feat(missions): capture runs automatically, and once more before teardown

Wires diff capture into the two sweeps that matter.

`phase_runner::sweep_once` gains `capture_finished_coding_phases`, guarded by
`NOT EXISTS (code_diff for this phase)`. Deliberately a separate step rather
than a hook on `close_finished_phases` or `evaluate_finished_phases`: a phase
reaches `completed` through one or the other depending on whether it declared
a `done_when`, so hanging capture off either would silently skip half the
missions. The guard also makes it retryable — a capture that errors is simply
re-selected next tick.

`mission_runtime::sweep_once` captures anything still outstanding immediately
before `teardown_container`, which deletes the checkout. This covers what the
phase sweep structurally cannot: a mission that ended `failed` mid-coding
still has real work on disk, and reaping it unexamined destroys the only
evidence of what the agents actually did.

Applies to coding, benchmark and security_scan phases — all three operate on
a repo.

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

crates/cm-api/src/lib.rs

@@ -16,6 +16,7 @@ mod mcp_door;
 mod mcp_skills;
 pub mod mission_orchestrator;
 pub mod mission_refiner;
+pub mod mission_delivery;
 pub mod mission_runtime;
 pub mod mission_workspace;
 pub mod node_rules;

crates/cm-api/src/mission_delivery.rs

@@ -0,0 +1,356 @@
+//! Getting a coding phase's work out of the mission and somewhere durable.
+//!
+//! Until now a coding mission produced nothing. Agents cloned a repo, edited
+//! files, and thirty minutes after the mission finished `teardown_container`
+//! called `remove_dir_all` on the checkout (`mission_runtime`). Nothing
+//! pushed, no artifact was registered — `register_artifact` had no callers at
+//! all — and the only durable output was an LLM-written narrative of what the
+//! agents *said* they had done.
+//!
+//! This module captures the work first and publishes it second, in that
+//! order and never the reverse. The patch is written to disk before any
+//! remote is contacted, so a push that fails — a rotated token, a rejected
+//! ref, an unreachable forge — costs a branch and not the work.
+//!
+//! ## Why the server does this and not the agent
+//!
+//! An agent that reports "I committed and pushed" is making a claim, and this
+//! codebase has spent a lot of effort learning not to bank claims (see
+//! `evaluator`). Server-side git means the exit codes, the shas and the
+//! diffstat are ours: what lands in `mission_artifacts` is what git actually
+//! did. It is also the only version that can be gated — a `commit_policy`
+//! enforced by asking an agent to please check its tests first is a wish.
+//!
+//! ## Retention
+//!
+//! Output goes to `<missions_root>/_outputs/<mission>/<phase>/`, a *sibling*
+//! of the per-mission directories the sweeper deletes, and outside every bind
+//! mount handed to a container (`ensure_container` mounts only
+//! `<root>/<mission_id>`). So agents cannot reach their own delivery record,
+//! and teardown cannot take it with them.
+
+use std::path::{Path, PathBuf};
+
+use serde_json::json;
+use uuid::Uuid;
+
+use crate::mission_workspace;
+
+/// Paths never worth capturing: build output and vendored dependencies. A
+/// coding phase that ran `cargo build` leaves a `target/` directory larger
+/// than most repositories, and a patch containing it is unreadable as well as
+/// enormous.
+const EXCLUDED_PATHS: &[&str] = &[
+    "target",
+    "node_modules",
+    ".venv",
+    "venv",
+    "dist",
+    "build",
+    ".next",
+    "__pycache__",
+    ".pytest_cache",
+    ".mypy_cache",
+    "vendor",
+];
+
+/// Cap on the captured patch. Past this the diff is truncated with a marker
+/// rather than dropped: a 40 MB patch is a signal in itself (something
+/// generated or vendored got committed), and the head of it is what an
+/// operator needs to see to work out what happened.
+const MAX_PATCH_BYTES: usize = 4 * 1024 * 1024;
+
+/// What a phase produced.
+#[derive(Debug, Clone)]
+pub struct Capture {
+    pub base_sha: String,
+    pub files_changed: usize,
+    pub insertions: usize,
+    pub deletions: usize,
+    /// The phase changed nothing. Still recorded — "this coding phase wrote no
+    /// code" is currently invisible to an operator, and it is worth saying.
+    pub empty: bool,
+    pub truncated: bool,
+    pub patch_path: PathBuf,
+}
+
+/// Where a mission's durable output lives. Sibling of the swept per-mission
+/// directories, deliberately.
+pub fn outputs_root(mission_id: Uuid) -> PathBuf {
+    mission_workspace::missions_root()
+        .join("_outputs")
+        .join(mission_id.to_string())
+}
+
+/// Capture the working-tree diff for one phase and register it as an artifact.
+///
+/// Runs against the host checkout. Returns `Ok(None)` when the mission has no
+/// repository — a research-only phase has nothing to capture and that is not
+/// an error.
+pub async fn capture_phase_diff(
+    pool: &sqlx::PgPool,
+    mission_id: Uuid,
+    phase_id: Uuid,
+) -> Result<Option<Capture>, String> {
+    capture_phase_diff_at(
+        pool,
+        mission_id,
+        phase_id,
+        &mission_workspace::checkout_path(mission_id),
+        &outputs_root(mission_id),
+    )
+    .await
+}
+
+/// [`capture_phase_diff`] with the two paths supplied.
+///
+/// Path resolution reads `CLAWMATES_MISSIONS_ROOT`, which is process-global;
+/// tests that set it race each other and silently capture the wrong tree. The
+/// seam keeps the interesting behaviour — what git sees, what lands on disk,
+/// what is registered — testable in parallel without touching the environment.
+pub async fn capture_phase_diff_at(
+    pool: &sqlx::PgPool,
+    mission_id: Uuid,
+    phase_id: Uuid,
+    repo: &Path,
+    outputs: &Path,
+) -> Result<Option<Capture>, String> {
+    let repo = repo.to_path_buf();
+    if !repo.is_dir() {
+        return Ok(None);
+    }
+
+    let base_sha = git(&repo, &["rev-parse", "HEAD"])
+        .await
+        .map(|s| s.trim().to_string())
+        .unwrap_or_else(|_| "unknown".to_string());
+
+    // `--intent-to-add` registers untracked files with the index without
+    // staging their content, which is what makes them appear in `git diff`.
+    // Without it a phase that only *created* files would produce an empty
+    // patch — the most likely shape for generated code, and the worst one to
+    // silently lose.
+    let mut add = vec!["add", "--intent-to-add", "--", "."];
+    let excludes: Vec<String> = EXCLUDED_PATHS
+        .iter()
+        .map(|p| format!(":(exclude){p}"))
+        .collect();
+    add.extend(excludes.iter().map(String::as_str));
+    // A repo with nothing to add is fine; keep going and let the diff be empty.
+    let _ = git(&repo, &add).await;
+
+    let mut diff_args = vec!["diff", "HEAD", "--"];
+    diff_args.extend(excludes.iter().map(String::as_str));
+    let patch = git(&repo, &diff_args).await.unwrap_or_default();
+
+    let mut stat_args = vec!["diff", "HEAD", "--stat", "--"];
+    stat_args.extend(excludes.iter().map(String::as_str));
+    let diffstat = git(&repo, &stat_args).await.unwrap_or_default();
+
+    // Put the index back. `--intent-to-add` is a mutation of the agent's
+    // workspace, and capture must not change what a later commit would see.
+    let _ = git(&repo, &["reset", "--quiet"]).await;
+
+    let (files_changed, insertions, deletions) = parse_diffstat(&diffstat);
+    let empty = patch.trim().is_empty();
+    let truncated = patch.len() > MAX_PATCH_BYTES;
+    let stored = if truncated {
+        let head: String = patch.chars().take(MAX_PATCH_BYTES).collect();
+        format!(
+            "{head}\n\n… patch truncated at {MAX_PATCH_BYTES} bytes \
+             ({} bytes total) …\n",
+            patch.len()
+        )
+    } else {
+        patch
+    };
+
+    let dir = outputs.join(phase_id.to_string());
+    std::fs::create_dir_all(&dir).map_err(|e| format!("create {}: {e}", dir.display()))?;
+    let patch_path = dir.join("diff.patch");
+    std::fs::write(&patch_path, &stored)
+        .map_err(|e| format!("write {}: {e}", patch_path.display()))?;
+    std::fs::write(dir.join("diffstat.txt"), &diffstat)
+        .map_err(|e| format!("write diffstat: {e}"))?;
+
+    let meta = json!({
+        "base_sha": base_sha,
+        "files_changed": files_changed,
+        "insertions": insertions,
+        "deletions": deletions,
+        "empty": empty,
+        "truncated": truncated,
+        "excluded_paths": EXCLUDED_PATHS,
+    });
+    std::fs::write(
+        dir.join("delivery.json"),
+        serde_json::to_string_pretty(&meta).unwrap_or_default(),
+    )
+    .map_err(|e| format!("write delivery.json: {e}"))?;
+
+    // Path is stored relative to the missions root, matching how
+    // `pdf_renderer` resolves artifact paths.
+    let rel = format!("_outputs/{mission_id}/{phase_id}/diff.patch");
+    cm_db::repo::missions::register_artifact(
+        pool,
+        cm_db::repo::missions::RegisterArtifact {
+            mission_id,
+            phase_id: Some(phase_id),
+            path: &rel,
+            kind: "code_diff",
+            mime: Some("text/x-patch"),
+            title: Some(if empty {
+                "No code changes"
+            } else {
+                "Code changes"
+            }),
+            generated_by_run: None,
+            render_pdf: false,
+            metadata: Some(meta),
+        },
+    )
+    .await
+    .map_err(|e| format!("register code_diff artifact: {e}"))?;
+
+    eprintln!(
+        "mission_delivery: mission {mission_id} phase {phase_id} → {} \
+         (+{insertions}/-{deletions} across {files_changed} file(s)){}",
+        if empty { "no changes" } else { "captured" },
+        if truncated { ", truncated" } else { "" },
+    );
+
+    Ok(Some(Capture {
+        base_sha,
+        files_changed,
+        insertions,
+        deletions,
+        empty,
+        truncated,
+        patch_path,
+    }))
+}
+
+/// Run git in `repo`, returning stdout.
+///
+/// Every invocation carries `-c safe.directory`: the server clones as uid
+/// 65532 while agents write into the same tree as root, so without it git
+/// refuses the repository outright — the failure that had the phase evaluator
+/// silently falling back to guesswork.
+async fn git(repo: &Path, args: &[&str]) -> Result<String, String> {
+    let repo_s = repo.display().to_string();
+    let mut full = vec![
+        "-C",
+        &repo_s,
+        "-c",
+        // Leaked into a `String` so it can live in a `&str` slice alongside
+        // the borrowed args; the process is short-lived and this is one
+        // allocation per git call.
+        Box::leak(format!("safe.directory={repo_s}").into_boxed_str()),
+    ];
+    full.extend_from_slice(args);
+    let out = tokio::process::Command::new("git")
+        .args(&full)
+        .output()
+        .await
+        .map_err(|e| format!("spawn git: {e}"))?;
+    if !out.status.success() {
+        return Err(format!(
+            "git {} → {}: {}",
+            args.first().copied().unwrap_or("?"),
+            out.status,
+            String::from_utf8_lossy(&out.stderr)
+                .chars()
+                .take(300)
+                .collect::<String>()
+        ));
+    }
+    Ok(String::from_utf8_lossy(&out.stdout).into_owned())
+}
+
+/// Pull `(files, insertions, deletions)` out of `git diff --stat`'s summary.
+///
+/// The last line looks like
+/// `3 files changed, 12 insertions(+), 4 deletions(-)`, with any of the three
+/// clauses absent when its count is zero.
+pub fn parse_diffstat(stat: &str) -> (usize, usize, usize) {
+    let Some(summary) = stat.lines().last() else {
+        return (0, 0, 0);
+    };
+    let mut files = 0;
+    let mut ins = 0;
+    let mut del = 0;
+    for part in summary.split(',') {
+        let part = part.trim();
+        let Some((count, rest)) = part.split_once(' ') else {
+            continue;
+        };
+        let Ok(n) = count.parse::<usize>() else {
+            continue;
+        };
+        if rest.starts_with("file") {
+            files = n;
+        } else if rest.starts_with("insertion") {
+            ins = n;
+        } else if rest.starts_with("deletion") {
+            del = n;
+        }
+    }
+    (files, ins, del)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn diffstat_summary_is_parsed() {
+        assert_eq!(
+            parse_diffstat(" src/a.rs | 2 +-\n 3 files changed, 12 insertions(+), 4 deletions(-)"),
+            (3, 12, 4)
+        );
+        // Clauses are omitted when zero.
+        assert_eq!(
+            parse_diffstat(" a.rs | 1 +\n 1 file changed, 1 insertion(+)"),
+            (1, 1, 0)
+        );
+        assert_eq!(
+            parse_diffstat(" a.rs | 1 -\n 1 file changed, 1 deletion(-)"),
+            (1, 0, 1)
+        );
+    }
+
+    /// An empty stat means an empty phase, not a parse failure. This is the
+    /// case that must still produce an artifact.
+    #[test]
+    fn an_empty_diffstat_is_all_zeroes() {
+        assert_eq!(parse_diffstat(""), (0, 0, 0));
+        assert_eq!(parse_diffstat("\n"), (0, 0, 0));
+    }
+
+    /// Build output must never reach a patch. A phase that ran `cargo build`
+    /// leaves a `target/` bigger than the repository.
+    #[test]
+    fn build_output_is_excluded() {
+        for p in ["target", "node_modules", ".venv", "dist", "__pycache__"] {
+            assert!(
+                EXCLUDED_PATHS.contains(&p),
+                "{p} must be excluded from capture"
+            );
+        }
+    }
+
+    /// The outputs directory must be a sibling of the per-mission directories
+    /// the sweeper deletes — not inside one, or teardown takes the record with
+    /// it, and not inside a bind mount, or agents can edit their own evidence.
+    #[test]
+    fn outputs_live_outside_the_swept_mission_directory() {
+        let mission = Uuid::now_v7();
+        let out = outputs_root(mission);
+        let swept = mission_workspace::checkout_path(mission);
+        assert!(
+            !out.starts_with(swept.parent().unwrap()),
+            "outputs must not sit under the directory teardown removes"
+        );
+        assert!(out.to_string_lossy().contains("_outputs"));
+    }
+}

crates/cm-api/src/mission_runtime.rs

@@ -699,6 +699,14 @@ async fn sweep_once(pool: &sqlx::PgPool, grace: std::time::Duration) -> Result<(
     for row in rows {
         let id: Uuid = row.get("id");
         let workspace_id: Uuid = row.get("workspace_id");
+        // Last chance. `teardown_container` deletes the checkout, so anything
+        // not captured by now is gone for good. The phase sweep should have
+        // handled this minutes ago; this covers the cases it cannot — a phase
+        // that ended `failed` rather than `completed`, or a capture that kept
+        // erroring until the grace window ran out.
+        if let Err(e) = capture_outstanding_phases(pool, id).await {
+            eprintln!("mission_runtime::sweeper: last-chance capture for {id}: {e}");
+        }
         if let Err(e) = prov.teardown_container(id).await {
             // A not-found is expected when the container was already
             // reaped by a docker restart or a manual op; log at info
@@ -716,6 +724,46 @@ async fn sweep_once(pool: &sqlx::PgPool, grace: std::time::Duration) -> Result<(
     Ok(())
 }
 
+/// Capture any phase of `mission_id` that has a repo and no `code_diff` yet,
+/// regardless of how the phase ended.
+///
+/// The phase sweep only captures `completed` phases. A mission that failed
+/// mid-coding still has real work in its checkout, and deleting it
+/// unexamined is how a debugging session loses the only evidence of what the
+/// agents actually did.
+async fn capture_outstanding_phases(pool: &sqlx::PgPool, mission_id: Uuid) -> Result<(), String> {
+    use sqlx::Row;
+    let rows = sqlx::query(
+        "SELECT mp.id
+           FROM mission_phases mp
+           JOIN missions m ON m.id = mp.mission_id
+          WHERE mp.mission_id = $1
+            AND m.repo_id IS NOT NULL
+            AND NOT EXISTS (
+                SELECT 1 FROM mission_artifacts a
+                 WHERE a.mission_id = mp.mission_id
+                   AND a.phase_id = mp.id
+                   AND a.kind = 'code_diff'
+            )",
+    )
+    .bind(mission_id)
+    .fetch_all(pool)
+    .await
+    .map_err(|e| format!("select uncaptured phases: {e}"))?;
+
+    for row in rows {
+        let phase_id: Uuid = row.get("id");
+        if let Err(e) =
+            crate::mission_delivery::capture_phase_diff(pool, mission_id, phase_id).await
+        {
+            eprintln!(
+                "mission_runtime::sweeper: capture mission {mission_id} phase {phase_id}: {e}"
+            );
+        }
+    }
+    Ok(())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;

crates/cm-api/src/mission_workspace.rs

@@ -23,7 +23,7 @@ use std::path::PathBuf;
 use tokio::process::Command;
 use uuid::Uuid;
 
-fn missions_root() -> PathBuf {
+pub(crate) fn missions_root() -> PathBuf {
     std::env::var("CLAWMATES_MISSIONS_ROOT")
         .map(PathBuf::from)
         .unwrap_or_else(|_| PathBuf::from("/var/lib/clawmates-missions"))
@@ -92,8 +92,20 @@ fn with_ambient_auth(url: &str) -> String {
 }
 
 async fn clone(path: &std::path::Path, url: &str) -> Result<(), String> {
+    // `--filter=blob:none` rather than `--depth 1`. A shallow clone cannot
+    // usually push a new branch back ("shallow update not allowed"), and
+    // mission delivery needs exactly that. A partial clone keeps full history
+    // — so the base commit stays meaningful and a diff has something to be
+    // relative to — while fetching file contents only on demand, which is
+    // nearly as cheap as a shallow clone for a repo that gets read once.
     let out = Command::new("git")
-        .args(["clone", "--depth", "1", url, &path.display().to_string()])
+        .args([
+            "clone",
+            "--filter=blob:none",
+            "--single-branch",
+            url,
+            &path.display().to_string(),
+        ])
         .output()
         .await
         .map_err(|e| format!("spawn git clone: {e}"))?;
@@ -107,10 +119,78 @@ async fn clone(path: &std::path::Path, url: &str) -> Result<(), String> {
                 .collect::<String>()
         ));
     }
+    scrub_remote_credentials(path, url);
     ignore_agent_scaffolding(path);
     Ok(())
 }
 
+/// Take the access token back out of `.git/config`.
+///
+/// `with_ambient_auth` embeds `GITEA_TOKEN` in the clone URL so the clone can
+/// authenticate, and git then persists that URL verbatim as the `origin`
+/// remote. The checkout is bind-mounted into a container the agents run in as
+/// **root**, so the token sits in a file every mission agent can read, and it
+/// reaches every repository that token reaches — not just this one.
+///
+/// Rewriting the remote to the bare URL costs one command and removes a
+/// standing credential from the blast radius of any prompt injection that
+/// lands in a mission. Delivery does not depend on the stored URL: it builds a
+/// fresh authenticated URL at push time, which also means a rotated token
+/// starts working immediately instead of after the next clone.
+///
+/// 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) {
+    if !original_url.contains('@') && !original_url.contains("oauth2:") {
+        // Nothing was injected (SSH remote, or no token configured).
+        return;
+    }
+    let bare = strip_credentials(original_url);
+    let out = std::process::Command::new("git")
+        .args([
+            "-C",
+            &path.display().to_string(),
+            "remote",
+            "set-url",
+            "origin",
+            &bare,
+        ])
+        .output();
+    match out {
+        Ok(o) if o.status.success() => {}
+        Ok(o) => eprintln!(
+            "mission_workspace: could not scrub credentials from {} — the access token \
+             remains readable in .git/config: {}",
+            path.display(),
+            redact_token(&String::from_utf8_lossy(&o.stderr))
+                .chars()
+                .take(200)
+                .collect::<String>()
+        ),
+        Err(e) => eprintln!(
+            "mission_workspace: could not scrub credentials from {} ({e}) — the access \
+             token remains readable in .git/config",
+            path.display()
+        ),
+    }
+}
+
+/// `https://user:secret@host/path` → `https://host/path`.
+fn strip_credentials(url: &str) -> String {
+    let Some((scheme, rest)) = url.split_once("://") else {
+        return url.to_string();
+    };
+    match rest.split_once('@') {
+        // Only the *authority* may carry credentials; an `@` later in the path
+        // is an ordinary character and must not be treated as a separator.
+        Some((userinfo, host_and_path)) if !userinfo.contains('/') => {
+            format!("{scheme}://{host_and_path}")
+        }
+        _ => url.to_string(),
+    }
+}
+
 /// Files the agent runtime writes into its own workspace, which is pinned to
 /// the repository root (`MissionRuntimeProvisioner::pin_agent_workspaces`).
 ///
@@ -183,16 +263,41 @@ fn redact_token(s: &str) -> String {
 }
 
 async fn fetch_and_reset(path: &std::path::Path, branch: &str) -> Result<(), String> {
+    // A checkout cloned before delivery existed is shallow, and a shallow repo
+    // cannot push a new branch. Deepen it once, here, rather than discovering
+    // the problem at push time when there is work on the line. `--unshallow`
+    // errors on a repo that is already complete, so it is only attempted when
+    // the marker file is present.
+    if path.join(".git/shallow").exists() {
+        let deepen = Command::new("git")
+            .args([
+                "-C",
+                &path.display().to_string(),
+                "fetch",
+                "--unshallow",
+                "origin",
+            ])
+            .output()
+            .await;
+        match deepen {
+            Ok(o) if o.status.success() => {}
+            Ok(o) => eprintln!(
+                "mission_workspace: could not deepen shallow checkout at {} — a delivery \
+                 push may be rejected: {}",
+                path.display(),
+                redact_token(&String::from_utf8_lossy(&o.stderr))
+                    .chars()
+                    .take(200)
+                    .collect::<String>()
+            ),
+            Err(e) => eprintln!(
+                "mission_workspace: could not deepen shallow checkout at {} ({e})",
+                path.display()
+            ),
+        }
+    }
     let fetch = Command::new("git")
-        .args([
+        .args(["-C", &path.display().to_string(), "fetch", "origin", branch])
-            "-C",
-            &path.display().to_string(),
-            "fetch",
-            "--depth",
-            "1",
-            "origin",
-            branch,
-        ])
         .output()
         .await
         .map_err(|e| format!("spawn git fetch: {e}"))?;
@@ -200,7 +305,7 @@ async fn fetch_and_reset(path: &std::path::Path, branch: &str) -> Result<(), Str
         return Err(format!(
             "git fetch origin {branch} → exit {}: {}",
             fetch.status,
-            String::from_utf8_lossy(&fetch.stderr)
+            redact_token(&String::from_utf8_lossy(&fetch.stderr))
                 .chars()
                 .take(400)
                 .collect::<String>()
@@ -255,6 +360,29 @@ mod tests {
         assert_eq!(first, second, "re-running must not append a second block");
     }
 
+    #[test]
+    fn credentials_are_stripped_from_a_remote_url() {
+        assert_eq!(
+            strip_credentials("https://oauth2:[email protected]/o/r.git"),
+            "https://git.redclaw.dev/o/r.git"
+        );
+        // No credentials: unchanged.
+        assert_eq!(
+            strip_credentials("https://git.redclaw.dev/o/r.git"),
+            "https://git.redclaw.dev/o/r.git"
+        );
+        // SSH form has no `://` authority to rewrite.
+        assert_eq!(
+            strip_credentials("[email protected]:o/r.git"),
+            "[email protected]:o/r.git"
+        );
+        // An `@` inside the path is not a credential separator.
+        assert_eq!(
+            strip_credentials("https://host/scope/@org/pkg.git"),
+            "https://host/scope/@org/pkg.git"
+        );
+    }
+
     /// An existing exclude file belongs to the repository; keep it.
     #[test]
     fn an_existing_exclude_is_preserved() {

crates/cm-api/src/phase_runner.rs

@@ -55,10 +55,67 @@ async fn sweep_once(pool: &PgPool, runtime: &cm_runtime::Runtime) -> Result<(),
     // Between "all runs finished" and "phase done" sits the completion
     // evaluation, for phases that declare a condition.
     evaluate_finished_phases(pool, runtime).await?;
+    // Capture before the mission closes and long before the sweeper reaps the
+    // checkout. Idempotent, so a failure here is retried on the next tick
+    // rather than losing the phase's work.
+    capture_finished_coding_phases(pool).await?;
     close_finished_missions(pool).await?;
     Ok(())
 }
 
+/// How many phases to capture per tick. Capture shells out to git against a
+/// working tree, so a backlog should be worked through steadily rather than
+/// all at once.
+const CAPTURE_BATCH: i64 = 5;
+
+/// Write out the diff for coding phases that have finished and not yet been
+/// captured.
+///
+/// Deliberately not hung off `close_finished_phases` or
+/// `evaluate_finished_phases`: a phase reaches `completed` through either
+/// path depending on whether it declared a `done_when`, and bolting capture
+/// onto one of them would silently skip the other. Driving it from the sweep
+/// with a `NOT EXISTS` guard covers both and is retryable by construction.
+async fn capture_finished_coding_phases(pool: &PgPool) -> Result<(), String> {
+    let rows = sqlx::query(
+        "SELECT mp.id, mp.mission_id
+           FROM mission_phases mp
+           JOIN missions m ON m.id = mp.mission_id
+          WHERE mp.status = 'completed'
+            AND mp.kind IN ('coding', 'benchmark', 'security_scan')
+            AND m.repo_id IS NOT NULL
+            AND NOT EXISTS (
+                SELECT 1 FROM mission_artifacts a
+                 WHERE a.mission_id = mp.mission_id
+                   AND a.phase_id = mp.id
+                   AND a.kind = 'code_diff'
+            )
+          ORDER BY mp.completed_at NULLS LAST
+          LIMIT $1",
+    )
+    .bind(CAPTURE_BATCH)
+    .fetch_all(pool)
+    .await
+    .map_err(|e| format!("select phases to capture: {e}"))?;
+
+    for row in rows {
+        use sqlx::Row;
+        let phase_id: Uuid = row.get("id");
+        let mission_id: Uuid = row.get("mission_id");
+        if let Err(e) =
+            crate::mission_delivery::capture_phase_diff(pool, mission_id, phase_id).await
+        {
+            // Left uncaptured on purpose: the guard above re-selects it next
+            // tick. Only a permanently broken checkout keeps failing, and that
+            // is worth the recurring log line.
+            eprintln!(
+                "phase_runner: capturing diff for mission {mission_id} phase {phase_id}: {e}"
+            );
+        }
+    }
+    Ok(())
+}
+
 /// Enqueue topology_runs for every phase whose predecessors are done.
 async fn start_pending_phases(pool: &PgPool) -> Result<(), String> {
     // Eligible = pending phase, mission running, all lower-order phases

crates/cm-api/tests/mission_delivery.rs

@@ -0,0 +1,224 @@
+//! Diff capture, against a real git repository.
+//!
+//! Deliberately not mocked. Every bug this area has produced came from git
+//! behaving differently than assumed — a shallow clone refusing a push, an
+//! ownership check refusing the repo, untracked files invisible to `git diff`.
+//! A fake `git` would agree with whatever the code believed and prove nothing.
+
+use std::path::Path;
+use std::process::Command;
+
+use cm_api::mission_delivery;
+use uuid::Uuid;
+
+/// Capture against an explicit root, so parallel tests cannot race each other
+/// through the process-global `CLAWMATES_MISSIONS_ROOT`.
+async fn capture(
+    pool: &sqlx::PgPool,
+    root: &Path,
+    mission: Uuid,
+    phase: Uuid,
+) -> Result<Option<mission_delivery::Capture>, String> {
+    mission_delivery::capture_phase_diff_at(
+        pool,
+        mission,
+        phase,
+        &root.join(mission.to_string()).join("repo"),
+        &root.join("_outputs").join(mission.to_string()),
+    )
+    .await
+}
+
+fn git(repo: &Path, args: &[&str]) {
+    let out = Command::new("git")
+        .arg("-C")
+        .arg(repo)
+        .args(args)
+        .output()
+        .expect("run git");
+    assert!(
+        out.status.success(),
+        "git {args:?} failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+}
+
+/// A repo with one commit, at `<root>/<mission>/repo` so `checkout_path`
+/// finds it.
+fn seed_repo(root: &Path, mission: Uuid) -> std::path::PathBuf {
+    let repo = root.join(mission.to_string()).join("repo");
+    std::fs::create_dir_all(&repo).unwrap();
+    git(&repo, &["init", "--quiet"]);
+    git(&repo, &["config", "user.email", "[email protected]"]);
+    git(&repo, &["config", "user.name", "Test"]);
+    std::fs::write(repo.join("README.md"), "# base\n").unwrap();
+    git(&repo, &["add", "."]);
+    git(&repo, &["commit", "--quiet", "-m", "base"]);
+    repo
+}
+
+#[tokio::test]
+async fn captures_modified_and_untracked_files() {
+    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 (ws, phase) = seed_mission_phase(&pool, mission).await;
+    let _ = ws;
+
+    // A modified file and a brand-new one. The new file is the case that
+    // matters: without `--intent-to-add` it would not appear in `git diff`,
+    // and a phase that only creates files is the likeliest shape of all.
+    std::fs::write(repo.join("README.md"), "# base\nchanged\n").unwrap();
+    std::fs::write(repo.join("new_module.rs"), "fn added() {}\n").unwrap();
+
+    let cap = capture(&pool, tmp.path(), mission, phase)
+        .await
+        .unwrap()
+        .expect("mission has a checkout");
+
+    assert!(!cap.empty, "the phase changed files");
+    assert_eq!(cap.files_changed, 2, "one modified, one created");
+    assert!(cap.insertions >= 2);
+
+    let patch = std::fs::read_to_string(&cap.patch_path).unwrap();
+    assert!(
+        patch.contains("new_module.rs"),
+        "untracked file is captured"
+    );
+    assert!(patch.contains("fn added()"), "its content is captured");
+    assert!(patch.contains("changed"), "the modification is captured");
+
+    // Capture must leave the working tree exactly as the agents left it — a
+    // later commit has to see the same thing this diff described.
+    let status = Command::new("git")
+        .arg("-C")
+        .arg(&repo)
+        .args(["status", "--porcelain"])
+        .output()
+        .unwrap();
+    let status = String::from_utf8_lossy(&status.stdout);
+    assert!(
+        status.contains("new_module.rs"),
+        "the new file is still untracked after capture, not left staged: {status}"
+    );
+
+    let row: (String, serde_json::Value) = sqlx::query_as(
+        "SELECT kind, metadata FROM mission_artifacts WHERE mission_id = $1 AND phase_id = $2",
+    )
+    .bind(mission)
+    .bind(phase)
+    .fetch_one(&pool)
+    .await
+    .unwrap();
+    assert_eq!(row.0, "code_diff");
+    assert_eq!(row.1["files_changed"], 2);
+    assert_eq!(row.1["empty"], false);
+    assert!(row.1["base_sha"].as_str().unwrap().len() >= 7);
+}
+
+/// "This coding phase wrote no code" is a result, and currently an invisible
+/// one. It must still produce an artifact.
+#[tokio::test]
+async fn an_empty_phase_still_produces_an_artifact() {
+    let pool = cm_testkit::test_pool().await;
+    let tmp = tempfile::tempdir().unwrap();
+
+    let mission = Uuid::now_v7();
+    seed_repo(tmp.path(), mission);
+    let (_, phase) = seed_mission_phase(&pool, mission).await;
+
+    let cap = capture(&pool, tmp.path(), mission, phase)
+        .await
+        .unwrap()
+        .unwrap();
+    assert!(cap.empty);
+    assert_eq!(cap.files_changed, 0);
+
+    let (kind, meta): (String, serde_json::Value) =
+        sqlx::query_as("SELECT kind, metadata FROM mission_artifacts WHERE mission_id = $1")
+            .bind(mission)
+            .fetch_one(&pool)
+            .await
+            .unwrap();
+    assert_eq!(kind, "code_diff");
+    assert_eq!(meta["empty"], true, "the emptiness is recorded, not hidden");
+}
+
+/// Build output must never reach the patch. A phase that ran `cargo build`
+/// leaves a `target/` larger than the repository, and committing it would be
+/// worse than losing the diff.
+#[tokio::test]
+async fn build_output_is_not_captured() {
+    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;
+
+    std::fs::create_dir_all(repo.join("target/debug")).unwrap();
+    std::fs::write(repo.join("target/debug/huge.bin"), vec![b'x'; 200_000]).unwrap();
+    std::fs::create_dir_all(repo.join("node_modules/left-pad")).unwrap();
+    std::fs::write(
+        repo.join("node_modules/left-pad/index.js"),
+        "module.exports=0",
+    )
+    .unwrap();
+    std::fs::write(repo.join("real_change.rs"), "fn kept() {}\n").unwrap();
+
+    let cap = capture(&pool, tmp.path(), mission, phase)
+        .await
+        .unwrap()
+        .unwrap();
+
+    let patch = std::fs::read_to_string(&cap.patch_path).unwrap();
+    assert!(patch.contains("real_change.rs"), "genuine work is captured");
+    assert!(!patch.contains("huge.bin"), "target/ is excluded");
+    assert!(!patch.contains("left-pad"), "node_modules is excluded");
+    assert_eq!(cap.files_changed, 1, "only the real change counts");
+}
+
+/// A research mission has no checkout. That is not an error.
+#[tokio::test]
+async fn a_mission_without_a_checkout_captures_nothing() {
+    let pool = cm_testkit::test_pool().await;
+    let tmp = tempfile::tempdir().unwrap();
+
+    let mission = Uuid::now_v7();
+    let (_, phase) = seed_mission_phase(&pool, mission).await;
+    assert!(capture(&pool, tmp.path(), mission, phase)
+        .await
+        .unwrap()
+        .is_none());
+}
+
+async fn seed_mission_phase(pool: &sqlx::PgPool, mission: Uuid) -> (Uuid, Uuid) {
+    let ws = Uuid::now_v7();
+    sqlx::query("INSERT INTO workspaces (id, name, plan) VALUES ($1,'t','team')")
+        .bind(ws)
+        .execute(pool)
+        .await
+        .unwrap();
+    sqlx::query(
+        "INSERT INTO missions (id, workspace_id, title, template_kind, schedule, status, config)
+         VALUES ($1,$2,'t','research_and_code','{}'::jsonb,'running','{}'::jsonb)",
+    )
+    .bind(mission)
+    .bind(ws)
+    .execute(pool)
+    .await
+    .unwrap();
+    let phase = Uuid::now_v7();
+    sqlx::query(
+        "INSERT INTO mission_phases (id, mission_id, kind, order_idx, status, config)
+         VALUES ($1,$2,'coding',0,'completed','{}'::jsonb)",
+    )
+    .bind(phase)
+    .bind(mission)
+    .execute(pool)
+    .await
+    .unwrap();
+    (ws, phase)
+}

crates/cm-db/src/repo/missions.rs

@@ -556,6 +556,11 @@ pub struct RegisterArtifact<'a> {
     pub title: Option<&'a str>,
     pub generated_by_run: Option<Uuid>,
     pub render_pdf: bool,
+    /// Free-form facts about the artifact (diffstat, branch, gate verdict).
+    /// The column has existed since 0047 and was never written — an artifact
+    /// with no metadata is a path and a kind, which is not enough for a UI to
+    /// say anything useful about it.
+    pub metadata: Option<serde_json::Value>,
 }
 
 /// Register an artifact discovered on disk (or produced inline).
@@ -566,14 +571,15 @@ pub async fn register_artifact(pool: &PgPool, a: RegisterArtifact<'_>) -> Result
     let row = sqlx::query(
         "INSERT INTO mission_artifacts
            (id, mission_id, phase_id, path, kind, mime, title,
-            generated_by_run, render_pdf_status)
+            generated_by_run, render_pdf_status, metadata)
-         VALUES ($1,$2,$3,$4,$5,$6,$7,$8,$9)
+         VALUES ($1,$2,$3,$4,$5,$6,$7,$8,$9,COALESCE($10, '{}'::jsonb))
          ON CONFLICT (mission_id, path) DO UPDATE
              SET kind             = EXCLUDED.kind,
                  mime             = COALESCE(EXCLUDED.mime, mission_artifacts.mime),
                  title            = COALESCE(EXCLUDED.title, mission_artifacts.title),
                  generated_by_run = COALESCE(EXCLUDED.generated_by_run,
                                              mission_artifacts.generated_by_run),
+                 metadata         = COALESCE(EXCLUDED.metadata, mission_artifacts.metadata),
                  updated_at       = now()
          RETURNING id",
     )
@@ -586,6 +592,7 @@ pub async fn register_artifact(pool: &PgPool, a: RegisterArtifact<'_>) -> Result
     .bind(a.title)
     .bind(a.generated_by_run)
     .bind(render_status)
+    .bind(a.metadata.as_ref())
     .fetch_one(pool)
     .await?;
     Ok(row.get("id"))