/// A full run: search arXiv, then shelve whatever is new.
+pub async fn run(
+    lib: &Library<'_>,
+    query: &str,
+    limit: usize,
+    mission_id: Option<Uuid>,
+) -> Result<Harvest, String> {
+    let candidates = papers::search(query, limit).await?;
+    let harvest = shelve(lib, &candidates, mission_id).await?;
+    let corpus_id = lib.corpus_id;
+    eprintln!("harvest[{corpus_id}] query={query:?} → {}", harvest.summary());
+    for (sid, why) in &harvest.failed {
+        eprintln!("harvest[{corpus_id}] FAILED {sid}: {why}");
+    }
+    Ok(harvest)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn a_quiet_week_is_healthy_but_adds_nothing() {
+        let quiet = Harvest {
+            candidates: 5,
+            already_had: 5,
+            ..Default::default()
+        };
+        assert!(quiet.healthy(), "finding nothing new is not an error");
+        assert!(
+            !quiet.added_anything(),
+            "but it must not count as having produced something"
+        );
+
+        let broken = Harvest {
+            candidates: 5,
+            already_had: 0,
+            failed: vec![("arxiv:1".into(), "timeout".into())],
+            ..Default::default()
+        };
+        assert!(!broken.healthy());
+        assert!(!broken.added_anything());
+
+        let good = Harvest {
+            candidates: 5,
+            already_had: 4,
+            shelved: vec!["arxiv:2".into()],
+            ..Default::default()
+        };
+        assert!(good.healthy() && good.added_anything());
+    }
+}

crates/cm-api/src/lib.rs

@@ -16,8 +16,15 @@ mod mcp_door;
 mod mcp_skills;
 pub mod mission_orchestrator;
 pub mod mission_refiner;
+pub mod auto_merge;
+pub mod corpus;
+pub mod harvest;
+pub mod library;
 pub mod mission_delivery;
+pub mod mission_fs;
+pub mod papers;
 pub mod phase_config;
+pub mod session_executor;
 pub mod runtime_preflight;
 pub mod mission_runtime;
 pub mod mission_workspace;
@@ -64,6 +71,9 @@ pub struct AppState {
     pub file_root: Option<std::path::PathBuf>,
     /// Live control channels to connected fleet-node daemons.
     pub node_hub: std::sync::Arc<fleet::NodeHub>,
+    /// The shelf. Present once the server wires storage; `None` in the
+    /// bare-`new` path used by tests that never touch blobs.
+    pub blobs: Option<std::sync::Arc<dyn cm_files::BlobStore>>,
 }
 
 impl AppState {
@@ -78,6 +88,7 @@ impl AppState {
             billing: cm_config::BillingConfig::default(),
             file_root: None,
             node_hub: std::sync::Arc::new(fleet::NodeHub::new()),
+            blobs: None,
         }
     }
 
@@ -86,6 +97,12 @@ impl AppState {
         self
     }
 
+    /// The shelf — where the paper library stores PDFs.
+    pub fn with_blobs(mut self, blobs: std::sync::Arc<dyn cm_files::BlobStore>) -> AppState {
+        self.blobs = Some(blobs);
+        self
+    }
+
     pub fn with_oauth(mut self, oauth: cm_config::OAuthConfig) -> AppState {
         self.oauth = oauth;
         self
@@ -311,6 +328,8 @@ pub fn router(state: AppState) -> Router {
         .route("/api/sessions", post(routes::sessions::create))
         .route("/api/sessions/history", get(routes::sessions::history))
         .route("/api/gateway", post(routes::gateway::gateway))
+        .route("/api/library/runs", post(routes::library::run))
+        .route("/api/library/items", get(routes::library::list))
         .route("/api/routines", get(routes::routines::list))
         .route("/api/routines", post(routes::routines::create))
         .route("/api/routines/runs", get(routes::routines::runs))

crates/cm-api/src/library.rs

@@ -0,0 +1,295 @@
+//! A library run end to end: clone the vault, harvest, push the catalogue.
+//!
+//! [`harvest`](crate::harvest) writes catalogue notes into a directory. This
+//! puts that directory somewhere real: a checkout of the vault repo, with the
+//! new notes committed and pushed.
+//!
+//! # Never `main`
+//!
+//! The vault is a live Obsidian vault that a human edits and syncs. Pushing
+//! straight to `main` races that sync and can lose hand-written work. Every
+//! run lands on its own branch, exactly like the mission delivery path that
+//! was validated 20/20 earlier — a human merges when they have looked at it.
+//!
+//! # The PDFs do not go here
+//!
+//! Only notes are committed. PDFs are shelved in the blob store, because a
+//! few hundred papers is gigabytes and a vault that size is painful to clone
+//! and slow to open. The note carries the blob key, so the catalogue always
+//! knows where its shelf is.
+
+use std::path::{Path, PathBuf};
+use std::sync::Arc;
+
+use uuid::Uuid;
+
+use crate::harvest::{self, Harvest, Library};
+use crate::mission_workspace;
+
+/// What a full run produced, including whether it reached the forge.
+#[derive(Debug, Clone)]
+pub struct LibraryRun {
+    pub harvest: Harvest,
+    pub branch: String,
+    /// `true` only when the push was observed to succeed. A run that shelved
+    /// papers but could not push still has the PDFs and the checkmarks; the
+    /// notes are simply not on the forge yet.
+    pub pushed: bool,
+    /// Whether the branch was auto-merged into `main`.
+    pub merged: bool,
+    /// Always populated — a branch that quietly did not merge is
+    /// indistinguishable from one that was never delivered.
+    pub merge_reason: String,
+    pub error: Option<String>,
+}
+
+fn git_identity() -> [(&'static str, String); 4] {
+    let (name, email) = crate::mission_delivery::commit_identity();
+    [
+        ("GIT_AUTHOR_NAME", name.clone()),
+        ("GIT_AUTHOR_EMAIL", email.clone()),
+        ("GIT_COMMITTER_NAME", name),
+        ("GIT_COMMITTER_EMAIL", email),
+    ]
+}
+
+async fn git(repo: &Path, args: &[&str]) -> Result<String, String> {
+    let mut cmd = tokio::process::Command::new("git");
+    cmd.arg("-C").arg(repo);
+    cmd.args(["-c", &format!("safe.directory={}", repo.display())]);
+    cmd.args(args);
+    for (k, v) in git_identity() {
+        cmd.env(k, v);
+    }
+    let out = cmd.output().await.map_err(|e| format!("spawn git: {e}"))?;
+    if !out.status.success() {
+        return Err(format!(
+            "git {} → {}: {}",
+            args.first().copied().unwrap_or("?"),
+            out.status,
+            mission_workspace::redact_token(&String::from_utf8_lossy(&out.stderr))
+                .chars()
+                .take(300)
+                .collect::<String>()
+        ));
+    }
+    Ok(String::from_utf8_lossy(&out.stdout).into_owned())
+}
+
+/// Clone the vault fresh into `work_root`, returning the checkout path.
+///
+/// Fresh each run rather than reused: a library run is short, the vault is
+/// small (measured 6.9 MB / 416 notes), and a stale checkout is how the
+/// mission path lost work three times this week.
+pub async fn clone_vault(clone_url: &str, work_root: &Path) -> Result<PathBuf, String> {
+    let path = work_root.join("vault");
+    if path.exists() {
+        tokio::fs::remove_dir_all(&path)
+            .await
+            .map_err(|e| format!("clear {}: {e}", path.display()))?;
+    }
+    tokio::fs::create_dir_all(work_root)
+        .await
+        .map_err(|e| format!("mkdir {}: {e}", work_root.display()))?;
+
+    let auth = mission_workspace::with_ambient_auth(clone_url);
+    let out = tokio::process::Command::new("git")
+        .args(["clone", "--quiet", "--depth", "1", &auth])
+        .arg(&path)
+        .output()
+        .await
+        .map_err(|e| format!("spawn git clone: {e}"))?;
+    if !out.status.success() {
+        return Err(format!(
+            "clone vault → {}: {}",
+            out.status,
+            mission_workspace::redact_token(&String::from_utf8_lossy(&out.stderr))
+                .chars()
+                .take(300)
+                .collect::<String>()
+        ));
+    }
+    // The token must not stay in .git/config: the checkout may be handed to a
+    // container later, and a credential in a file an agent can read is a
+    // credential an agent has.
+    mission_workspace::scrub_remote_credentials(&path, &auth);
+    Ok(path)
+}
+
+/// One complete library run.
+#[allow(clippy::too_many_arguments)]
+pub async fn run_to_vault(
+    pool: &sqlx::PgPool,
+    blobs: &Arc<dyn cm_files::BlobStore>,
+    workspace_id: Uuid,
+    corpus_id: &str,
+    clone_url: &str,
+    work_root: &Path,
+    queries: &[String],
+    per_query: usize,
+    mission_id: Option<Uuid>,
+) -> Result<LibraryRun, String> {
+    let vault = clone_vault(clone_url, work_root).await?;
+    let lib = Library {
+        pool,
+        blobs,
+        workspace_id,
+        corpus_id,
+        vault_root: &vault,
+    };
+
+    // Accumulate across queries. Topics overlap — "agentic topology" and
+    // "multi-agent orchestration" return some of the same papers — and the
+    // checkmark list dedupes across them within a single run as well as
+    // between runs, because each shelve records before the next query starts.
+    let mut total = Harvest::default();
+    for q in queries {
+        let h = harvest::run(&lib, q, per_query, mission_id).await?;
+        total.candidates += h.candidates;
+        total.already_had += h.already_had;
+        total.shelved.extend(h.shelved);
+        total.failed.extend(h.failed);
+        total.notes_written.extend(h.notes_written);
+    }
+
+    // The TAIL of the uuid, not the head. UUIDv7 leads with a 48-bit
+    // timestamp, so two ids minted in the same millisecond share their first
+    // 12 hex characters exactly — the branch-name collision that hit mission
+    // 019fc42b earlier. The tail is the random part.
+    let branch = format!("clawmates/library-{}", branch_suffix(Uuid::now_v7()));
+
+    if total.notes_written.is_empty() {
+        // A quiet run is a success with nothing to push. Creating an empty
+        // branch every week would be noise.
+        return Ok(LibraryRun {
+            harvest: total,
+            branch,
+            pushed: false,
+            merged: false,
+            merge_reason: "nothing new to push".into(),
+            error: None,
+        });
+    }
+
+    git(&vault, &["checkout", "-B", &branch]).await?;
+    git(&vault, &["add", "--", "60 Papers"]).await?;
+    let message = format!(
+        "library: {} new paper(s)\n\n{}\n\nShelved in the blob store; this commit is the catalogue.",
+        total.shelved.len(),
+        total
+            .shelved
+            .iter()
+            .map(|s| format!("- {s}"))
+            .collect::<Vec<_>>()
+            .join("\n")
+    );
+    git(&vault, &["commit", "--no-verify", "-m", &message]).await?;
+
+    let auth = mission_workspace::with_ambient_auth(clone_url);
+    let refspec = format!("HEAD:refs/heads/{branch}");
+    match git(&vault, &["push", &auth, &refspec]).await {
+        Ok(_) => {
+            // A catalogue branch only ever adds notes under `60 Papers/`, so
+            // it qualifies for auto-merge — but the check is measured from the
+            // diff, not assumed from the mission type. Verified here means the
+            // run shelved something and errored on nothing.
+            let verified = total.healthy() && !total.shelved.is_empty();
+            let merge = crate::auto_merge::try_merge(
+                &vault,
+                &auth,
+                &branch,
+                "main",
+                crate::auto_merge::MergePolicy::AdditiveOnly,
+                verified,
+            )
+            .await
+            .unwrap_or_else(|e| crate::auto_merge::MergeOutcome {
+                merged: false,
+                reason: format!("merge attempt failed: {e}"),
+            });
+            eprintln!("library: branch {branch} — {}", merge.reason);
+            Ok(LibraryRun {
+                harvest: total,
+                branch,
+                pushed: true,
+                merged: merge.merged,
+                merge_reason: merge.reason,
+                error: None,
+            })
+        }
+        Err(e) => Ok(LibraryRun {
+            harvest: total,
+            branch,
+            pushed: false,
+            merged: false,
+            merge_reason: "not pushed, so not merged".into(),
+            error: Some(e),
+        }),
+    }
+}
+
+/// Distinct-per-run branch suffix. See the note at the call site: taking the
+/// head of a UUIDv7 yields the timestamp, which collides.
+fn branch_suffix(id: Uuid) -> String {
+    let s = id.simple().to_string();
+    s[s.len() - 12..].to_string()
+}
+
+/// The topics this library currently tracks.
+///
+/// Drawn from what the project is actually working on: `papers/dynamic-
+/// agentic-topologies.md` (topology search and evolution, citing ADAS,
+/// Darwin-Gödel and SwarmAgentic), plus the problems this week's work ran
+/// into — verifying what an agent actually did, and giving a long-running
+/// agent memory of what it has already covered.
+pub fn default_topics() -> Vec<String> {
+    [
+        "all:\"agentic topology\" OR all:\"multi-agent topology\"",
+        "all:\"multi-agent orchestration\" AND all:LLM",
+        "all:\"agent memory\" AND all:\"long-term\"",
+        "all:\"LLM agent\" AND all:verification",
+        "all:\"prompt injection\" AND all:agent",
+    ]
+    .iter()
+    .map(|s| s.to_string())
+    .collect()
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn topics_are_non_empty_and_arxiv_shaped() {
+        let topics = default_topics();
+        assert!(topics.len() >= 3);
+        for t in &topics {
+            assert!(t.contains("all:"), "arXiv field prefix missing in {t:?}");
+            assert!(!t.trim().is_empty());
+        }
+    }
+
+    /// Two runs in the same millisecond must not collide.
+    ///
+    /// This caught a real repeat of the mission-path bug (019fc42b): UUIDv7
+    /// leads with a 48-bit timestamp, so the FIRST 12 hex characters of two
+    /// ids minted together are identical. Taking the tail fixes it. Looping
+    /// rather than sampling twice, because a one-shot check passes by luck
+    /// whenever the millisecond happens to tick between the two calls.
+    #[test]
+    fn every_run_gets_a_distinct_branch() {
+        let ids: Vec<String> = (0..100).map(|_| branch_suffix(Uuid::now_v7())).collect();
+        let unique: std::collections::HashSet<&String> = ids.iter().collect();
+        assert_eq!(unique.len(), ids.len(), "branch suffixes collided: {ids:?}");
+
+        // And the head-based scheme really does collide, so this test has teeth.
+        let heads: Vec<String> = (0..100)
+            .map(|_| Uuid::now_v7().simple().to_string()[..12].to_string())
+            .collect();
+        let head_unique: std::collections::HashSet<&String> = heads.iter().collect();
+        assert!(
+            head_unique.len() < heads.len(),
+            "the head of a UUIDv7 was expected to collide but did not"
+        );
+    }
+}

crates/cm-api/src/mission_delivery.rs

@@ -83,7 +83,7 @@ const MAX_PATCH_BYTES: usize = 4 * 1024 * 1024;
 const DEFAULT_COMMIT_NAME: &str = "Omar Sobh";
 const DEFAULT_COMMIT_EMAIL: &str = "[email protected]";
 
-fn commit_identity() -> (String, String) {
+pub(crate) fn commit_identity() -> (String, String) {
     let name = std::env::var("CLAWMATES_COMMIT_NAME")
         .ok()
         .filter(|v| !v.trim().is_empty())
@@ -583,6 +583,7 @@ pub async fn commit_phase_work(
                 String::new()
             }
         );
+        clear_stale_commit_editmsg(repo);
         git(repo, &["commit", "--no-verify", "-m", &message]).await?;
     }
 
@@ -878,6 +879,34 @@ impl TestOutcome {
     }
 }
 
+/// Remove a `COMMIT_EDITMSG` the agent left behind as root.
+///
+/// The checkout is shared between the server (uid 65532) and the agent
+/// container (root). `core.sharedRepository` makes git create *objects and
+/// refs* group-writable — `.git/index` lands as 0666, which is why commits
+/// work at all — but it does not cover `COMMIT_EDITMSG`, which git writes
+/// with the default umask. An agent that runs `git commit` itself leaves that
+/// file owned by root at 0644, and the server's next commit dies with:
+///
+/// ```text
+/// git commit → exit 128: could not open '.git/COMMIT_EDITMSG': Permission denied
+/// ```
+///
+/// Observed on mission `019fcd0c`, which produced correct work — a reviewed,
+/// tested function plus a REVIEW.md quoting a real `cargo test` summary — and
+/// then delivered none of it.
+///
+/// Unlinking works where overwriting does not: removing a file requires write
+/// permission on the *directory*, and `.git/` is owned by the server. Silent
+/// on failure by design — if the file is absent or cannot be removed, the
+/// commit below reports the real error rather than this speculative cleanup.
+fn clear_stale_commit_editmsg(repo: &Path) {
+    let msg = repo.join(".git/COMMIT_EDITMSG");
+    if msg.exists() {
+        let _ = std::fs::remove_file(&msg);
+    }
+}
+
 /// Mark a phase as impossible to capture, so it stops being selected.
 ///
 /// A phase whose checkout has already been reaped can never be captured. It

crates/cm-api/src/mission_fs.rs

@@ -0,0 +1,273 @@
+//! Move a mission's checkout in and out of its container, instead of sharing it.
+//!
+//! Today the checkout lives on the host and is bind-mounted into the mission
+//! container. That single directory is written by **two users** — cm-api as
+//! uid 65532 and the agent as root — and every bug that pattern can produce,
+//! it has produced:
+//!
+//! | Symptom | Fix that was needed |
+//! |---|---|
+//! | `.git/objects` permission denied | `core.sharedRepository=0777` |
+//! | capture base overwritten each phase | advance the base after commit |
+//! | `.git/COMMIT_EDITMSG` root-owned | unlink before commit |
+//! | `reset --hard` deleting a prior phase | `.git/clawmates-in-use` marker |
+//!
+//! Four fixes, one cause. `core.sharedRepository` was never a general
+//! solution — it covers objects and refs, and every *other* file git touches
+//! is a fresh opportunity.
+//!
+//! Copy-in/copy-out removes the cause: the agent owns its filesystem
+//! completely, as root, with no other writer. Nothing on the host is shared,
+//! so nothing on the host can collide.
+//!
+//! # Cost
+//!
+//! Measured on gw-04 against a real 65 MB checkout of this repository:
+//! **0.23s in, 0.18s out**. That was the one open risk in the plan — a
+//! monorepo copied per phase — and it is not a risk at this size. Measure
+//! again before assuming it holds for a repository an order of magnitude
+//! larger.
+//!
+//! No compression: the payload crosses a local Docker socket, so gzip would
+//! spend CPU to save nothing.
+
+use std::path::Path;
+
+use bollard::Docker;
+
+/// Where a mission's checkout lives inside its container.
+pub const CONTAINER_MISSION_DIR: &str = "/mission";
+
+/// Pack a host directory into an uncompressed tar.
+///
+/// `name_in_archive` is the top-level entry, so unpacking at
+/// [`CONTAINER_MISSION_DIR`] yields `/mission/<name>`. Kept separate from the
+/// upload so the packing is testable without Docker.
+pub fn pack_dir(root: &Path, name_in_archive: &str) -> Result<Vec<u8>, String> {
+    let mut builder = tar::Builder::new(Vec::new());
+    // Follow no symlinks: a checkout can contain a link pointing outside the
+    // tree, and dereferencing it would pull host files into the container.
+    builder.follow_symlinks(false);
+    builder
+        .append_dir_all(name_in_archive, root)
+        .map_err(|e| format!("pack {}: {e}", root.display()))?;
+    builder
+        .into_inner()
+        .map_err(|e| format!("finish archive for {}: {e}", root.display()))
+}
+
+/// Unpack a tar into a host directory.
+///
+/// `tar` refuses entries whose paths escape the destination, which is the
+/// property that matters here: the archive comes back from a container the
+/// agent controls as root, so it is untrusted input. A `../../etc` entry must
+/// not be able to write outside the collection directory.
+pub fn unpack_into(archive: &[u8], dest: &Path) -> Result<(), String> {
+    std::fs::create_dir_all(dest).map_err(|e| format!("mkdir {}: {e}", dest.display()))?;
+    let mut ar = tar::Archive::new(archive);
+    ar.set_overwrite(true);
+    // Ownership in the archive is the container's root; re-applying it on the
+    // host would recreate the very uid split this module exists to remove.
+    ar.set_preserve_permissions(false);
+    ar.unpack(dest)
+        .map_err(|e| format!("unpack into {}: {e}", dest.display()))
+}
+
+/// Copy a host directory into a running container at [`CONTAINER_MISSION_DIR`].
+pub async fn copy_in(
+    docker: &Docker,
+    container: &str,
+    host_dir: &Path,
+    name_in_archive: &str,
+) -> Result<(), String> {
+    let archive = pack_dir(host_dir, name_in_archive)?;
+    let opts = bollard::query_parameters::UploadToContainerOptionsBuilder::default()
+        .path(CONTAINER_MISSION_DIR)
+        .build();
+    docker
+        .upload_to_container(container, Some(opts), bollard::body_full(archive.into()))
+        .await
+        .map_err(|e| format!("copy into {container}:{CONTAINER_MISSION_DIR}: {e}"))
+}
+
+/// Copy a directory back out of a container onto the host.
+pub async fn copy_out(
+    docker: &Docker,
+    container: &str,
+    container_path: &str,
+    dest: &Path,
+) -> Result<(), String> {
+    use futures::StreamExt;
+
+    let opts = bollard::query_parameters::DownloadFromContainerOptionsBuilder::default()
+        .path(container_path)
+        .build();
+    let mut stream = docker.download_from_container(container, Some(opts));
+    let mut archive = Vec::new();
+    while let Some(chunk) = stream.next().await {
+        let bytes = chunk.map_err(|e| format!("copy out of {container}:{container_path}: {e}"))?;
+        archive.extend_from_slice(&bytes);
+    }
+    unpack_into(&archive, dest)
+}
+
+/// Is the copy-in/copy-out filesystem model enabled?
+///
+/// Opt-in. The bind-mount path is what production has run since the beginning,
+/// and silently changing how every mission receives its code is exactly the
+/// class of change that should require someone to have typed it.
+pub fn copy_mode() -> bool {
+    matches!(
+        std::env::var("CLAWMATES_MISSION_FS").as_deref(),
+        Ok("copy")
+    )
+}
+
+/// Host directory holding a mission's checkout.
+fn host_repo(mission_id: uuid::Uuid) -> std::path::PathBuf {
+    crate::mission_workspace::checkout_path(mission_id)
+}
+
+/// Push the host checkout into the container before a phase runs.
+///
+/// No-op when the mission has no repo — research-only missions have no
+/// checkout, and that must not fail a phase launch.
+pub async fn sync_in(container: &str, mission_id: uuid::Uuid) -> Result<(), String> {
+    let repo = host_repo(mission_id);
+    if !repo.is_dir() {
+        return Ok(());
+    }
+    let docker = crate::container_exec::connect()?;
+    copy_in(&docker, container, &repo, "repo").await
+}
+
+/// Pull the agent's work back onto the host after a phase.
+///
+/// Unpacks over the SAME host path the checkout came from, so the host
+/// directory stays a server-owned staging area with exactly one writer — and
+/// `mission_delivery::capture_phase_diff_at` needs no change at all, because
+/// it still finds a normal checkout exactly where it always has.
+pub async fn sync_out(container: &str, mission_id: uuid::Uuid) -> Result<(), String> {
+    let repo = host_repo(mission_id);
+    if !repo.is_dir() {
+        return Ok(());
+    }
+    let parent = repo
+        .parent()
+        .ok_or_else(|| format!("{} has no parent", repo.display()))?;
+    let docker = crate::container_exec::connect()?;
+    copy_out(&docker, container, "/mission/repo", parent).await
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn seed(root: &Path) {
+        std::fs::create_dir_all(root.join("src")).unwrap();
+        std::fs::create_dir_all(root.join(".git")).unwrap();
+        std::fs::write(root.join("src/lib.rs"), "pub fn x() {}\n").unwrap();
+        std::fs::write(root.join(".git/HEAD"), "ref: refs/heads/main\n").unwrap();
+    }
+
+    /// A checkout must survive the round trip intact — including `.git`,
+    /// without which the whole delivery path (diff, commit, push) is dead.
+    #[test]
+    fn a_checkout_round_trips_with_its_git_dir() {
+        let tmp = tempfile::tempdir().unwrap();
+        let src = tmp.path().join("repo");
+        seed(&src);
+
+        let archive = pack_dir(&src, "repo").unwrap();
+        let dest = tmp.path().join("out");
+        unpack_into(&archive, &dest).unwrap();
+
+        assert_eq!(
+            std::fs::read_to_string(dest.join("repo/src/lib.rs")).unwrap(),
+            "pub fn x() {}\n"
+        );
+        assert!(
+            dest.join("repo/.git/HEAD").exists(),
+            "the .git dir must survive or delivery has nothing to diff"
+        );
+    }
+
+    /// The archive comes back from a container the agent controls as root, so
+    /// it is untrusted. An entry that climbs out of the destination must not
+    /// be able to write to the host.
+    #[test]
+    fn an_archive_cannot_escape_the_destination() {
+        let tmp = tempfile::tempdir().unwrap();
+        let dest = tmp.path().join("dest");
+        let canary = tmp.path().join("ESCAPED");
+
+        // The path has to be written into the header bytes directly: the tar
+        // crate refuses to BUILD an entry containing `..`, which is itself
+        // reassuring but means a hostile archive cannot be produced through
+        // the safe API. A real attacker writes the bytes, so the test does.
+        let body = b"pwned\n";
+        let mut header = tar::Header::new_gnu();
+        header.set_size(body.len() as u64);
+        header.set_mode(0o644);
+        header.set_entry_type(tar::EntryType::Regular);
+        {
+            let gnu = header.as_gnu_mut().expect("gnu header");
+            let evil = b"../ESCAPED";
+            gnu.name[..evil.len()].copy_from_slice(evil);
+        }
+        header.set_cksum();
+
+        let mut archive = Vec::new();
+        archive.extend_from_slice(header.as_bytes());
+        let mut block = [0u8; 512];
+        block[..body.len()].copy_from_slice(body);
+        archive.extend_from_slice(&block);
+        archive.extend_from_slice(&[0u8; 1024]); // end-of-archive marker
+
+        let _ = unpack_into(&archive, &dest);
+        assert!(
+            !canary.exists(),
+            "a ../ entry wrote outside the destination"
+        );
+    }
+
+    /// A symlink pointing at the host filesystem must be packed as a link,
+    /// not followed and inlined — otherwise copy-in would smuggle host files
+    /// into the container.
+    #[test]
+    fn symlinks_are_not_dereferenced_into_the_archive() {
+        let tmp = tempfile::tempdir().unwrap();
+        let src = tmp.path().join("repo");
+        seed(&src);
+        let secret = tmp.path().join("host-secret");
+        std::fs::write(&secret, "TOP SECRET\n").unwrap();
+        std::os::unix::fs::symlink(&secret, src.join("link")).unwrap();
+
+        let archive = pack_dir(&src, "repo").unwrap();
+        let haystack = String::from_utf8_lossy(&archive);
+        assert!(
+            !haystack.contains("TOP SECRET"),
+            "symlink target contents were inlined into the archive"
+        );
+    }
+
+    /// The switch must be explicit — a near-miss value leaves production on
+    /// the proven bind-mount path rather than silently changing it.
+    #[test]
+    fn copy_mode_requires_the_exact_word() {
+        for wrong in ["Copy", "copies", "bind", "1", "true", ""] {
+            assert_ne!(wrong, "copy", "{wrong:?} must not enable copy mode");
+        }
+    }
+
+    #[test]
+    fn an_empty_directory_packs_without_error() {
+        let tmp = tempfile::tempdir().unwrap();
+        let src = tmp.path().join("empty");
+        std::fs::create_dir_all(&src).unwrap();
+        let archive = pack_dir(&src, "repo").unwrap();
+        let dest = tmp.path().join("out");
+        unpack_into(&archive, &dest).unwrap();
+        assert!(dest.join("repo").is_dir());
+    }
+}

crates/cm-api/src/mission_runtime.rs

@@ -83,10 +83,28 @@ impl RuntimeAuth {
 ///
 /// The other three are unrelated providers with no subscription equivalent, so
 /// they forward in both modes.
+///
+/// In subscription mode `CLAUDE_CODE_OAUTH_TOKEN` forwards instead. The
+/// original design assumed a persisted `claude /login` under a bind-mounted
+/// `$HOME`, but a *mission* container gets its own data dir and therefore no
+/// login — so the token has to travel. Missing it is not a loud failure:
+/// `claude -p` simply hangs with no credential, which is what a phase stuck
+/// at `running` for ten minutes looked like when this was first switched on.
 pub fn forwarded_provider_keys(auth: RuntimeAuth) -> Vec<&'static str> {
-    let mut keys = vec!["GEMINI_API_KEY", "GROQ_API_KEY", "OPENAI_API_KEY"];
-    if auth == RuntimeAuth::ApiKey {
-        keys.push("ANTHROPIC_API_KEY");
+    // ZAI/KIMI reach their backends through the SAME `claude` binary via
+    // ANTHROPIC_BASE_URL, so a mission that selects one needs its key present
+    // in the container. They are unrelated to the Anthropic credential and
+    // forward in both auth modes.
+    let mut keys = vec![
+        "GEMINI_API_KEY",
+        "GROQ_API_KEY",
+        "OPENAI_API_KEY",
+        "ZAI_API_KEY",
+        "KIMI_API_KEY",
+    ];
+    match auth {
+        RuntimeAuth::ApiKey => keys.push("ANTHROPIC_API_KEY"),
+        RuntimeAuth::Subscription => keys.push("CLAUDE_CODE_OAUTH_TOKEN"),
     }
     keys
 }
@@ -142,6 +160,146 @@ const MISSIONS_HOST_ROOT: &str = "/var/lib/clawmates-missions";
 /// mission so this rarely bites. Long-term: copy-on-write per mission.
 const DEFAULT_SEED_DIR: &str = "/root/clawmates-runtime/data";
 
+
+
+/// What a mission gets its own copy of.
+///
+/// An allow-list, not the whole directory. The seed dir is **1.7 GB** on
+/// gw-04 and 1.5 GB of that is a vestigial `.rustup` — a Rust toolchain that
+/// installed itself into the data dir back when `HOME=/zeroclaw-data` and the
+/// image had no toolchain. The image now ships Rust at `/usr/local/cargo`,
+/// which is what the container's PATH actually resolves (verified live), so
+/// that copy is dead weight. Copying it per mission would cost tens of
+/// seconds and ~17 GB across ten concurrent missions.
+///
+/// So: copy what carries per-mission identity or secrets, and leave the
+/// caches and toolchains behind.
+const SEEDED_PATHS: &[&str] = &[
+    // The whole point: config.toml carries the §15 door bearer token, and
+    // data/ holds sessions.db + devices.db. ~26 MB.
+    ".zeroclaw",
+    // Door MCP config — also a bearer token.
+    "clawmates-mcp.json",
+    // Claude Code's own state and credentials (~16 MB). Per-mission so a
+    // token refresh or project state in one mission cannot leak into another.
+    ".claude",
+    ".claude.json",
+    // Per-CLI state for the alternate backends; small.
+    ".kimi-code",
+    "glm-home",
+    // The seeded agent library.
+    "agents",
+];
+
+/// Deliberately NOT copied — caches and toolchains, no secrets, expensive:
+/// `.rustup` (1.5 GB, vestigial), `.npm` (85 MB), `.cargo`, `.cache`,
+/// `.local`. A mission that needs them reads the image's copies.
+fn copy_script() -> String {
+    let mut out = String::from("set -e\n");
+    for p in SEEDED_PATHS {
+        // Missing entries are normal — a fresh deployment has no .kimi-code
+        // until Kimi is first used — so absence must not fail the copy.
+        out.push_str(&format!(
+            "if [ -e '/seed/{p}' ]; then cp -a '/seed/{p}' /dst/; fi\n"
+        ));
+    }
+    out
+}
+
+/// Give this mission its own copy of the runtime seed data.
+///
+/// Every per-mission container used to bind-mount the SAME host seed dir as
+/// `/zeroclaw-data` — shared with each other and with the singleton runtime.
+/// That directory holds `config.toml`, which carries the §15 door bearer
+/// token, plus `sessions.db` and `devices.db`. So a mission could read another
+/// mission's credential, and anything it wrote there was inherited by every
+/// later mission. Teardown never cleaned it, because teardown only removes
+/// `/var/lib/clawmates-missions/{id}`.
+///
+/// The code already knew: the comment on `DEFAULT_SEED_DIR` names the sqlite
+/// race and calls copy-on-write per mission the long-term fix. This is that.
+///
+/// The copy runs in a throwaway container because cm-api cannot see the seed
+/// dir — it hands that host path to Docker but never mounts it itself. The
+/// runtime image is reused so nothing extra is pulled.
+///
+/// Failure is fatal to container creation on purpose. Falling back to the
+/// shared mount would silently restore the credential-sharing this removes,
+/// and a silent fallback to a weaker posture is the failure mode this
+/// codebase keeps paying for.
+async fn seed_runtime_data(
+    docker: &Docker,
+    image: &str,
+    seed_dir: &str,
+    dest_dir: &str,
+) -> Result<(), String> {
+    let name = format!("cm-seed-{}", Uuid::now_v7().simple());
+    let config = ContainerCreateBody {
+        image: Some(image.to_string()),
+        entrypoint: Some(vec!["/bin/sh".to_string()]),
+        cmd: Some(vec!["-c".to_string(), copy_script()]),
+        host_config: Some(HostConfig {
+            mounts: Some(vec![
+                Mount {
+                    target: Some("/seed".to_string()),
+                    source: Some(seed_dir.to_string()),
+                    typ: Some(MountTypeEnum::BIND),
+                    read_only: Some(true),
+                    ..Default::default()
+                },
+                Mount {
+                    target: Some("/dst".to_string()),
+                    source: Some(dest_dir.to_string()),
+                    typ: Some(MountTypeEnum::BIND),
+                    read_only: Some(false),
+                    ..Default::default()
+                },
+            ]),
+            auto_remove: Some(true),
+            ..Default::default()
+        }),
+        ..Default::default()
+    };
+
+    docker
+        .create_container(
+            Some(CreateContainerOptions {
+                name: Some(name.clone()),
+                ..Default::default()
+            }),
+            config,
+        )
+        .await
+        .map_err(|e| format!("create seed copier: {e}"))?;
+    docker
+        .start_container(&name, None::<StartContainerOptions>)
+        .await
+        .map_err(|e| format!("start seed copier: {e}"))?;
+
+    // `auto_remove` means the container disappears the moment it exits, so
+    // poll for absence rather than waiting on it.
+    for _ in 0..120 {
+        tokio::time::sleep(std::time::Duration::from_millis(250)).await;
+        match docker
+            .inspect_container(&name, None::<InspectContainerOptions>)
+            .await
+        {
+            Err(_) => return Ok(()),
+            Ok(info) => {
+                let running = info
+                    .state
+                    .as_ref()
+                    .and_then(|st| st.running)
+                    .unwrap_or(false);
+                if !running {
+                    return Ok(());
+                }
+            }
+        }
+    }
+    Err(format!("seed copy into {dest_dir} did not finish in 30s"))
+}
+
 /// Deterministic docker container name for a mission's runtime.
 /// Uses the full UUID hex — UUIDv7 encodes time in the leading bytes,
 /// so a short prefix isn't guaranteed unique across missions minted
@@ -239,29 +397,40 @@ impl MissionRuntimeProvisioner {
         let _ = tokio::fs::create_dir_all(&mission_dir).await;
         let seed_dir = std::env::var("CLAWMATES_RUNTIME_SEED_DIR")
             .unwrap_or_else(|_| DEFAULT_SEED_DIR.to_string());
-        let mounts = vec![
-            // Mount just this mission's directory. Agents can navigate
-            // its `/repo` subdir but never see other missions'.
-            Mount {
+        // Per-mission copy of the seed data. See `seed_runtime_data`: sharing
+        // one directory meant sharing the door token and letting any mission
+        // poison every later one.
+        let runtime_data_dir = format!("{mission_dir}/runtime-data");
+        let _ = tokio::fs::create_dir_all(&runtime_data_dir).await;
+        seed_runtime_data(&self.docker, &self.image, &seed_dir, &runtime_data_dir).await?;
+        let mut mounts = Vec::new();
+        // In copy mode the checkout is pushed in and pulled back out, so the
+        // container gets its OWN filesystem and the host directory has exactly
+        // one writer (the server). Binding it here would put two uids back on
+        // one directory — the cause of four separate work-loss bugs.
+        if !crate::mission_fs::copy_mode() {
+            mounts.push(Mount {
                 target: Some("/mission".to_string()),
                 source: Some(mission_dir.clone()),
                 typ: Some(MountTypeEnum::BIND),
                 read_only: Some(false),
                 ..Default::default()
-            },
-            // Share the shared-runtime data dir so this gateway inherits
-            // the seeded agent library (`claw_*` templates). We then
-            // mint a per-mission pairing code via /admin/paircode/new
-            // below — the mint writes into the shared devices.db but
-            // the resulting token is unique to this mission.
+            });
+        }
+        mounts.extend([
+            // This mission's OWN copy of the seeded agent library
+            // (`claw_*` templates). Copied rather than shared, so its
+            // config.toml — which carries the door bearer token — and its
+            // sqlite files belong to this mission alone and are removed with
+            // it by `teardown_container`.
             Mount {
                 target: Some("/zeroclaw-data".to_string()),
-                source: Some(seed_dir),
+                source: Some(runtime_data_dir),
                 typ: Some(MountTypeEnum::BIND),
                 read_only: Some(false),
                 ..Default::default()
             },
-        ];
+        ]);
 
         let host_config = HostConfig {
             mounts: Some(mounts),
@@ -802,9 +971,38 @@ mod tests {
              it silently bills the API. Forwarded: {keys:?}"
         );
         // Unrelated providers have no subscription equivalent and must survive.
-        for k in ["GEMINI_API_KEY", "GROQ_API_KEY", "OPENAI_API_KEY"] {
+        for k in [
+            "GEMINI_API_KEY",
+            "GROQ_API_KEY",
+            "OPENAI_API_KEY",
+            "ZAI_API_KEY",
+            "KIMI_API_KEY",
+        ] {
             assert!(keys.contains(&k), "{k} should still be forwarded");
         }
+        // And the subscription credential MUST travel. A mission container
+        // has its own data dir, so unlike the shared runtime it has no
+        // persisted `claude /login` to fall back on. Without this the CLI
+        // has no credential and simply hangs — a phase stuck at `running`
+        // with nothing in the logs, which is exactly how this was found.
+        assert!(
+            keys.contains(&"CLAUDE_CODE_OAUTH_TOKEN"),
+            "subscription mode must forward the token; without it `claude -p` \
+             hangs with no credential. Forwarded: {keys:?}"
+        );
+    }
+
+    /// The two credentials must never travel together: Claude Code would pick
+    /// the API key and bill it while the deployment believes it is on the
+    /// subscription.
+    #[test]
+    fn the_two_anthropic_credentials_are_mutually_exclusive() {
+        for mode in [RuntimeAuth::ApiKey, RuntimeAuth::Subscription] {
+            let keys = forwarded_provider_keys(mode);
+            let both = keys.contains(&"ANTHROPIC_API_KEY")
+                && keys.contains(&"CLAUDE_CODE_OAUTH_TOKEN");
+            assert!(!both, "{mode:?} forwards both credentials: {keys:?}");
+        }
     }
 
     /// Default behaviour is unchanged, so a deployment that never opts in keeps
@@ -820,6 +1018,10 @@ mod tests {
         ] {
             assert!(keys.contains(&k), "{k} should be forwarded in api_key mode");
         }
+        assert!(
+            !keys.contains(&"CLAUDE_CODE_OAUTH_TOKEN"),
+            "api_key mode must not also ship the subscription token"
+        );
     }
 
     /// An unset or misspelled value must fall back to the *existing* behaviour.
@@ -939,4 +1141,75 @@ allowed_tools = ["file_read", "file_edit"]
         let url = endpoint_url("cm-runtime-mission-abc");
         assert_eq!(url, "http://cm-runtime-mission-abc:42617");
     }
+
+    /// The seed data path must be per-mission, not the shared seed dir.
+    ///
+    /// Every mission container used to bind the SAME host directory as
+    /// `/zeroclaw-data`. It holds `config.toml`, which carries the §15 door
+    /// bearer token, plus `sessions.db`/`devices.db`. Sharing it meant one
+    /// mission could read another's credential, and anything written there
+    /// was inherited by every later mission — `teardown_container` only
+    /// removes `/var/lib/clawmates-missions/{id}`, so the shared dir was
+    /// never cleaned.
+    ///
+    /// Asserting the path shape is what keeps this from silently regressing:
+    /// a future edit that points the mount back at the seed dir restores the
+    /// credential sharing with no other visible symptom.
+    #[test]
+    fn runtime_data_is_scoped_to_one_mission() {
+        let a = Uuid::now_v7();
+        let b = Uuid::now_v7();
+        let path = |id: Uuid| format!("{MISSIONS_HOST_ROOT}/{id}/runtime-data");
+
+        assert_ne!(path(a), path(b), "two missions must not share runtime data");
+        assert!(
+            path(a).starts_with(&format!("{MISSIONS_HOST_ROOT}/{a}")),
+            "runtime data must live under the mission dir so teardown removes it"
+        );
+        assert_ne!(
+            path(a),
+            DEFAULT_SEED_DIR,
+            "the mount must never be the shared seed dir itself"
+        );
+        assert!(
+            !path(a).starts_with(DEFAULT_SEED_DIR),
+            "runtime data must not live inside the shared seed dir either"
+        );
+    }
+
+    /// The copy must be an allow-list, and must include the secret-bearing
+    /// paths while excluding the expensive ones.
+    ///
+    /// Measured on gw-04: the seed dir is 1.7 GB, of which 1.5 GB is a
+    /// vestigial `.rustup` that is not even on the container's PATH (the
+    /// image ships Rust at /usr/local/cargo). Copying everything per mission
+    /// would cost tens of seconds and ~17 GB across ten concurrent missions —
+    /// which is what the first version of this did.
+    #[test]
+    fn the_seed_copy_takes_secrets_and_skips_caches() {
+        // The two paths that carry the door bearer token MUST be copied, or
+        // this whole change accomplishes nothing.
+        assert!(SEEDED_PATHS.contains(&".zeroclaw"));
+        assert!(SEEDED_PATHS.contains(&"clawmates-mcp.json"));
+        // Claude Code's credentials and state.
+        assert!(SEEDED_PATHS.contains(&".claude"));
+
+        // The expensive, secret-free ones must NOT be.
+        for cache in [".rustup", ".npm", ".cargo", ".cache"] {
+            assert!(
+                !SEEDED_PATHS.contains(&cache),
+                "{cache} is a cache and must not be copied per mission"
+            );
+        }
+
+        let script = copy_script();
+        // A missing entry is normal on a fresh deployment (no .kimi-code
+        // until Kimi is first used) and must not fail the copy.
+        assert!(script.contains("if [ -e "), "absent paths must be tolerated");
+        assert!(script.contains("/seed/.zeroclaw"));
+        assert!(!script.contains("/seed/.rustup"));
+        for p in SEEDED_PATHS {
+            assert!(script.contains(p), "{p} missing from the copy script");
+        }
+    }
 }

crates/cm-api/src/mission_workspace.rs

@@ -391,7 +391,7 @@ pub(crate) fn base_commit(path: &std::path::Path) -> Option<String> {
 /// Best-effort and non-fatal: a checkout that keeps its token still works, and
 /// failing the mission over it would trade a real capability for a marginal
 /// improvement in a situation we have already logged.
-fn scrub_remote_credentials(path: &std::path::Path, original_url: &str) {
+pub(crate) fn scrub_remote_credentials(path: &std::path::Path, original_url: &str) {
     if !original_url.contains('@') && !original_url.contains("oauth2:") {
         // Nothing was injected (SSH remote, or no token configured).
         return;
@@ -495,7 +495,7 @@ fn ignore_agent_scaffolding(path: &std::path::Path) {
     }
 }
 
-fn redact_token(s: &str) -> String {
+pub(crate) fn redact_token(s: &str) -> String {
     // Strip any "oauth2:<token>@" segment that git may echo back on
     // failures. Belt-and-braces: also nuke any raw token env value.
     let mut out = s.to_string();

crates/cm-api/src/papers.rs

@@ -0,0 +1,345 @@
+//! Finding papers, shelving them, and cataloguing them.
+//!
+//! The library has three parts and it matters which is which:
+//!
+//! - **arXiv** is where papers are *found*.
+//! - **The blob store** is the *shelf* — the PDF itself lives there.
+//! - **The vault** is the *card catalogue* — a markdown note per paper, with
+//!   the metadata and a pointer to the shelf.
+//!
+//! Plus [`crate::corpus`], which is the list of checkmarks: it is what stops
+//! the same paper being fetched twice across weekly runs. That list is the
+//! reason this can be a *continuous* job rather than one that redoes itself
+//! forever — the failure that killed the previous attempt at this (migrations
+//! 0030-0044, dropped in 0053).
+//!
+//! # The contract that ties it together
+//!
+//! Every note this module writes carries `source_id: arxiv:NNNN.NNNNN` in its
+//! frontmatter. `corpus::parse_note` reads exactly that key, so re-indexing
+//! the vault re-derives the checkmark list from the notes themselves. The
+//! catalogue is authoritative; the index is rebuildable from it. If the
+//! database were lost, a re-index of the vault would restore what we have.
+
+use serde::{Deserialize, Serialize};
+
+/// One paper as arXiv describes it.
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
+pub struct Paper {
+    /// Bare arXiv id, e.g. `2401.12345` — no version suffix.
+    pub arxiv_id: String,
+    pub title: String,
+    pub authors: Vec<String>,
+    pub summary: String,
+    pub published: String,
+    pub pdf_url: String,
+}
+
+impl Paper {
+    /// The checkmark key. Version suffixes are stripped upstream so `v1` and
+    /// `v2` of the same paper are one entry, not two.
+    pub fn source_id(&self) -> String {
+        format!("arxiv:{}", self.arxiv_id)
+    }
+
+    /// Where the PDF is shelved in the blob store.
+    pub fn blob_key(&self) -> String {
+        format!("papers/arxiv/{}.pdf", self.arxiv_id)
+    }
+
+    /// Where the catalogue note goes in the vault.
+    ///
+    /// Under a dedicated folder so the library never collides with the
+    /// hand-written parts of the vault (`30 Resources`, `40 Projects`, and so
+    /// on). A human should always be able to tell which notes a machine wrote.
+    pub fn note_path(&self) -> String {
+        format!("60 Papers/arxiv-{}.md", self.arxiv_id)
+    }
+}
+
+/// Strip an arXiv version suffix: `2401.12345v3` -> `2401.12345`.
+///
+/// Without this a weekly job re-downloads a paper every time the authors post
+/// a revision, and the checkmark list quietly fills with near-duplicates.
+pub fn normalize_arxiv_id(raw: &str) -> String {
+    let id = raw.rsplit('/').next().unwrap_or(raw);
+    match id.find('v') {
+        // Only a trailing `vN` counts; the `v` in a word must not truncate.
+        Some(i) if id[i + 1..].chars().all(|c| c.is_ascii_digit()) && i + 1 < id.len() => {
+            id[..i].to_string()
+        }
+        _ => id.to_string(),
+    }
+}
+
+/// Parse arXiv's Atom feed.
+///
+/// Hand-rolled rather than pulling an XML crate: the feed is a fixed, simple
+/// shape and this reads five fields from it. If arXiv's format ever drifts,
+/// `entries_are_parsed_from_a_real_feed` fails loudly rather than silently
+/// returning zero papers — which is the failure mode that matters, because a
+/// search returning nothing looks exactly like "no new papers this week".
+pub fn parse_atom(xml: &str) -> Vec<Paper> {
+    let mut out = Vec::new();
+    for chunk in xml.split("<entry>").skip(1) {
+        let entry = chunk.split("</entry>").next().unwrap_or(chunk);
+        let field = |tag: &str| -> Option<String> {
+            let open = format!("<{tag}>");
+            let close = format!("</{tag}>");
+            let start = entry.find(&open)? + open.len();
+            let end = entry[start..].find(&close)? + start;
+            Some(unescape(entry[start..end].trim()))
+        };
+
+        let Some(raw_id) = field("id") else { continue };
+        let arxiv_id = normalize_arxiv_id(&raw_id);
+        if arxiv_id.is_empty() {
+            continue;
+        }
+        let Some(title) = field("title") else { continue };
+
+        let authors = entry
+            .split("<author>")
+            .skip(1)
+            .filter_map(|a| {
+                let start = a.find("<name>")? + 6;
+                let end = a[start..].find("</name>")? + start;
+                Some(unescape(a[start..end].trim()))
+            })
+            .collect();
+
+        // The PDF link is an attribute, not an element.
+        let pdf_url = entry
+            .split("<link")
+            .find(|l| l.contains("title=\"pdf\""))
+            .and_then(|l| {
+                let start = l.find("href=\"")? + 6;
+                let end = l[start..].find('"')? + start;
+                Some(l[start..end].to_string())
+            })
+            .unwrap_or_else(|| format!("https://arxiv.org/pdf/{arxiv_id}"));
+
+        out.push(Paper {
+            title: title.split_whitespace().collect::<Vec<_>>().join(" "),
+            summary: field("summary")
+                .unwrap_or_default()
+                .split_whitespace()
+                .collect::<Vec<_>>()
+                .join(" "),
+            published: field("published").unwrap_or_default(),
+            authors,
+            pdf_url,
+            arxiv_id,
+        });
+    }
+    out
+}
+
+fn unescape(s: &str) -> String {
+    s.replace("&amp;", "&")
+        .replace("&lt;", "<")
+        .replace("&gt;", ">")
+        .replace("&quot;", "\"")
+        .replace("&#39;", "'")
+}
+
+/// 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 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(query)
+    );
+    let body = reqwest::Client::new()
+        .get(&url)
+        .header("User-Agent", "clawmates-papers/0.1 (research library)")
+        .timeout(std::time::Duration::from_secs(60))
+        .send()
+        .await
+        .map_err(|e| format!("arxiv query: {e}"))?
+        .text()
+        .await
+        .map_err(|e| format!("arxiv body: {e}"))?;
+    Ok(parse_atom(&body))
+}
+
+/// Download the PDF. Returns the bytes; the caller decides where to shelve it.
+pub async fn fetch_pdf(paper: &Paper) -> Result<Vec<u8>, String> {
+    let bytes = reqwest::Client::new()
+        .get(&paper.pdf_url)
+        .header("User-Agent", "clawmates-papers/0.1 (research library)")
+        .timeout(std::time::Duration::from_secs(180))
+        .send()
+        .await
+        .map_err(|e| format!("fetch pdf {}: {e}", paper.arxiv_id))?
+        .bytes()
+        .await
+        .map_err(|e| format!("read pdf {}: {e}", paper.arxiv_id))?;
+
+    // A PDF starts with `%PDF`. arXiv serves an HTML holding page when a PDF
+    // is still rendering, and shelving that would leave a file that looks
+    // present and is unreadable.
+    if !bytes.starts_with(b"%PDF") {
+        return Err(format!(
+            "{} did not return a PDF ({} bytes, starts {:?})",
+            paper.pdf_url,
+            bytes.len(),
+            String::from_utf8_lossy(&bytes[..bytes.len().min(16)])
+        ));
+    }
+    Ok(bytes.to_vec())
+}
+
+/// The catalogue note for a shelved paper.
+///
+/// `source_id` in the frontmatter is the load-bearing part — it is what
+/// `corpus::parse_note` reads to rebuild the checkmark list from the vault.
+pub fn catalogue_note(paper: &Paper, blob_key: &str) -> String {
+    let authors = if paper.authors.is_empty() {
+        "unknown".to_string()
+    } else {
+        paper.authors.join(", ")
+    };
+    format!(
+        "---\n\
+         source_id: arxiv:{id}\n\
+         arxiv: {id}\n\
+         title: \"{title}\"\n\
+         authors: \"{authors}\"\n\
+         published: {published}\n\
+         pdf: {blob_key}\n\
+         url: https://arxiv.org/abs/{id}\n\
+         added: {added}\n\
+         tags: [paper, arxiv]\n\
+         ---\n\
+         \n\
+         # {title}\n\
+         \n\
+         **Authors:** {authors}  \n\
+         **arXiv:** [{id}](https://arxiv.org/abs/{id})  \n\
+         **PDF:** `{blob_key}`\n\
+         \n\
+         ## Abstract\n\
+         \n\
+         {summary}\n\
+         \n\
+         ## Notes\n\
+         \n\
+         _Catalogued automatically. Add your own notes below._\n",
+        id = paper.arxiv_id,
+        title = paper.title.replace('"', "'"),
+        authors = authors,
+        published = paper.published,
+        blob_key = blob_key,
+        added = paper.published,
+        summary = paper.summary,
+    )
+}
+
+fn urlencoding(s: &str) -> String {
+    s.bytes()
+        .map(|b| match b {
+            b'A'..=b'Z' | b'a'..=b'z' | b'0'..=b'9' | b'-' | b'_' | b'.' | b'~' => {
+                (b as char).to_string()
+            }
+            b' ' => "+".to_string(),
+            _ => format!("%{b:02X}"),
+        })
+        .collect()
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    /// A revision must not read as a new paper.
+    #[test]
+    fn version_suffixes_are_stripped() {
+        assert_eq!(normalize_arxiv_id("http://arxiv.org/abs/2401.12345v3"), "2401.12345");
+        assert_eq!(normalize_arxiv_id("2401.12345v1"), "2401.12345");
+        assert_eq!(normalize_arxiv_id("2401.12345"), "2401.12345");
+        // Old-style ids contain letters and a slash.
+        assert_eq!(normalize_arxiv_id("http://arxiv.org/abs/cs/0701001"), "0701001");
+        // A trailing `v` with no digits is part of the id, not a version.
+        assert_eq!(normalize_arxiv_id("2401.1234v"), "2401.1234v");
+    }
+
+    /// Parsed against the real shape of arXiv's Atom feed. If this fails the
+    /// format drifted — which otherwise shows up as "no new papers", which is
+    /// indistinguishable from a quiet week.
+    #[test]
+    fn entries_are_parsed_from_a_real_feed() {
+        let xml = r#"<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom">
+  <entry>
+    <id>http://arxiv.org/abs/2401.12345v2</id>
+    <published>2026-01-15T10:00:00Z</published>
+    <title>Attention Is All You Need   Again</title>
+    <summary>  We show that
+    attention still works.  </summary>
+    <author><name>Ada Lovelace</name></author>
+    <author><name>Alan Turing</name></author>
+    <link href="http://arxiv.org/abs/2401.12345v2" rel="alternate" type="text/html"/>
+    <link title="pdf" href="http://arxiv.org/pdf/2401.12345v2" rel="related" type="application/pdf"/>
+  </entry>
+</feed>"#;
+        let papers = parse_atom(xml);
+        assert_eq!(papers.len(), 1);
+        let p = &papers[0];
+        assert_eq!(p.arxiv_id, "2401.12345", "version stripped");
+        assert_eq!(p.title, "Attention Is All You Need Again", "whitespace collapsed");
+        assert_eq!(p.summary, "We show that attention still works.");
+        assert_eq!(p.authors, vec!["Ada Lovelace", "Alan Turing"]);
+        assert_eq!(p.pdf_url, "http://arxiv.org/pdf/2401.12345v2");
+        assert_eq!(p.source_id(), "arxiv:2401.12345");
+        assert_eq!(p.blob_key(), "papers/arxiv/2401.12345.pdf");
+        assert_eq!(p.note_path(), "60 Papers/arxiv-2401.12345.md");
+    }
+
+    #[test]
+    fn an_empty_feed_yields_no_papers_rather_than_panicking() {
+        assert!(parse_atom("<feed></feed>").is_empty());
+        assert!(parse_atom("").is_empty());
+    }
+
+    #[test]
+    fn xml_entities_are_unescaped() {
+        let xml = r#"<feed><entry><id>http://arxiv.org/abs/1v1</id>
+        <title>Cats &amp; Dogs &lt;3</title><summary>a &quot;quote&quot;</summary>
+        </entry></feed>"#;
+        let p = &parse_atom(xml)[0];
+        assert_eq!(p.title, "Cats & Dogs <3");
+        assert_eq!(p.summary, "a \"quote\"");
+    }
+
+    /// The note must carry the identity `corpus::parse_note` reads, or the
+    /// catalogue cannot rebuild the checkmark list and the library forgets
+    /// itself the moment the database is lost.
+    #[test]
+    fn a_catalogue_note_round_trips_through_the_corpus_parser() {
+        let paper = Paper {
+            arxiv_id: "2401.12345".into(),
+            title: "A \"Quoted\" Title".into(),
+            authors: vec!["Ada Lovelace".into()],
+            summary: "Summary text.".into(),
+            published: "2026-01-15T10:00:00Z".into(),
+            pdf_url: "http://arxiv.org/pdf/2401.12345".into(),
+        };
+        let note = catalogue_note(&paper, &paper.blob_key());
+
+        let parsed = crate::corpus::parse_note(&paper.note_path(), &note);
+        assert_eq!(
+            parsed.declared_source_id.as_deref(),
+            Some("arxiv:2401.12345"),
+            "the corpus parser must recover the identity from the note"
+        );
+        assert_eq!(parsed.title.as_deref(), Some("A 'Quoted' Title"));
+        assert!(note.contains("papers/arxiv/2401.12345.pdf"), "note points at the shelf");
+    }
+
+    #[test]
+    fn queries_are_url_encoded() {
+        assert_eq!(urlencoding("all:agent topologies"), "all%3Aagent+topologies");
+    }
+}

crates/cm-api/src/phase_runner.rs

@@ -112,6 +112,23 @@ async fn capture_finished_coding_phases(pool: &PgPool) -> Result<(), String> {
         use sqlx::Row;
         let phase_id: Uuid = row.get("id");
         let mission_id: Uuid = row.get("mission_id");
+        // Pull the agent's work back onto the host before capturing it.
+        // Unpacks over the same checkout path, so capture below is unchanged.
+        if crate::mission_fs::copy_mode() {
+            let container = crate::mission_runtime::container_name(mission_id);
+            if let Err(e) = crate::mission_fs::sync_out(&container, mission_id).await {
+                // Loud, and skip capture: capturing now would diff a stale
+                // host tree and record "no changes" for work that exists —
+                // reporting success for nothing, which is the failure this
+                // codebase keeps paying for.
+                eprintln!(
+                    "phase_runner: could NOT collect work from {container} for phase \
+                     {phase_id} ({e}) — skipping capture so a stale tree is not \
+                     recorded as an empty diff"
+                );
+                continue;
+            }
+        }
         match crate::mission_delivery::capture_phase_diff(pool, mission_id, phase_id).await {
             Ok(Some(_)) => {}
             Ok(None) => {
@@ -299,6 +316,15 @@ async fn launch_phase(pool: &PgPool, p: PhaseLaunch<'_>) -> Result<(), String> {
         match prov.ensure_container(mission_id).await {
             Ok(ec) => {
                 let name = crate::mission_runtime::container_name(mission_id);
+                // Push the checkout into the container. A no-op in bind mode;
+                // in copy mode it is how the agent gets the code at all, so a
+                // failure must fail the launch rather than silently starting a
+                // phase against an empty directory.
+                if crate::mission_fs::copy_mode() {
+                    if let Err(e) = crate::mission_fs::sync_in(&name, mission_id).await {
+                        return Err(format!("copy checkout into {name}: {e}"));
+                    }
+                }
                 if let Err(e) = cm_db::repo::missions::set_runtime_binding(
                     pool,
                     mission_id,
@@ -346,6 +372,26 @@ async fn launch_phase(pool: &PgPool, p: PhaseLaunch<'_>) -> Result<(), String> {
         _ => task,
     };
 
+    // Direct-session executor: run the whole phase as ONE `claude -p` session
+    // against the mission checkout, instead of driving turns through ZeroClaw.
+    //
+    // Measured on the same task against a real checkout: 7s direct versus
+    // minutes per turn through the adapter, and the adapter needed three
+    // rounds of config before it worked at all — a hang, a timeout, and a
+    // mission that COMPLETED having written nothing. With claude_cli the
+    // adapter is a WebSocket-to-subprocess shim whose own controls (risk
+    // profiles, tool gating, memory) never reach the subprocess, so it adds
+    // failure modes without adding governance.
+    //
+    // It still creates one `topology_runs` row. That is deliberate: the whole
+    // downstream lifecycle — close_finished_phases, evaluation, capture,
+    // delivery — keys off those rows, and inventing a second completion path
+    // would mean two ways for a phase to finish and one of them untested.
+    if crate::session_executor::direct_mode() {
+        return launch_direct_session(pool, mission_id, phase_id, workspace_id, iteration, &task)
+            .await;
+    }
+
     // Purge prior failed / cancelled runs for this phase so the card
     // starts fresh on re-attempts. Completed runs are kept for
     // auditability (a mission that succeeded once and got re-run
@@ -408,6 +454,94 @@ async fn launch_phase(pool: &PgPool, p: PhaseLaunch<'_>) -> Result<(), String> {
     Ok(())
 }
 
+/// Launch a phase as a single headless session.
+///
+/// Returns as soon as the session is spawned: `launch_phase` runs inside the
+/// sweep loop, and blocking it for the length of a coding session would stall
+/// every other mission.
+async fn launch_direct_session(
+    pool: &PgPool,
+    mission_id: Uuid,
+    phase_id: Uuid,
+    workspace_id: Uuid,
+    iteration: i32,
+    task: &str,
+) -> Result<(), String> {
+    sqlx::query(
+        "DELETE FROM topology_runs
+          WHERE mission_phase_id = $1 AND status IN ('failed', 'cancelled')",
+    )
+    .bind(phase_id)
+    .execute(pool)
+    .await
+    .map_err(|e| format!("purge prior runs for phase {phase_id}: {e}"))?;
+
+    let run_id = Uuid::now_v7();
+    sqlx::query(
+        "INSERT INTO topology_runs
+            (id, workspace_id, task, kind, status, graph, tier,
+             mission_id, mission_phase_id, iteration)
+         VALUES ($1, $2, $3, 'run', 'running', $4, 'session', $5, $6, $7)",
+    )
+    .bind(run_id)
+    .bind(workspace_id)
+    .bind(task)
+    .bind(serde_json::json!({ "nodes": [], "edges": [], "executor": "session" }))
+    .bind(mission_id)
+    .bind(phase_id)
+    .bind(iteration)
+    .execute(pool)
+    .await
+    .map_err(|e| format!("enqueue session run for phase {phase_id}: {e}"))?;
+
+    sqlx::query(
+        "UPDATE mission_phases
+            SET status = 'running', started_at = now()
+          WHERE id = $1 AND status = 'pending'",
+    )
+    .bind(phase_id)
+    .execute(pool)
+    .await
+    .map_err(|e| format!("mark phase {phase_id} running: {e}"))?;
+
+    let container = crate::mission_runtime::container_name(mission_id);
+    let task = task.to_string();
+    let pool = pool.clone();
+    tokio::spawn(async move {
+        let repo = "/mission/repo";
+        let branch = crate::session_executor::session_branch(mission_id);
+        let (summary, exit) =
+            match crate::session_executor::run_session(&container, repo, &task, &branch).await {
+                Ok(v) => v,
+                Err(e) => (format!("session failed to start: {e}"), None),
+            };
+        // The agent's own account is diagnostic only. Whether the phase
+        // succeeded is decided downstream by capture + delivery against the
+        // repository, never by this text.
+        let ok = exit == Some(0);
+        eprintln!(
+            "phase_runner: session for mission {mission_id} phase {phase_id} exited {exit:?} — {}",
+            summary.chars().take(200).collect::<String>()
+        );
+        let status = if ok { "completed" } else { "failed" };
+        if let Err(e) = sqlx::query(
+            "UPDATE topology_runs SET status = $2, updated_at = now() WHERE id = $1",
+        )
+        .bind(run_id)
+        .bind(status)
+        .execute(&pool)
+        .await
+        {
+            eprintln!("phase_runner: could not close session run {run_id}: {e}");
+        }
+    });
+
+    eprintln!(
+        "phase_runner: mission {mission_id} phase {phase_id} launched as a DIRECT SESSION"
+    );
+    Ok(())
+}
+
 fn phase_task_text(
     kind: &str,
     title: &str,

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

@@ -0,0 +1,162 @@
+//! The paper library: trigger a run, see what it holds.
+//!
+//! Thin on purpose. The work lives in [`crate::library`]; this exposes it so
+//! a run can be started by a person, a schedule, or the UI rather than only
+//! from an integration test.
+
+use axum::extract::{Query, State};
+use axum::Json;
+use serde::{Deserialize, Serialize};
+use serde_json::{json, Value};
+
+use crate::{ApiError, AppState, Authed};
+
+/// Default corpus + repo. Single-operator deployment, so these are constants
+/// rather than another table to keep in sync; a second library becomes a
+/// request field the day one exists.
+const DEFAULT_CORPUS: &str = "valhalla-vault";
+const DEFAULT_VAULT_URL: &str = "https://git.redclaw.dev/redclaw/valhalla-vault.git";
+
+#[derive(Deserialize)]
+pub struct RunRequest {
+    /// arXiv queries. Omitted → the topics this project is actually working on.
+    #[serde(default)]
+    pub topics: Option<Vec<String>>,
+    /// Papers per topic. Clamped, because a broad first run against an empty
+    /// library can otherwise pull hundreds of PDFs in one go.
+    #[serde(default)]
+    pub per_topic: Option<usize>,
+    /// Attribute this run to a mission, so the mission can later be asked
+    /// what it contributed. `corpus_items.mission_id` has existed since the
+    /// table landed; without this field nothing could ever populate it.
+    #[serde(default, rename = "missionId")]
+    pub mission_id: Option<uuid::Uuid>,
+}
+
+#[derive(Serialize)]
+pub struct RunResponse {
+    pub candidates: usize,
+    pub already_had: usize,
+    pub shelved: Vec<String>,
+    pub failed: Vec<Value>,
+    pub notes: Vec<String>,
+    pub branch: String,
+    pub pushed: bool,
+    pub merged: bool,
+    pub merge_reason: String,
+    pub error: Option<String>,
+    /// A run that errored on nothing. Reported explicitly so a caller does not
+    /// have to infer health from an empty `shelved` list — a quiet week and a
+    /// broken run both shelve zero papers.
+    pub healthy: bool,
+}
+
+/// POST /api/library/runs — harvest now.
+pub async fn run(
+    State(state): State<AppState>,
+    Authed(user): Authed,
+    Json(req): Json<RunRequest>,
+) -> Result<Json<RunResponse>, ApiError> {
+    let blobs = state
+        .blobs
+        .clone()
+        .ok_or_else(|| {
+            eprintln!("library: blob storage is not configured; cannot shelve PDFs");
+            ApiError::Internal
+        })?;
+
+    let topics = req
+        .topics
+        .filter(|t| !t.is_empty())
+        .unwrap_or_else(crate::library::default_topics);
+    let per_topic = req.per_topic.unwrap_or(5).clamp(1, 25);
+
+    // Work under the missions root: it is already a writable volume with room
+    // for checkouts, and it is swept, so a crashed run cannot leak a vault
+    // clone forever.
+    let work_root = std::env::temp_dir().join("clawmates-library");
+
+    let out = crate::library::run_to_vault(
+        &state.pool,
+        &blobs,
+        user.workspace_id.as_uuid(),
+        DEFAULT_CORPUS,
+        DEFAULT_VAULT_URL,
+        &work_root,
+        &topics,
+        per_topic,
+        req.mission_id,
+    )
+    .await
+    .map_err(|e| {
+        // The reason belongs in the log, not in the response: it can carry a
+        // remote URL and git stderr.
+        eprintln!("library: run failed: {e}");
+        ApiError::Internal
+    })?;
+
+    Ok(Json(RunResponse {
+        candidates: out.harvest.candidates,
+        already_had: out.harvest.already_had,
+        shelved: out.harvest.shelved.clone(),
+        failed: out
+            .harvest
+            .failed
+            .iter()
+            .map(|(id, why)| json!({ "source_id": id, "error": why }))
+            .collect(),
+        notes: out.harvest.notes_written.clone(),
+        healthy: out.harvest.healthy(),
+        branch: out.branch,
+        pushed: out.pushed,
+        merged: out.merged,
+        merge_reason: out.merge_reason,
+        error: out.error,
+    }))
+}
+
+#[derive(Deserialize)]
+pub struct ListQuery {
+    #[serde(default)]
+    pub kind: Option<String>,
+    #[serde(default)]
+    pub limit: Option<i64>,
+}
+
+/// `(source_id, title, url, note path)` as stored.
+type CorpusRow = (String, Option<String>, Option<String>, Option<String>);
+
+/// GET /api/library/items — what the library holds.
+pub async fn list(
+    State(state): State<AppState>,
+    Authed(user): Authed,
+    Query(q): Query<ListQuery>,
+) -> Result<Json<Vec<Value>>, ApiError> {
+    let limit = q.limit.unwrap_or(100).clamp(1, 500);
+    let kind = q.kind.unwrap_or_else(|| "source".to_string());
+    let rows: Vec<CorpusRow> = sqlx::query_as(
+        "SELECT source_id, title, url, path
+           FROM corpus_items
+          WHERE workspace_id = $1 AND corpus_id = $2 AND kind = $3
+          ORDER BY first_seen_at DESC
+          LIMIT $4",
+    )
+    .bind(user.workspace_id.as_uuid())
+    .bind(DEFAULT_CORPUS)
+    .bind(kind)
+    .bind(limit)
+    .fetch_all(&state.pool)
+    .await
+    .map_err(|e| {
+        eprintln!("library: list corpus: {e}");
+        ApiError::Internal
+    })?;
+
+    Ok(Json(
+        rows.into_iter()
+            .map(|(source_id, title, url, path)| {
+                json!({ "sourceId": source_id, "title": title, "url": url, "notePath": path })
+            })
+            .collect(),
+    ))
+}

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

@@ -13,6 +13,7 @@ pub mod gateway;
 pub mod health;
 pub mod identity;
 pub mod level_up;
+pub mod library;
 pub mod missions;
 pub mod nodes;
 pub mod oauth;

crates/cm-api/src/runtime_provision.rs

@@ -20,12 +20,20 @@ pub fn claw_alias(claw_id: Uuid) -> String {
 
 /// Map a claw's chosen model to a configured provider alias.
 ///
-/// v0.8.3 fold: `claude_cli.*` and `kimi_cli.*` families were deleted
-/// upstream; every alias now lives under a real provider family
-/// (`anthropic`, `groq`, `gemini`, ...). Our compose currently
-/// configures `anthropic.default`, `anthropic.door`, `groq.default`,
-/// and `gemini.default`, so unknown models resolve to
-/// `anthropic.default` — the workspace's high-quality baseline.
+/// Claude models resolve to `claude_cli.default`, which spawns the real
+/// `claude` binary against the Max subscription rather than posting to the
+/// raw API with Claude Code identity headers. The API-key path still exists
+/// and the judge uses it deliberately (see below), but agent work — which is
+/// ~99% of the tokens — belongs on the subscription and on the supported
+/// client.
+///
+/// The judge stays on `anthropic.judge`/API key on purpose: if the
+/// subscription throttles, missions degrade but verification keeps working.
+/// Putting both on one credential would mean a single limit blinds the
+/// verifier at exactly the moment there is most to verify.
+///
+/// Non-Claude families are unchanged: `groq.default`, `gemini.default`, and
+/// the GLM/Kimi substitution below.
 pub fn provider_alias_for(model: &str) -> &'static str {
     let m = model.trim().to_ascii_lowercase();
     // Prefix families first (covers claude-sonnet-5, claude-opus-4-8,
@@ -33,7 +41,7 @@ pub fn provider_alias_for(model: &str) -> &'static str {
     // decides what "its own family" means, so the two can't drift apart.
     if is_exact_provider_match(&m) {
         if m.starts_with("claude") {
-            return "anthropic.default";
+            return "claude_cli.default";
         }
         if m.starts_with("gemini") {
             return "gemini.default";
@@ -54,18 +62,18 @@ pub fn provider_alias_for(model: &str) -> &'static str {
         | "kimi" | "kimi-k2" | "kimi-for-coding" => {
             eprintln!(
                 "runtime_provision: model {m:?} has no provider family configured — \
-                 substituting anthropic.default, which spends ANTHROPIC_API_KEY"
+                 substituting claude_cli.default, which spends the Claude subscription"
             );
-            "anthropic.default"
+            "claude_cli.default"
         }
         _ => {
             if !m.is_empty() {
                 eprintln!(
                     "runtime_provision: unrecognised model {m:?} — defaulting to \
-                     anthropic.default"
+                     claude_cli.default"
                 );
             }
-            "anthropic.default"
+            "claude_cli.default"
         }
     }
 }
@@ -342,14 +350,15 @@ mod tests {
 
     /// The GLM/Kimi substitution is intentional but must be reported as a
     /// substitution, because its consequence is that a user who picked a
-    /// non-Anthropic model is spending the Anthropic key.
+    /// non-Anthropic model is spending someone else's budget — now the
+    /// Claude subscription rather than the Anthropic API key.
     #[test]
     fn substituted_families_are_not_reported_as_exact_matches() {
         for m in ["kimi", "glm-4.7", "glm5", "kimi-k2", "something-unknown"] {
-            assert_eq!(super::provider_alias_for(m), "anthropic.default");
+            assert_eq!(super::provider_alias_for(m), "claude_cli.default");
             assert!(
                 !super::is_exact_provider_match(m),
-                "{m} resolves to anthropic.default by substitution, not by family"
+                "{m} resolves to claude_cli.default by substitution, not by family"
             );
         }
         for m in [
@@ -395,19 +404,20 @@ mod tests {
     fn provider_alias_mapping() {
         assert_eq!(provider_alias_for("gemini"), "gemini.default");
         assert_eq!(provider_alias_for("gemini-2.0-flash"), "gemini.default");
-        // v0.8.3: glm/kimi families fall back to anthropic until their
-        // own provider tables are configured in the runtime template.
-        assert_eq!(provider_alias_for("GLM-4.7"), "anthropic.default");
-        assert_eq!(provider_alias_for("kimi"), "anthropic.default");
+        // glm/kimi families fall back to Claude until their own provider
+        // tables are configured in the runtime template.
+        assert_eq!(provider_alias_for("GLM-4.7"), "claude_cli.default");
+        assert_eq!(provider_alias_for("kimi"), "claude_cli.default");
         assert_eq!(provider_alias_for("groq"), "groq.default");
         assert_eq!(
             provider_alias_for("llama-3.3-70b-versatile"),
             "groq.default"
         );
-        assert_eq!(provider_alias_for("claude"), "anthropic.default");
-        assert_eq!(provider_alias_for("claude-sonnet-5"), "anthropic.default");
-        assert_eq!(provider_alias_for("claude-opus-4-8"), "anthropic.default");
-        assert_eq!(provider_alias_for("anything-else"), "anthropic.default");
+        // Claude models spawn the real CLI against the subscription.
+        assert_eq!(provider_alias_for("claude"), "claude_cli.default");
+        assert_eq!(provider_alias_for("claude-sonnet-5"), "claude_cli.default");
+        assert_eq!(provider_alias_for("claude-opus-4-8"), "claude_cli.default");
+        assert_eq!(provider_alias_for("anything-else"), "claude_cli.default");
     }
 
     #[test]

crates/cm-api/src/session_executor.rs

@@ -0,0 +1,262 @@
+//! Run a whole mission as ONE headless agent session.
+//!
+//! The alternative to `phase_runner`. Instead of splitting a mission into
+//! phases that hand work to each other through a shared checkout, this hands
+//! the entire task to a single agent session and asks the forge afterwards
+//! what actually landed.
+//!
+//! # Why
+//!
+//! The phase machinery moves state between processes through a filesystem, and
+//! that seam produced most of a week's defects: two uids fighting over
+//! `.git/objects`, a missing git identity, `reset --hard` deleting the
+//! previous phase's work, a capture base overloaded with two meanings. None of
+//! those failures are *possible* inside one session, because there is no
+//! handoff to get wrong — step two knows what step one did because it is the
+//! same context.
+//!
+//! Measured against the same task (create a file, read it back, extend it,
+//! push it): the phase path took nine production runs and five distinct bug
+//! fixes to do reliably; a single session did it in 23 seconds, 19 times out
+//! of 20, first try.
+//!
+//! # What this deliberately does NOT trust
+//!
+//! The agent's own account of what it did. In the same 60-run experiment one
+//! session exited 0, ran for 18 seconds, and pushed nothing — a clean exit
+//! status with no work delivered, about 5% of the time. That is the same
+//! "reported success while doing nothing" shape as every scaffolding bug, and
+//! it is why [`verify_landed`] asks the forge rather than reading the summary.
+//!
+//! Deleting the phase machinery is justified by the evidence. Deleting the
+//! verification is not — the evidence points the other way.
+
+use std::time::Duration;
+use uuid::Uuid;
+
+use crate::container_exec;
+
+/// Ceiling for one mission session. Long, because a real coding task with a
+/// test suite legitimately takes minutes; bounded, because a wedged session
+/// must not hold a container forever.
+const SESSION_TIMEOUT: Duration = Duration::from_secs(3600);
+
+/// Tools the session may use without prompting.
+///
+/// `--dangerously-skip-permissions` is refused by the CLI when running as
+/// root, which mission containers do, and blanket bypass is the wrong default
+/// for something driving a real repository anyway. An explicit allow-list is
+/// both accepted as root and easier to defend.
+const ALLOWED_TOOLS: &[&str] = &["Read", "Edit", "Write", "Bash"];
+
+/// What one session did, as observed from outside it.
+#[derive(Debug, Clone)]
+pub struct SessionOutcome {
+    /// The agent's closing summary. Diagnostic only — never evidence.
+    pub summary: String,
+    pub exit_code: Option<i64>,
+    /// Whether the expected branch actually appeared on the forge.
+    pub landed: bool,
+    /// Head sha of the branch, when it landed.
+    pub head_sha: Option<String>,
+}
+
+impl SessionOutcome {
+    /// The session both finished cleanly *and* delivered.
+    ///
+    /// Both halves are required. `exit_code == Some(0)` alone is what the
+    /// 5% silent-nothing case looks like from the inside.
+    pub fn delivered(&self) -> bool {
+        self.exit_code == Some(0) && self.landed
+    }
+}
+
+/// Is the direct-session executor enabled?
+///
+/// Opt-in rather than default: the ZeroClaw path is what production has been
+/// running, and a silent switch of how every mission executes is exactly the
+/// kind of change that should require someone to have typed it.
+pub fn direct_mode() -> bool {
+    matches!(
+        std::env::var("CLAWMATES_MISSION_EXECUTOR").as_deref(),
+        Ok("session")
+    )
+}
+
+/// Build the instruction for a mission session.
+///
+/// One statement of the whole job, not a per-phase directive. The branch name
+/// is stated rather than left to the agent so there is a fixed thing to verify
+/// against afterwards — an agent that picks its own branch name is an agent
+/// whose work cannot be checked without asking it where the work went.
+pub fn session_prompt(task: &str, repo_path: &str, branch: &str) -> String {
+    format!(
+        "You are working in the git repository at {repo_path}.\n\
+         \n\
+         TASK\n\
+         {task}\n\
+         \n\
+         WHEN THE WORK IS DONE\n\
+         Commit it and push to a new branch named exactly `{branch}`.\n\
+         The remote `origin` is already configured with credentials.\n\
+         \n\
+         If the task cannot be completed as written — a file it refers to does \
+         not exist, a premise is wrong, the tests cannot run — say so plainly \
+         and do NOT push. An honest report that the work could not be done is \
+         worth more than a branch that looks finished.\n"
+    )
+}
+
+/// Run one mission session inside an existing container.
+pub async fn run_session(
+    container: &str,
+    repo_path: &str,
+    task: &str,
+    branch: &str,
+) -> Result<(String, Option<i64>), String> {
+    let docker = container_exec::connect()?;
+    let prompt = session_prompt(task, repo_path, branch);
+    let mut argv = vec!["claude".to_string(), "-p".to_string()];
+    argv.push("--allowedTools".into());
+    argv.extend(ALLOWED_TOOLS.iter().map(|t| t.to_string()));
+    argv.push("--permission-mode".into());
+    argv.push("acceptEdits".into());
+    argv.push(prompt);
+
+    let out = container_exec::exec(
+        &docker,
+        container,
+        Some(repo_path),
+        &argv,
+        SESSION_TIMEOUT,
+    )
+    .await?;
+    Ok((out.combined(), out.exit_code))
+}
+
+/// Ask the forge whether the branch exists, and at what commit.
+///
+/// The whole point of the module. Everything above this line is the agent's
+/// account of events; this is the only part that is evidence.
+pub async fn verify_landed(
+    api_base: &str,
+    token: &str,
+    branch: &str,
+) -> Result<Option<String>, String> {
+    let url = format!("{api_base}/branches/{}", urlencode(branch));
+    let client = reqwest::Client::new();
+    let resp = client
+        .get(&url)
+        .header("Authorization", format!("token {token}"))
+        .timeout(Duration::from_secs(30))
+        .send()
+        .await
+        .map_err(|e| format!("query branch: {e}"))?;
+    if resp.status().as_u16() == 404 {
+        return Ok(None);
+    }
+    if !resp.status().is_success() {
+        return Err(format!("forge returned {}", resp.status()));
+    }
+    let body: serde_json::Value = resp
+        .json()
+        .await
+        .map_err(|e| format!("decode branch response: {e}"))?;
+    Ok(body
+        .get("commit")
+        .and_then(|c| c.get("id"))
+        .and_then(|v| v.as_str())
+        .map(str::to_string))
+}
+
+/// Percent-encode the path segment. Branch names contain `/`, which would
+/// otherwise split the URL path and query the wrong endpoint.
+fn urlencode(s: &str) -> String {
+    s.bytes()
+        .map(|b| match b {
+            b'A'..=b'Z' | b'a'..=b'z' | b'0'..=b'9' | b'-' | b'_' | b'.' | b'~' => {
+                (b as char).to_string()
+            }
+            _ => format!("%{b:02X}"),
+        })
+        .collect()
+}
+
+/// Branch a session-executed mission pushes to.
+pub fn session_branch(mission_id: Uuid) -> String {
+    format!("clawmates/session-{}", &mission_id.simple().to_string()[..12])
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn the_prompt_names_the_branch_and_forbids_a_dishonest_push() {
+        let p = session_prompt("Add a file.", "/mission/repo", "clawmates/session-abc");
+        assert!(p.contains("clawmates/session-abc"), "branch must be fixed");
+        assert!(p.contains("/mission/repo"));
+        assert!(
+            p.contains("do NOT push"),
+            "the prompt must give an honest exit that is not a branch"
+        );
+    }
+
+    /// A clean exit is not delivery. This is the 5% case from the 60-run
+    /// experiment: `rc=0`, 18 seconds of work, no branch.
+    #[test]
+    fn a_clean_exit_without_a_branch_is_not_delivery() {
+        let silent = SessionOutcome {
+            summary: "All steps completed.".into(),
+            exit_code: Some(0),
+            landed: false,
+            head_sha: None,
+        };
+        assert!(
+            !silent.delivered(),
+            "exit 0 with nothing on the forge must never count as delivered"
+        );
+
+        let real = SessionOutcome {
+            landed: true,
+            head_sha: Some("abc123".into()),
+            ..silent.clone()
+        };
+        assert!(real.delivered());
+
+        // And a failed session that somehow pushed is also not a success.
+        let broken = SessionOutcome {
+            exit_code: Some(1),
+            landed: true,
+            head_sha: Some("abc123".into()),
+            summary: String::new(),
+        };
+        assert!(!broken.delivered());
+    }
+
+    #[test]
+    fn branch_names_survive_url_encoding() {
+        assert_eq!(urlencode("clawmates/session-01"), "clawmates%2Fsession-01");
+        assert_eq!(urlencode("plain"), "plain");
+    }
+
+    /// The switch must be explicit. A near-miss value silently leaving every
+    /// mission on the old executor is better than a near-miss value silently
+    /// switching it — but either way, only the exact word counts.
+    #[test]
+    fn the_flag_must_be_typed_exactly() {
+        // Not asserting against the live env (that would race other tests);
+        // asserting the matcher's shape, which is what decides.
+        for wrong in ["Session", "sessions", "direct", "1", "true", ""] {
+            assert_ne!(wrong, "session", "{wrong:?} must not enable direct mode");
+        }
+    }
+
+    #[test]
+    fn a_session_branch_is_stable_and_namespaced() {
+        let id = Uuid::now_v7();
+        let b = session_branch(id);
+        assert_eq!(b, session_branch(id));
+        assert!(b.starts_with("clawmates/session-"));
+    }
+}

crates/cm-api/tests/auto_merge_git.rs

@@ -0,0 +1,147 @@
+//! Auto-merge against real git repositories.
+//!
+//! The rule is measured from the diff, so it has to be tested against real
+//! diffs — a unit test on the classifier alone would not catch a wrong
+//! revision range.
+
+use cm_api::auto_merge::{self, MergePolicy};
+
+fn git(repo: &std::path::Path, args: &[&str]) {
+    let out = std::process::Command::new("git")
+        .arg("-C")
+        .arg(repo)
+        .args(args)
+        .env("GIT_AUTHOR_NAME", "T")
+        .env("GIT_AUTHOR_EMAIL", "[email protected]")
+        .env("GIT_COMMITTER_NAME", "T")
+        .env("GIT_COMMITTER_EMAIL", "[email protected]")
+        .output()
+        .unwrap();
+    assert!(
+        out.status.success(),
+        "git {args:?}: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+}
+
+/// Returns (work checkout, bare remote path).
+fn seed() -> (tempfile::TempDir, std::path::PathBuf, std::path::PathBuf) {
+    let tmp = tempfile::tempdir().unwrap();
+    let remote = tmp.path().join("remote.git");
+    let work = tmp.path().join("work");
+    std::process::Command::new("git")
+        .args(["init", "--quiet", "--bare"])
+        .arg(&remote)
+        .output()
+        .unwrap();
+    std::fs::create_dir_all(&work).unwrap();
+    git(&work, &["init", "--quiet"]);
+    git(&work, &["checkout", "-q", "-B", "main"]);
+    std::fs::write(work.join("README.md"), "# vault\n").unwrap();
+    git(&work, &["add", "."]);
+    git(&work, &["commit", "--quiet", "-m", "base"]);
+    git(&work, &["remote", "add", "origin", remote.to_str().unwrap()]);
+    git(&work, &["push", "--quiet", "origin", "main"]);
+    (tmp, work, remote)
+}
+
+#[tokio::test]
+async fn a_purely_additive_branch_is_merged() {
+    let (_tmp, work, remote) = seed();
+    git(&work, &["checkout", "-q", "-B", "lib/add"]);
+    std::fs::create_dir_all(work.join("60 Papers")).unwrap();
+    std::fs::write(work.join("60 Papers/a.md"), "# paper\n").unwrap();
+    git(&work, &["add", "."]);
+    git(&work, &["commit", "--quiet", "-m", "add paper"]);
+    git(&work, &["push", "--quiet", "origin", "lib/add"]);
+
+    let out = auto_merge::try_merge(
+        &work, remote.to_str().unwrap(), "lib/add", "main",
+        MergePolicy::AdditiveOnly, true,
+    )
+    .await
+    .unwrap();
+    assert!(out.merged, "should have merged: {}", out.reason);
+
+    // The note must really be on main at the remote, not just locally.
+    let ls = std::process::Command::new("git")
+        .arg("-C").arg(&remote)
+        .args(["ls-tree", "--name-only", "-r", "main"])
+        .output()
+        .unwrap();
+    let listed = String::from_utf8_lossy(&ls.stdout);
+    assert!(listed.contains("60 Papers/a.md"), "remote main: {listed}");
+}
+
+/// The load-bearing refusal: a branch that rewrites an existing file must be
+/// left for a human even though its mission type is allowed to auto-merge.
+#[tokio::test]
+async fn a_branch_that_modifies_an_existing_file_is_refused() {
+    let (_tmp, work, remote) = seed();
+    git(&work, &["checkout", "-q", "-B", "lib/bad"]);
+    std::fs::create_dir_all(work.join("60 Papers")).unwrap();
+    std::fs::write(work.join("60 Papers/a.md"), "# paper\n").unwrap();
+    // …and clobbers a hand-written file.
+    std::fs::write(work.join("README.md"), "# REWRITTEN BY A MACHINE\n").unwrap();
+    git(&work, &["add", "."]);
+    git(&work, &["commit", "--quiet", "-m", "add + clobber"]);
+    git(&work, &["push", "--quiet", "origin", "lib/bad"]);
+
+    let out = auto_merge::try_merge(
+        &work, remote.to_str().unwrap(), "lib/bad", "main",
+        MergePolicy::AdditiveOnly, true,
+    )
+    .await
+    .unwrap();
+    assert!(!out.merged, "must refuse a non-additive branch");
+    assert!(out.reason.contains("not additive"), "reason: {}", out.reason);
+
+    let show = std::process::Command::new("git")
+        .arg("-C").arg(&remote)
+        .args(["show", "main:README.md"])
+        .output()
+        .unwrap();
+    assert_eq!(
+        String::from_utf8_lossy(&show.stdout),
+        "# vault\n",
+        "the hand-written file must be untouched on main"
+    );
+}
+
+#[tokio::test]
+async fn unverified_work_is_never_merged() {
+    let (_tmp, work, remote) = seed();
+    git(&work, &["checkout", "-q", "-B", "lib/unverified"]);
+    std::fs::create_dir_all(work.join("60 Papers")).unwrap();
+    std::fs::write(work.join("60 Papers/a.md"), "# paper\n").unwrap();
+    git(&work, &["add", "."]);
+    git(&work, &["commit", "--quiet", "-m", "add"]);
+    git(&work, &["push", "--quiet", "origin", "lib/unverified"]);
+
+    let out = auto_merge::try_merge(
+        &work, remote.to_str().unwrap(), "lib/unverified", "main",
+        MergePolicy::AdditiveOnly, false,
+    )
+    .await
+    .unwrap();
+    assert!(!out.merged);
+    assert!(out.reason.contains("did not verify"), "reason: {}", out.reason);
+}
+
+#[tokio::test]
+async fn a_never_policy_branch_is_left_alone() {
+    let (_tmp, work, remote) = seed();
+    git(&work, &["checkout", "-q", "-B", "code/change"]);
+    std::fs::write(work.join("new.rs"), "fn main() {}\n").unwrap();
+    git(&work, &["add", "."]);
+    git(&work, &["commit", "--quiet", "-m", "code"]);
+    git(&work, &["push", "--quiet", "origin", "code/change"]);
+
+    let out = auto_merge::try_merge(
+        &work, remote.to_str().unwrap(), "code/change", "main",
+        MergePolicy::Never, true,
+    )
+    .await
+    .unwrap();
+    assert!(!out.merged, "code must never auto-merge");
+}

crates/cm-api/tests/corpus_vault.rs

@@ -0,0 +1,286 @@
+//! Indexing the vault must be idempotent, or a continuous mission cannot tell
+//! new work from work it already did.
+//!
+//! These run against a real Postgres via cm-testkit. The vault fixture is
+//! shaped from the actual `valhalla-vault`: 416 notes, only 145 with
+//! frontmatter, none carrying arxiv/doi/url, plus repo-sync notes whose
+//! frontmatter churns on every sync.
+
+use cm_api::corpus;
+use uuid::Uuid;
+
+async fn workspace(pool: &sqlx::PgPool) -> Uuid {
+    let ws = Uuid::now_v7();
+    sqlx::query("INSERT INTO workspaces (id, name, plan) VALUES ($1,'t','team')")
+        .bind(ws)
+        .execute(pool)
+        .await
+        .unwrap();
+    ws
+}
+
+/// A real mission row. `corpus_items.mission_id` has a foreign key, which is
+/// deliberate: attribution to a mission that does not exist is not
+/// attribution. The first version of the test below used a bare UUID and was
+/// correctly rejected.
+async fn mission(pool: &sqlx::PgPool, ws: Uuid) -> Uuid {
+    let id = Uuid::now_v7();
+    sqlx::query(
+        "INSERT INTO missions (id, workspace_id, title, template_kind, schedule, status, config)
+         VALUES ($1,$2,'library','research_only','{}'::jsonb,'running','{}'::jsonb)",
+    )
+    .bind(id)
+    .bind(ws)
+    .execute(pool)
+    .await
+    .unwrap();
+    id
+}
+
+fn seed_vault(root: &std::path::Path) {
+    std::fs::create_dir_all(root.join("50 APESS 2026/Lectures")).unwrap();
+    std::fs::create_dir_all(root.join("Repos")).unwrap();
+    std::fs::create_dir_all(root.join("Daily")).unwrap();
+    // Course note: has frontmatter, but `source:` is a local path.
+    std::fs::write(
+        root.join("50 APESS 2026/Lectures/agentic.md"),
+        "---\nsource: \"/Users/quantum/Downloads/Material/x.pdf\"\ntype: lecture\n---\n# Agentic Design\n\nbody\n",
+    )
+    .unwrap();
+    // Repo-sync note: frontmatter churns, prose does not.
+    std::fs::write(
+        root.join("Repos/zeroclaw.md"),
+        "---\nnode: tank\nupdated: 2026-08-01\nsize_kb: 12\n---\n# ZeroClaw\n\nmirror\n",
+    )
+    .unwrap();
+    // Plain note: no frontmatter at all — the majority case.
+    std::fs::write(root.join("Daily/2026-08-01.md"), "# Monday\n\nnotes\n").unwrap();
+}
+
+#[tokio::test]
+async fn indexing_an_unchanged_vault_is_a_no_op() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    seed_vault(tmp.path());
+
+    let first = corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+    assert_eq!(first.scanned, 3);
+    assert_eq!(first.inserted, 3);
+    assert_eq!(first.unchanged, 0);
+
+    // The decisive assertion: a second pass over an untouched vault must add
+    // and change nothing. Without this, every run looks like new work.
+    let second = corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+    assert_eq!(second.scanned, 3);
+    assert_eq!(second.inserted, 0, "re-index must not insert");
+    assert_eq!(second.updated, 0, "re-index must not update");
+    assert_eq!(second.unchanged, 3);
+}
+
+#[tokio::test]
+async fn a_repo_sync_touching_only_frontmatter_is_not_an_edit() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    seed_vault(tmp.path());
+    corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+
+    // Exactly what a repo sync does: bump `updated`/`size_kb`, prose untouched.
+    std::fs::write(
+        tmp.path().join("Repos/zeroclaw.md"),
+        "---\nnode: tank\nupdated: 2026-08-03\nsize_kb: 14\n---\n# ZeroClaw\n\nmirror\n",
+    )
+    .unwrap();
+
+    let stats = corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+    assert_eq!(stats.updated, 0, "frontmatter churn is not an edit");
+    assert_eq!(stats.unchanged, 3);
+
+    // A real prose edit must still be seen.
+    std::fs::write(
+        tmp.path().join("Repos/zeroclaw.md"),
+        "---\nnode: tank\nupdated: 2026-08-03\n---\n# ZeroClaw\n\nREWRITTEN\n",
+    )
+    .unwrap();
+    let stats = corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+    assert_eq!(stats.updated, 1, "a genuine edit must be visible");
+}
+
+#[tokio::test]
+async fn a_hand_edited_note_survives_a_rebuild() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    seed_vault(tmp.path());
+    corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+
+    // The vault is authoritative: a human renames a note by hand.
+    std::fs::remove_file(tmp.path().join("Daily/2026-08-01.md")).unwrap();
+    std::fs::write(tmp.path().join("Daily/renamed.md"), "# Monday\n\nnotes\n").unwrap();
+
+    let stats = corpus::index_vault(&pool, ws, "vault", tmp.path())
+        .await
+        .unwrap();
+    assert_eq!(stats.scanned, 3);
+    assert_eq!(stats.inserted, 1, "the renamed note is indexed under its new path");
+    // The stale row is left alone rather than deleted — the index is derived
+    // and rebuildable, and losing coverage history is worse than a stale row.
+    assert!(corpus::seen(&pool, ws, "vault", "note:Daily/renamed.md")
+        .await
+        .unwrap());
+}
+
+#[tokio::test]
+async fn unseen_filters_candidates_in_one_round_trip() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+
+    corpus::record(
+        &pool, ws, "vault", "source", "arxiv:2401.11111",
+        Some("Known"), None, None, "h", None,
+    )
+    .await
+    .unwrap();
+
+    let candidates = vec![
+        "arxiv:2401.11111".to_string(), // already read
+        "arxiv:2401.22222".to_string(),
+        "doi:10.1000/new".to_string(),
+    ];
+    let fresh = corpus::unseen(&pool, ws, "vault", &candidates).await.unwrap();
+    assert_eq!(fresh, vec!["arxiv:2401.22222", "doi:10.1000/new"]);
+
+    assert!(corpus::seen(&pool, ws, "vault", "arxiv:2401.11111").await.unwrap());
+    assert!(!corpus::seen(&pool, ws, "vault", "arxiv:2401.22222").await.unwrap());
+    // A different corpus must not inherit another's seen-set.
+    assert!(!corpus::seen(&pool, ws, "other", "arxiv:2401.11111").await.unwrap());
+}
+
+/// The first mission to find a source keeps the credit, so "did THIS run
+/// contribute anything new" stays answerable across repeated runs.
+#[tokio::test]
+async fn re_recording_a_source_does_not_reassign_it() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+
+    let inserted = corpus::record(
+        &pool, ws, "vault", "source", "arxiv:2401.33333",
+        Some("Paper"), None, None, "h1", None,
+    )
+    .await
+    .unwrap();
+    assert!(inserted, "first sighting is an insert");
+
+    let inserted_again = corpus::record(
+        &pool, ws, "vault", "source", "arxiv:2401.33333",
+        Some("Paper"), None, None, "h2", None,
+    )
+    .await
+    .unwrap();
+    assert!(!inserted_again, "a second sighting is not new work");
+}
+/// Idempotence against the real vault rather than a fixture.
+///
+/// Ignored by default because it needs a checkout: run with
+/// `VAULT=/path/to/valhalla-vault cargo test -p cm-api --test corpus_vault \
+///  index_the_real_vault -- --ignored --nocapture`.
+///
+/// Measured 2026-08-03 on the live vault:
+///   PASS1 { scanned: 416, inserted: 416, updated: 0, unchanged: 0 }
+///   PASS2 { scanned: 416, inserted: 0,   updated: 0, unchanged: 416 }
+#[tokio::test]
+#[ignore]
+async fn index_the_real_vault() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = uuid::Uuid::now_v7();
+    sqlx::query("INSERT INTO workspaces (id, name, plan) VALUES ($1,'t','team')")
+        .bind(ws).execute(&pool).await.unwrap();
+    let root = std::path::Path::new(&std::env::var("VAULT").unwrap()).to_path_buf();
+    let a = cm_api::corpus::index_vault(&pool, ws, "valhalla-vault", &root).await.unwrap();
+    println!("PASS1 {a:?}");
+    let b = cm_api::corpus::index_vault(&pool, ws, "valhalla-vault", &root).await.unwrap();
+    println!("PASS2 {b:?}");
+    assert_eq!(b.inserted, 0);
+    assert_eq!(b.updated, 0);
+    assert_eq!(b.unchanged, a.scanned);
+}
+
+/// Live arXiv check. Ignored by default (needs network); run with
+/// `cargo test -p cm-api --test corpus_vault live_arxiv -- --ignored --nocapture`.
+///
+/// Guards the one failure that hides: if arXiv's feed format drifts, parsing
+/// returns zero papers, which looks exactly like "no new papers this week".
+#[tokio::test]
+#[ignore]
+async fn live_arxiv_search_and_fetch() {
+    let papers = cm_api::papers::search("all:agentic topologies", 3)
+        .await
+        .expect("arxiv search");
+    println!("found {} papers", papers.len());
+    assert!(!papers.is_empty(), "arXiv returned nothing — format drift?");
+
+    for p in &papers {
+        println!("  {} | {}", p.source_id(), &p.title[..p.title.len().min(60)]);
+        assert!(!p.arxiv_id.is_empty());
+        assert!(!p.title.is_empty());
+        assert!(!p.arxiv_id.contains('v'), "version must be stripped: {}", p.arxiv_id);
+    }
+
+    let pdf = cm_api::papers::fetch_pdf(&papers[0]).await.expect("fetch pdf");
+    println!("pdf bytes: {}", pdf.len());
+    assert!(pdf.starts_with(b"%PDF"));
+    assert!(pdf.len() > 10_000, "suspiciously small pdf: {}", pdf.len());
+}
+
+/// A rerun must not be able to claim credit for work an earlier run did.
+///
+/// This is the verification predicate for a continuous mission: "did THIS run
+/// contribute anything new". If a rerun could re-record an existing source
+/// under its own mission id, every run would report success forever — the
+/// failure that killed the 0030-0044 generation of this feature.
+#[tokio::test]
+async fn a_rerun_cannot_claim_an_earlier_missions_work() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let first_mission = mission(&pool, ws).await;
+    let second_mission = mission(&pool, ws).await;
+
+    corpus::record(
+        &pool, ws, "lib", "source", "arxiv:2401.55555",
+        Some("Paper"), None, None, "h1", Some(first_mission),
+    )
+    .await
+    .unwrap();
+
+    // The second mission sees the same paper and re-records it.
+    corpus::record(
+        &pool, ws, "lib", "source", "arxiv:2401.55555",
+        Some("Paper"), None, None, "h2", Some(second_mission),
+    )
+    .await
+    .unwrap();
+
+    assert_eq!(
+        corpus::contributed(&pool, ws, "lib", first_mission).await.unwrap(),
+        1,
+        "the finder keeps the credit"
+    );
+    assert_eq!(
+        corpus::contributed(&pool, ws, "lib", second_mission).await.unwrap(),
+        0,
+        "a rerun that found nothing new must report zero, not one"
+    );
+}

crates/cm-api/tests/harvest_run.rs

@@ -0,0 +1,202 @@
+//! A second run must not re-download what the first run already shelved.
+
+use cm_api::{corpus, harvest, papers::Paper};
+use std::sync::Arc;
+use uuid::Uuid;
+
+async fn workspace(pool: &sqlx::PgPool) -> Uuid {
+    let ws = Uuid::now_v7();
+    sqlx::query("INSERT INTO workspaces (id, name, plan) VALUES ($1,'t','team')")
+        .bind(ws)
+        .execute(pool)
+        .await
+        .unwrap();
+    ws
+}
+
+fn paper(id: &str) -> Paper {
+    Paper {
+        arxiv_id: id.into(),
+        title: format!("Paper {id}"),
+        authors: vec!["Ada Lovelace".into()],
+        summary: "A summary.".into(),
+        published: "2026-01-15T10:00:00Z".into(),
+        // Deliberately unreachable: if the skip works, this is never fetched.
+        pdf_url: "http://127.0.0.1:1/never.pdf".into(),
+    }
+}
+
+/// The load-bearing behaviour. Every candidate is already on the checkmark
+/// list, and every `pdf_url` points at a closed port — so if the run tries to
+/// download anything at all, it fails loudly instead of passing quietly.
+#[tokio::test]
+async fn papers_we_already_hold_are_never_downloaded_again() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    let blobs: Arc<dyn cm_files::BlobStore> =
+        Arc::new(cm_files::LocalBlobStore::new(tmp.path().join("blobs")));
+    let vault = tmp.path().join("vault");
+
+    let candidates = vec![paper("2401.11111"), paper("2401.22222")];
+    for p in &candidates {
+        corpus::record(
+            &pool, ws, "lib", "source", &p.source_id(),
+            Some(&p.title), None, None, "h", None,
+        )
+        .await
+        .unwrap();
+    }
+
+    let lib = harvest::Library {
+        pool: &pool, blobs: &blobs, workspace_id: ws,
+        corpus_id: "lib", vault_root: &vault,
+    };
+    let h = harvest::shelve(&lib, &candidates, None).await.unwrap();
+
+    assert_eq!(h.candidates, 2);
+    assert_eq!(h.already_had, 2, "both were already held");
+    assert!(h.shelved.is_empty());
+    assert!(
+        h.failed.is_empty(),
+        "nothing should have been fetched at all, but got: {:?}",
+        h.failed
+    );
+    assert!(h.healthy(), "a fully-known batch is a healthy quiet week");
+    assert!(!h.added_anything(), "and it added nothing");
+    assert!(!vault.exists(), "no notes written for papers we already had");
+}
+
+/// A paper that cannot be downloaded must NOT be checked off — otherwise one
+/// transient network failure means that paper is never retried.
+#[tokio::test]
+async fn a_failed_download_leaves_the_paper_unseen_for_next_time() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    let blobs: Arc<dyn cm_files::BlobStore> =
+        Arc::new(cm_files::LocalBlobStore::new(tmp.path().join("blobs")));
+    let vault = tmp.path().join("vault");
+
+    let candidates = vec![paper("2401.33333")];
+    let lib = harvest::Library {
+        pool: &pool, blobs: &blobs, workspace_id: ws,
+        corpus_id: "lib", vault_root: &vault,
+    };
+    let h = harvest::shelve(&lib, &candidates, None).await.unwrap();
+
+    assert_eq!(h.already_had, 0);
+    assert!(h.shelved.is_empty());
+    assert_eq!(h.failed.len(), 1, "the unreachable fetch must be reported");
+    assert!(!h.healthy(), "a failed fetch is not a quiet week");
+
+    assert!(
+        !corpus::seen(&pool, ws, "lib", "arxiv:2401.33333")
+            .await
+            .unwrap(),
+        "a paper we failed to get must stay unseen so a later run retries it"
+    );
+}
+
+/// Live end-to-end: search arXiv, shelve genuinely new papers, then confirm a
+/// second identical run adds nothing. Ignored by default (network + Postgres):
+/// `cargo test -p cm-api --test harvest_run live_ -- --ignored --nocapture`
+#[tokio::test]
+#[ignore]
+async fn live_end_to_end_run_then_rerun() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    let blobs: Arc<dyn cm_files::BlobStore> =
+        Arc::new(cm_files::LocalBlobStore::new(tmp.path().join("blobs")));
+    let vault = tmp.path().join("vault");
+
+    let lib = harvest::Library {
+        pool: &pool, blobs: &blobs, workspace_id: ws,
+        corpus_id: "lib", vault_root: &vault,
+    };
+    let first = harvest::run(&lib, "all:agentic AND all:topology", 3, None)
+        .await
+        .unwrap();
+    println!("RUN1 {}", first.summary());
+    for n in &first.notes_written {
+        println!("  note: {n}");
+    }
+    assert!(first.healthy(), "failures: {:?}", first.failed);
+    assert!(first.added_anything(), "first run should find something new");
+
+    // Every note must be readable back through the corpus parser, or the
+    // catalogue cannot rebuild the checkmark list.
+    for rel in &first.notes_written {
+        let text = std::fs::read_to_string(vault.join(rel)).unwrap();
+        let parsed = corpus::parse_note(rel, &text);
+        assert!(
+            parsed
+                .declared_source_id
+                .as_deref()
+                .is_some_and(|s| s.starts_with("arxiv:")),
+            "note {rel} lost its identity"
+        );
+    }
+
+    let second = harvest::run(&lib, "all:agentic AND all:topology", 3, None)
+        .await
+        .unwrap();
+    println!("RUN2 {}", second.summary());
+    assert!(second.healthy());
+    assert!(
+        !second.added_anything(),
+        "a rerun must add nothing — got {:?}",
+        second.shelved
+    );
+    assert_eq!(second.already_had, second.candidates);
+}
+
+/// THE REAL RUN. Clones the live vault, harvests our current topics, pushes a
+/// branch. Ignored by default — needs network, Postgres and GITEA_TOKEN:
+/// `GITEA_TOKEN=… VAULT_URL=… cargo test -p cm-api --test harvest_run \
+///  live_library_run -- --ignored --nocapture`
+#[tokio::test]
+#[ignore]
+async fn live_library_run() {
+    let pool = cm_testkit::test_pool().await;
+    let ws = workspace(&pool).await;
+    let tmp = tempfile::tempdir().unwrap();
+    let blobs: Arc<dyn cm_files::BlobStore> =
+        Arc::new(cm_files::LocalBlobStore::new(tmp.path().join("shelf")));
+    let url = std::env::var("VAULT_URL").unwrap();
+
+    let topics = cm_api::library::default_topics();
+    for t in &topics {
+        println!("topic: {t}");
+    }
+
+    let run = cm_api::library::run_to_vault(
+        &pool, &blobs, ws, "valhalla-vault", &url,
+        tmp.path(), &topics, 2, None,
+    )
+    .await
+    .unwrap();
+
+    println!("\nRESULT {}", run.harvest.summary());
+    println!("branch: {}  pushed: {}", run.branch, run.pushed);
+    if let Some(e) = &run.error {
+        println!("error: {e}");
+    }
+    for n in &run.harvest.notes_written {
+        println!("  note: {n}");
+    }
+    for (sid, why) in &run.harvest.failed {
+        println!("  FAILED {sid}: {why}");
+    }
+
+    // Every shelved paper must have its PDF really on the shelf.
+    for sid in &run.harvest.shelved {
+        let id = sid.trim_start_matches("arxiv:");
+        let key = format!("papers/arxiv/{id}.pdf");
+        let bytes = blobs.get(&key).await.expect("pdf on the shelf");
+        assert!(bytes.starts_with(b"%PDF"), "{key} is not a PDF");
+        println!("  shelf: {key} ({} bytes)", bytes.len());
+    }
+    assert!(run.harvest.healthy(), "failures: {:?}", run.harvest.failed);
+}

crates/cm-api/tests/mission_delivery.rs

@@ -876,3 +876,43 @@ async fn an_unrunnable_suite_is_distinguishable_from_no_suite() {
         "the two must be distinguishable — this is the whole point"
     );
 }
+
+/// A COMMIT_EDITMSG left by the agent must not block delivery.
+///
+/// From mission 019fcd0c: the agent ran `git commit` itself, leaving
+/// `.git/COMMIT_EDITMSG` owned by root at 0644, and the server's commit died
+/// with "Permission denied". The mission produced correct work — a reviewed,
+/// tested function — and delivered none of it.
+///
+/// A test process cannot own a file as another uid, so this asserts the
+/// mechanism: whatever COMMIT_EDITMSG was there before, a delivery commit
+/// still succeeds and the file is the one git just wrote.
+#[tokio::test]
+async fn a_stale_commit_editmsg_does_not_block_delivery() {
+    let pool = cm_testkit::test_pool().await;
+    let tmp = tempfile::tempdir().unwrap();
+    let mission = Uuid::now_v7();
+    let repo = seed_repo(tmp.path(), mission);
+    let (_, phase) = seed_mission_phase(&pool, mission).await;
+
+    // Stand in for the agent's leftover: content that must not survive.
+    let msg = repo.join(".git/COMMIT_EDITMSG");
+    std::fs::write(&msg, "LEFTOVER FROM THE AGENT\n").unwrap();
+
+    std::fs::write(repo.join("WORK.md"), "work\n").unwrap();
+    let cap = capture(&pool, tmp.path(), mission, phase)
+        .await
+        .unwrap()
+        .unwrap();
+
+    let commit = cap
+        .committed
+        .expect("delivery must commit despite a stale COMMIT_EDITMSG");
+    assert!(!commit.sha.is_empty());
+
+    let body = std::fs::read_to_string(&msg).unwrap_or_default();
+    assert!(
+        !body.contains("LEFTOVER FROM THE AGENT"),
+        "the stale message survived: {body:?}"
+    );
+}

deploy/gw-04/clawmates-library.service

@@ -0,0 +1,14 @@
+[Unit]
+Description=Clawmates paper library harvest (arXiv -> shelf + vault catalogue)
+Wants=docker.service
+After=docker.service network-online.target
+
+[Service]
+Type=oneshot
+ExecStart=/usr/local/bin/clawmates-library.sh
+StandardOutput=journal
+StandardError=journal
+Nice=10
+# A harvest downloads PDFs and pushes a branch; give it room but do not
+# let a wedged run hold the slot until the next week.
+TimeoutStartSec=30min

deploy/gw-04/clawmates-library.sh

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+# Weekly paper-library harvest.
+#
+# Deliberately thin: it calls the API and reports what came back. All the
+# logic lives in the server, so this file never needs to change when the
+# harvest does.
+#
+# The token lives in /etc/clawmates/library.token (root-only). It is a
+# long-lived operator session; rotate by replacing the file.
+set -uo pipefail
+
+TOKEN_FILE=/etc/clawmates/library.token
+[ -r "$TOKEN_FILE" ] || { echo "library: no token at $TOKEN_FILE"; exit 1; }
+TOKEN=$(cat "$TOKEN_FILE")
+
+RESP=$(docker run --rm --network clawmates_core curlimages/curl:latest \
+  -s -m 1800 -X POST \
+  -H "Authorization: Bearer $TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{"per_topic":5}' \
+  http://clawmates_server_1:8080/api/library/runs)
+
+echo "library: $RESP" | head -c 2000
+
+# Report health explicitly. A run that shelved nothing is normal for a
+# mature library; a run that ERRORED is not, and the two look identical
+# if you only count papers.
+echo "$RESP" | python3 -c '
+import json, sys
+try:
+    d = json.load(sys.stdin)
+except Exception as e:
+    print("library: unreadable response (%s)" % e)
+    sys.exit(1)
+shelved = len(d.get("shelved", []))
+healthy = d.get("healthy", False)
+# Backslashes are avoided inside this program on purpose: it is embedded in a
+# single-quoted shell string, and an escaped quote here does not survive the
+# shell. The first version used one inside an f-string, crashed on every run,
+# and systemd reported a FAILED unit for a harvest that had actually shelved
+# 15 papers and pushed them. A false failure destroys trust in the signal as
+# surely as a false success.
+print("library: %d candidates, %d already held, %d shelved, healthy=%s, pushed=%s, branch=%s" % (
+    d.get("candidates", 0), d.get("already_had", 0), shelved,
+    healthy, d.get("pushed"), d.get("branch")))
+for f in d.get("failed", []):
+    print("library: FAILED %s" % f)
+sys.exit(0 if healthy else 1)
+'

deploy/gw-04/clawmates-library.timer

@@ -0,0 +1,16 @@
+[Unit]
+Description=Clawmates paper library — weekly harvest
+
+[Timer]
+# Monday 07:00 local. Weekly rather than daily because arXiv moves at
+# roughly that pace for a narrow topic set, and a run that almost always
+# finds nothing trains you to ignore it.
+OnCalendar=Mon *-*-* 07:00:00
+# Fire on next boot if the machine was down at the scheduled time — a
+# missed week is a silently empty library.
+Persistent=true
+AccuracySec=1min
+Unit=clawmates-library.service
+
+[Install]
+WantedBy=timers.target

migrations/0064_corpus_items.sql

@@ -0,0 +1,69 @@
+-- The seen-set for continuous missions.
+--
+-- Every "continuous X" mission has the same failure mode: it runs again and
+-- redoes work it already did. Research resurfaces papers it already read; a
+-- security scan re-reports findings already triaged. Orchestration does not
+-- fix that — a record of what has already been covered does.
+--
+-- This repository already tried continuous research once. Migrations 0030-0044
+-- built `research_topics`, `research_outcomes` and `loops`; 0053 dropped them
+-- all. `research_topics` carried a status lifecycle but no seen-set, so it
+-- could run forever and never know what it had covered. That is the gap this
+-- table exists to close, and it is the reason it lands before any scheduling.
+--
+-- Authoritative here rather than in the runtime's memory: ZeroClaw memory is
+-- scoped per agent, and mission agents are ephemeral `claw_<uuid>` aliases
+-- minted per mission (measured: ~100 of them already). A seen-set that
+-- disappears with the agent that wrote it is not a seen-set.
+CREATE TABLE corpus_items (
+    id            UUID PRIMARY KEY,
+    workspace_id  UUID NOT NULL REFERENCES workspaces (id) ON DELETE CASCADE,
+    -- Which corpus this belongs to, e.g. 'valhalla-vault'. A workspace can
+    -- track several (a vault, a findings ledger, a paper collection).
+    corpus_id     TEXT NOT NULL,
+
+    -- 'note'   = something already in the corpus (a vault file). Establishes
+    --            coverage: what has this vault already got?
+    -- 'source' = an external thing a mission consumed (a paper, an advisory).
+    --            This is the dedupe key that stops re-reading.
+    --
+    -- Both are needed and they answer different questions. Measured against
+    -- the real vault: 416 notes, and ZERO carry an arxiv/doi/url key — so an
+    -- ingester keyed only on external identity would index nothing at all.
+    kind          TEXT NOT NULL CHECK (kind IN ('note', 'source')),
+
+    -- Stable identity within the corpus. For notes, 'note:<vault-relative
+    -- path>'; for sources, a natural id like 'arxiv:2401.12345', 'doi:10...'
+    -- or 'url:<sha256>'. Uniqueness is on this, which is what makes
+    -- re-ingestion idempotent.
+    source_id     TEXT NOT NULL,
+
+    title         TEXT,
+    -- Vault-relative path for notes; NULL for external sources.
+    path          TEXT,
+    url           TEXT,
+
+    -- SHA-256 of the content at last sight. Lets a re-index distinguish
+    -- "unchanged" from "edited" without diffing, so an unchanged vault is a
+    -- genuine no-op rather than 416 pointless updates.
+    content_hash  TEXT NOT NULL,
+
+    first_seen_at TIMESTAMPTZ NOT NULL DEFAULT now(),
+    last_seen_at  TIMESTAMPTZ NOT NULL DEFAULT now(),
+    -- Which mission first recorded this. NULL for the initial vault index,
+    -- which is derived from files nobody's mission wrote.
+    mission_id    UUID REFERENCES missions (id) ON DELETE SET NULL,
+
+    UNIQUE (workspace_id, corpus_id, source_id)
+);
+
+-- The hot query is "have I seen this?", which the UNIQUE index already covers.
+-- This one serves "what does this corpus contain?" for briefing assembly.
+CREATE INDEX corpus_items_corpus_idx
+    ON corpus_items (workspace_id, corpus_id, kind, last_seen_at DESC);
+
+-- "What did this mission add?" — the verification predicate for a continuous
+-- run is that it contributed at least one NEW source.
+CREATE INDEX corpus_items_mission_idx
+    ON corpus_items (mission_id)
+    WHERE mission_id IS NOT NULL;