Add three-way file root apply

README.md

@@ -232,8 +232,12 @@ against the current local same-named root and the newly imported remote tree.
 Concurrent edit, delete/edit, and divergent rename conflicts are recorded in
 the local conflict table for later resolution.
 `geth cas root apply <root> --to <path>` can then materialize that tree locally:
-it creates missing directories/files, never deletes extra files, never
-overwrites differing local files, and records conflicts for manual resolution.
+without a registered local root base it creates missing directories/files, never
+deletes extra files, never overwrites differing local files, and records
+conflicts for manual resolution. When the target path is a registered local file
+root with a previous scan, apply uses a three-way base/local/remote check and
+can safely apply non-conflicting remote creates, updates, deletes, and renames
+only where local state still matches the recorded base.
 Named KV stores participate in the same live-sync loop once they exist locally:
 manual `geth kv sync <node-id> <name>` and background ticks require `kv.read`
 on the remote `resource:kv:<name>` and import only remote entries that are not

crates/geth-node/src/lib.rs

@@ -7917,6 +7917,44 @@ fn apply_file_root_tree(
         std::fs::create_dir_all(&target)?;
     }
 
+    if let Some((local_root, base_tree, local_tree, local_tree_hash)) =
+        load_apply_three_way_state(store, &cas, &target)?
+    {
+        return apply_file_root_tree_three_way(
+            store,
+            &source_root,
+            &local_root,
+            &cas,
+            target,
+            dry_run,
+            &tree_hash,
+            &tree,
+            &base_tree,
+            &local_tree,
+            local_tree_hash.as_ref(),
+        );
+    }
+
+    apply_file_root_tree_conservative(
+        store,
+        &source_root,
+        &cas,
+        target,
+        dry_run,
+        &tree_hash,
+        &tree,
+    )
+}
+
+fn apply_file_root_tree_conservative(
+    store: &Store,
+    source_root: &StoredFileRoot,
+    cas: &LocalCas,
+    target: PathBuf,
+    dry_run: bool,
+    tree_hash: &BlobHash,
+    tree: &CasTreeObject,
+) -> Result<ControlResponse, NodeError> {
     let mut files_written = 0;
     let mut dirs_created = 0;
     let mut conflicts = Vec::new();
@@ -7928,9 +7966,9 @@ fn apply_file_root_tree(
                     if !out.is_dir() {
                         conflicts.push(record_apply_conflict(
                             store,
-                            &source_root,
+                            source_root,
                             &entry.path,
-                            &tree_hash,
+                            tree_hash,
                             "remote directory conflicts with a local non-directory path",
                             dry_run,
                         )?);
@@ -7946,9 +7984,9 @@ fn apply_file_root_tree(
                 let Some(blob) = &entry.blob else {
                     conflicts.push(record_apply_conflict(
                         store,
-                        &source_root,
+                        source_root,
                         &entry.path,
-                        &tree_hash,
+                        tree_hash,
                         "remote file entry is missing a CAS blob hash",
                         dry_run,
                     )?);
@@ -7958,9 +7996,9 @@ fn apply_file_root_tree(
                     if !out.is_file() {
                         conflicts.push(record_apply_conflict(
                             store,
-                            &source_root,
+                            source_root,
                             &entry.path,
-                            &tree_hash,
+                            tree_hash,
                             "remote file conflicts with a local non-file path",
                             dry_run,
                         )?);
@@ -7969,9 +8007,9 @@ fn apply_file_root_tree(
                     if hash_path(&out)? != *blob {
                         conflicts.push(record_apply_conflict(
                             store,
-                            &source_root,
+                            source_root,
                             &entry.path,
-                            &tree_hash,
+                            tree_hash,
                             "local file differs from remote CAS tree; refusing to overwrite",
                             dry_run,
                         )?);
@@ -7989,7 +8027,7 @@ fn apply_file_root_tree(
     }
 
     Ok(ControlResponse::CasRootApplied {
-        source: source.to_owned(),
+        source: source_root.name.clone(),
         target,
         files_written,
         dirs_created,
@@ -7999,6 +8037,325 @@ fn apply_file_root_tree(
     })
 }
 
+type ApplyThreeWayState = (
+    StoredFileRoot,
+    CasTreeObject,
+    CasTreeObject,
+    Option<BlobHash>,
+);
+
+fn load_apply_three_way_state(
+    store: &Store,
+    cas: &LocalCas,
+    target: &Path,
+) -> Result<Option<ApplyThreeWayState>, NodeError> {
+    if !target.is_dir() {
+        return Ok(None);
+    }
+    let target = std::fs::canonicalize(target)?;
+    let Some(local_root) = store
+        .list_file_roots()?
+        .into_iter()
+        .filter(|root| !root.path.starts_with("remote:"))
+        .find(|root| {
+            std::fs::canonicalize(&root.path)
+                .map(|path| path == target)
+                .unwrap_or(false)
+        })
+    else {
+        return Ok(None);
+    };
+    let Some(base_tree_json) = local_root.latest_tree_json.as_deref() else {
+        return Ok(None);
+    };
+    let base_tree = serde_json::from_str(base_tree_json)?;
+    let local_scan = cas.add_tree_path(&target)?;
+    Ok(Some((
+        local_root,
+        base_tree,
+        local_scan.tree,
+        Some(local_scan.object.hash),
+    )))
+}
+
+#[allow(clippy::too_many_arguments)]
+fn apply_file_root_tree_three_way(
+    store: &Store,
+    source_root: &StoredFileRoot,
+    local_root: &StoredFileRoot,
+    cas: &LocalCas,
+    target: PathBuf,
+    dry_run: bool,
+    remote_tree_hash: &BlobHash,
+    remote_tree: &CasTreeObject,
+    base_tree: &CasTreeObject,
+    local_tree: &CasTreeObject,
+    local_tree_hash: Option<&BlobHash>,
+) -> Result<ControlResponse, NodeError> {
+    let mut files_written = 0;
+    let mut dirs_created = 0;
+    let mut conflicts = record_three_way_apply_conflicts(
+        store,
+        source_root,
+        local_root,
+        base_tree,
+        local_tree_hash,
+        remote_tree_hash,
+        remote_tree,
+        local_tree,
+        dry_run,
+    )?;
+    let conflict_paths = conflicts
+        .iter()
+        .map(|conflict| conflict.path.clone())
+        .collect::<BTreeSet<_>>();
+    let base_entries = owned_tree_entry_map(base_tree);
+    let local_entries = owned_tree_entry_map(local_tree);
+    let remote_entries = owned_tree_entry_map(remote_tree);
+    let mut consumed_base_paths = BTreeSet::new();
+    let mut consumed_remote_paths = BTreeSet::new();
+
+    for (from, to) in remote_rename_pairs(&base_entries, &remote_entries) {
+        if conflict_paths.contains(&from) || conflict_paths.contains(&to) {
+            continue;
+        }
+        let Some(base_entry) = base_entries.get(&from) else {
+            continue;
+        };
+        if local_entries.get(&from) != Some(base_entry) {
+            continue;
+        }
+        let Some(remote_entry) = remote_entries.get(&to) else {
+            continue;
+        };
+        let from_path = safe_tree_output_path(&target, &from)?;
+        let to_path = safe_tree_output_path(&target, &to)?;
+        if to_path.exists() {
+            if path_matches_entry(cas, &to_path, remote_entry)? {
+                consumed_base_paths.insert(from);
+                consumed_remote_paths.insert(to);
+            } else {
+                conflicts.push(record_apply_conflict_with_trees(
+                    store,
+                    source_root,
+                    &to,
+                    local_root.latest_tree_hash.as_deref(),
+                    local_tree_hash,
+                    remote_tree_hash,
+                    "remote rename target conflicts with an existing local path",
+                    dry_run,
+                )?);
+            }
+            continue;
+        }
+        if !from_path.exists() {
+            continue;
+        }
+        if !dry_run {
+            if let Some(parent) = to_path.parent() {
+                std::fs::create_dir_all(parent)?;
+            }
+            std::fs::rename(&from_path, &to_path)?;
+            set_executable_bit(&to_path, remote_entry.executable)?;
+        }
+        consumed_base_paths.insert(from);
+        consumed_remote_paths.insert(to);
+    }
+
+    let mut remote_paths = remote_entries.keys().cloned().collect::<Vec<_>>();
+    remote_paths.sort_by(|left, right| {
+        kind_order_for_apply(remote_entries.get(left))
+            .cmp(&kind_order_for_apply(remote_entries.get(right)))
+            .then_with(|| left.cmp(right))
+    });
+    for path in remote_paths {
+        if consumed_remote_paths.contains(&path) || conflict_paths.contains(&path) {
+            continue;
+        }
+        let Some(remote_entry) = remote_entries.get(&path) else {
+            continue;
+        };
+        let base_entry = base_entries.get(&path);
+        let local_entry = local_entries.get(&path);
+        if local_entry == Some(remote_entry) || base_entry == Some(remote_entry) {
+            continue;
+        }
+        if base_entry.is_some() && local_entry != base_entry {
+            continue;
+        }
+        if base_entry.is_none() && local_entry.is_some() {
+            conflicts.push(record_apply_conflict_with_trees(
+                store,
+                source_root,
+                &path,
+                local_root.latest_tree_hash.as_deref(),
+                local_tree_hash,
+                remote_tree_hash,
+                "remote create conflicts with an existing local path",
+                dry_run,
+            )?);
+            continue;
+        }
+        match remote_entry.kind {
+            CasTreeEntryKind::Directory => {
+                let out = safe_tree_output_path(&target, &path)?;
+                if !out.exists() {
+                    dirs_created += 1;
+                    if !dry_run {
+                        std::fs::create_dir_all(out)?;
+                    }
+                }
+            }
+            CasTreeEntryKind::File => {
+                let Some(blob) = &remote_entry.blob else {
+                    conflicts.push(record_apply_conflict_with_trees(
+                        store,
+                        source_root,
+                        &path,
+                        local_root.latest_tree_hash.as_deref(),
+                        local_tree_hash,
+                        remote_tree_hash,
+                        "remote file entry is missing a CAS blob hash",
+                        dry_run,
+                    )?);
+                    continue;
+                };
+                let out = safe_tree_output_path(&target, &path)?;
+                files_written += 1;
+                if !dry_run {
+                    let bytes = cas.read_bytes(blob)?;
+                    write_file_atomic(&out, &bytes)?;
+                    set_executable_bit(&out, remote_entry.executable)?;
+                }
+            }
+        }
+    }
+
+    let mut deleted_paths = base_entries
+        .keys()
+        .filter(|path| {
+            !remote_entries.contains_key(*path)
+                && !consumed_base_paths.contains(*path)
+                && !conflict_paths.contains(*path)
+        })
+        .cloned()
+        .collect::<Vec<_>>();
+    deleted_paths.sort_by(|left, right| right.cmp(left));
+    for path in deleted_paths {
+        let Some(base_entry) = base_entries.get(&path) else {
+            continue;
+        };
+        if local_entries.get(&path) != Some(base_entry) {
+            continue;
+        }
+        let out = safe_tree_output_path(&target, &path)?;
+        if dry_run || !out.exists() {
+            continue;
+        }
+        match base_entry.kind {
+            CasTreeEntryKind::Directory => {
+                let _ = std::fs::remove_dir(&out);
+            }
+            CasTreeEntryKind::File => {
+                std::fs::remove_file(&out)?;
+            }
+        }
+    }
+
+    Ok(ControlResponse::CasRootApplied {
+        source: source_root.name.clone(),
+        target,
+        files_written,
+        dirs_created,
+        conflicts,
+        dry_run,
+        note: "three-way file-root apply updated only paths where local state still matched the recorded base; ambiguous edits remain durable conflicts".to_owned(),
+    })
+}
+
+#[allow(clippy::too_many_arguments)]
+fn record_three_way_apply_conflicts(
+    store: &Store,
+    source_root: &StoredFileRoot,
+    local_root: &StoredFileRoot,
+    base_tree: &CasTreeObject,
+    local_tree_hash: Option<&BlobHash>,
+    remote_tree_hash: &BlobHash,
+    remote_tree: &CasTreeObject,
+    local_tree: &CasTreeObject,
+    dry_run: bool,
+) -> Result<Vec<FileConflict>, NodeError> {
+    geth_cas::detect_tree_conflicts(base_tree, local_tree, remote_tree)
+        .into_iter()
+        .map(|conflict| {
+            record_apply_conflict_with_trees(
+                store,
+                source_root,
+                &conflict.path,
+                local_root.latest_tree_hash.as_deref(),
+                local_tree_hash,
+                remote_tree_hash,
+                &conflict.detail,
+                dry_run,
+            )
+        })
+        .collect()
+}
+
+fn owned_tree_entry_map(tree: &CasTreeObject) -> BTreeMap<String, geth_cas::CasTreeEntry> {
+    tree.entries
+        .iter()
+        .map(|entry| (entry.path.clone(), entry.clone()))
+        .collect()
+}
+
+fn remote_rename_pairs(
+    base_entries: &BTreeMap<String, geth_cas::CasTreeEntry>,
+    remote_entries: &BTreeMap<String, geth_cas::CasTreeEntry>,
+) -> Vec<(String, String)> {
+    let mut pairs = Vec::new();
+    for (base_path, base_entry) in base_entries {
+        let Some(base_blob) = &base_entry.blob else {
+            continue;
+        };
+        if remote_entries.contains_key(base_path) {
+            continue;
+        }
+        if let Some((remote_path, _)) = remote_entries.iter().find(|(remote_path, remote_entry)| {
+            !base_entries.contains_key(*remote_path)
+                && remote_entry.blob.as_ref() == Some(base_blob)
+        }) {
+            pairs.push((base_path.clone(), remote_path.clone()));
+        }
+    }
+    pairs.sort();
+    pairs
+}
+
+fn path_matches_entry(
+    cas: &LocalCas,
+    path: &Path,
+    entry: &geth_cas::CasTreeEntry,
+) -> Result<bool, NodeError> {
+    match entry.kind {
+        CasTreeEntryKind::Directory => Ok(path.is_dir()),
+        CasTreeEntryKind::File => {
+            let Some(blob) = &entry.blob else {
+                return Ok(false);
+            };
+            Ok(path.is_file() && hash_path(path)? == *blob && cas.has(blob)?)
+        }
+    }
+}
+
+fn kind_order_for_apply(entry: Option<&geth_cas::CasTreeEntry>) -> u8 {
+    match entry.map(|entry| &entry.kind) {
+        Some(CasTreeEntryKind::Directory) => 0,
+        Some(CasTreeEntryKind::File) => 1,
+        None => 2,
+    }
+}
+
 fn safe_tree_output_path(root: &Path, relative: &str) -> Result<PathBuf, NodeError> {
     let relative_path = Path::new(relative);
     if relative_path.is_absolute() {
@@ -8052,6 +8409,45 @@ fn record_apply_conflict(
     file_conflict_from_stored(stored)
 }
 
+#[allow(clippy::too_many_arguments)]
+fn record_apply_conflict_with_trees(
+    store: &Store,
+    root: &StoredFileRoot,
+    path: &str,
+    base_tree: Option<&str>,
+    local_tree: Option<&BlobHash>,
+    remote_tree: &BlobHash,
+    detail: &str,
+    dry_run: bool,
+) -> Result<FileConflict, NodeError> {
+    let created_at = geth_store::now_ms();
+    let stored = StoredFileConflict {
+        conflict_id: generated_file_conflict_id(
+            &root.name,
+            path,
+            FileConflictKind::ConcurrentEdit.as_str(),
+            created_at,
+        ),
+        root_name: root.name.clone(),
+        resource_id: root.resource_id.clone(),
+        path: path.to_owned(),
+        kind: FileConflictKind::ConcurrentEdit.as_str().to_owned(),
+        status: FileConflictStatus::Open.as_str().to_owned(),
+        base_tree_hash: base_tree.map(ToOwned::to_owned),
+        local_tree_hash: local_tree.map(ToString::to_string),
+        remote_tree_hash: Some(remote_tree.to_string()),
+        detail: detail.to_owned(),
+        resolution: None,
+        resolution_note: None,
+        created_at_ms: created_at,
+        resolved_at_ms: None,
+    };
+    if !dry_run {
+        store.upsert_file_conflict(&stored)?;
+    }
+    file_conflict_from_stored(stored)
+}
+
 fn record_sync_tree_conflicts(
     store: &Store,
     local_root: &StoredFileRoot,

crates/geth/tests/bootstrap.rs

@@ -1651,6 +1651,174 @@ fn cas_file_root_apply_writes_missing_files_and_records_conflicts() {
     }
 }
 
+#[test]
+fn cas_file_root_apply_three_way_updates_deletes_and_renames_safe_changes() {
+    let home = tempfile::tempdir().expect("tempdir");
+    let paths = geth_config::GethPaths::from_home(home.path());
+    let node = geth_node::init_node(&paths).expect("init node");
+    let target_path = home.path().join("target-root");
+    std::fs::create_dir_all(&target_path).expect("create target root");
+    std::fs::write(target_path.join("update.txt"), b"base").expect("write base update");
+    std::fs::write(target_path.join("delete.txt"), b"base delete").expect("write base delete");
+    std::fs::write(target_path.join("rename.txt"), b"base rename").expect("write base rename");
+
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootAdd {
+            name: "shared".to_owned(),
+            path: target_path.clone(),
+        },
+    )
+    .expect("add local root");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootScan {
+            name: "shared".to_owned(),
+        },
+    )
+    .expect("scan local base");
+
+    let source_path = home.path().join("source-root");
+    std::fs::create_dir_all(&source_path).expect("create source root");
+    std::fs::write(source_path.join("update.txt"), b"remote").expect("write remote update");
+    std::fs::write(source_path.join("rename-new.txt"), b"base rename")
+        .expect("write remote rename");
+    std::fs::write(source_path.join("created.txt"), b"created").expect("write remote create");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootAdd {
+            name: "remote-node-peer-shared".to_owned(),
+            path: source_path,
+        },
+    )
+    .expect("add remote root");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootScan {
+            name: "remote-node-peer-shared".to_owned(),
+        },
+    )
+    .expect("scan remote root");
+
+    let response = geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootApply {
+            source: "remote-node-peer-shared".to_owned(),
+            target: target_path.clone(),
+            dry_run: false,
+        },
+    )
+    .expect("three-way apply");
+    match response {
+        geth_control::ControlResponse::CasRootApplied {
+            files_written,
+            conflicts,
+            note,
+            ..
+        } => {
+            assert_eq!(files_written, 2);
+            assert!(conflicts.is_empty());
+            assert!(note.contains("three-way"));
+        }
+        other => panic!("unexpected response: {other:?}"),
+    }
+
+    assert_eq!(
+        std::fs::read(target_path.join("update.txt")).expect("read updated"),
+        b"remote"
+    );
+    assert!(
+        !target_path.join("delete.txt").exists(),
+        "safe remote delete should remove unchanged local base file"
+    );
+    assert!(
+        !target_path.join("rename.txt").exists(),
+        "safe remote rename should remove old path"
+    );
+    assert_eq!(
+        std::fs::read(target_path.join("rename-new.txt")).expect("read renamed"),
+        b"base rename"
+    );
+    assert_eq!(
+        std::fs::read(target_path.join("created.txt")).expect("read created"),
+        b"created"
+    );
+}
+
+#[test]
+fn cas_file_root_apply_three_way_keeps_ambiguous_changes_as_conflicts() {
+    let home = tempfile::tempdir().expect("tempdir");
+    let paths = geth_config::GethPaths::from_home(home.path());
+    let node = geth_node::init_node(&paths).expect("init node");
+    let target_path = home.path().join("target-root");
+    std::fs::create_dir_all(&target_path).expect("create target root");
+    std::fs::write(target_path.join("note.txt"), b"base").expect("write base");
+
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootAdd {
+            name: "shared".to_owned(),
+            path: target_path.clone(),
+        },
+    )
+    .expect("add local root");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootScan {
+            name: "shared".to_owned(),
+        },
+    )
+    .expect("scan local base");
+    std::fs::write(target_path.join("note.txt"), b"local edit").expect("write local edit");
+
+    let source_path = home.path().join("source-root");
+    std::fs::create_dir_all(&source_path).expect("create source root");
+    std::fs::write(source_path.join("note.txt"), b"remote edit").expect("write remote edit");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootAdd {
+            name: "remote-node-peer-shared".to_owned(),
+            path: source_path,
+        },
+    )
+    .expect("add remote root");
+    geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootScan {
+            name: "remote-node-peer-shared".to_owned(),
+        },
+    )
+    .expect("scan remote root");
+
+    let response = geth_node::handle_request(
+        &node,
+        geth_control::ControlRequest::CasRootApply {
+            source: "remote-node-peer-shared".to_owned(),
+            target: target_path.clone(),
+            dry_run: false,
+        },
+    )
+    .expect("three-way conflict apply");
+    match response {
+        geth_control::ControlResponse::CasRootApplied { conflicts, .. } => {
+            assert_eq!(conflicts.len(), 1);
+            assert_eq!(conflicts[0].path, "note.txt");
+            assert_eq!(
+                conflicts[0].kind,
+                geth_cas::FileConflictKind::ConcurrentEdit
+            );
+            assert!(conflicts[0].base_tree.is_some());
+            assert!(conflicts[0].local_tree.is_some());
+            assert!(conflicts[0].remote_tree.is_some());
+        }
+        other => panic!("unexpected response: {other:?}"),
+    }
+    assert_eq!(
+        std::fs::read(target_path.join("note.txt")).expect("read local after conflict"),
+        b"local edit"
+    );
+}
+
 #[test]
 fn cas_file_conflict_record_list_and_resolve() {
     let home = tempfile::tempdir().expect("tempdir");

docs/architecture.md

@@ -161,12 +161,15 @@ watermarks. Repeated remote file-root syncs retain the previous imported remote
 tree as the base and compare base/local/remote tree state. When both local and
 remote roots changed, geth records durable concurrent edit, delete/edit, or
 divergent rename conflicts instead of applying remote content. `geth cas root
-apply <root> --to <path>` is the first conservative
-materialization path: it creates missing files and directories from the CAS tree,
-does not delete extra local files, does not overwrite differing local files, and
-records conflicts for manual resolution. The daemon also has durable local
-file-conflict records with explicit resolution choices; richer three-way apply
-will extend those records instead of silently applying ambiguous remote changes.
+apply <root> --to <path>` is conservative when the target has no registered
+base: it creates missing files and directories from the CAS tree, does not
+delete extra local files, does not overwrite differing local files, and records
+conflicts for manual resolution. When the target path matches a registered
+local root with a previous scan, apply uses that scan as the base for a
+three-way base/local/remote check. It can safely accept remote creates, updates,
+deletes, and renames only when the current local filesystem still matches the
+base; ambiguous paths remain durable conflicts. The daemon also has durable
+local file-conflict records with explicit resolution choices.
 
 As a bootstrap network path, `geth cas fetch <node-id> <hash>` dials an
 imported signed peer card over the daemon-owned Iroh control ALPN. The serving
@@ -176,7 +179,7 @@ before returning blob bytes. The requester verifies that the returned bytes hash
 to the requested BLAKE3 CAS hash before storing them. Successful fetches update
 durable local provider metadata keyed by CAS hash and peer node, which can be
 inspected through `geth cas providers <hash>`. Iroh-blobs provider/fetch
-integration and richer three-way file application are future work.
+integration is future work.
 
 `geth-db` currently registers local SQLite paths as DB resources and reports
 local-only sync status plus a read-only SQLite schema summary/hash. It also

docs/roadmap.md

@@ -40,12 +40,12 @@ Implementation order:
    - `[x]` `geth status` reports the current bootstrap backend, target crate,
      target version, and blocker for CAS, KV, and pubsub.
 
-3. `[ ]` Polish file sync reconciliation.
+3. `[x]` Polish file sync reconciliation.
    Acceptance criteria:
-   - `[ ]` Add a safe three-way apply path for non-conflicting
+   - `[x]` Add a safe three-way apply path for non-conflicting
      create/update/delete/rename changes.
-   - `[ ]` Keep ambiguous changes as durable conflicts.
-   - `[ ]` Add two-root integration coverage.
+   - `[x]` Keep ambiguous changes as durable conflicts.
+   - `[x]` Add two-root integration coverage.
 
 4. `[ ]` Replace JSON document state with durable Automerge documents.
    Acceptance criteria:
@@ -108,11 +108,11 @@ Implementation order:
 
 - `[~]` File sync reconciliation polish.
   Acceptance criteria:
-  - `[ ]` `cas root apply` has a richer three-way base/local/remote reconcile
+  - `[x]` `cas root apply` has a richer three-way base/local/remote reconcile
     path for safe updates and deletes.
-  - `[ ]` Ambiguous changes continue to produce durable conflicts instead of
+  - `[x]` Ambiguous changes continue to produce durable conflicts instead of
     overwriting local files.
-  - `[ ]` Tests cover create/update/delete/rename application across two local
+  - `[x]` Tests cover create/update/delete/rename application across two local
     roots.
 
 - `[~]` Durable Automerge documents.
@@ -717,8 +717,12 @@ and future group key evolution.
     and directories from a CAS tree without deleting extras or overwriting local
     edits.
   - `[x]` Apply records durable conflicts for differing local paths.
-  - `[ ]` Future completion adds a richer three-way apply using base/local/remote
-    trees for automatic safe updates and deletes.
+  - `[x]` `geth cas root apply <root> --to <path>` uses a registered local
+    root's previous scan as the base for automatic safe creates, updates,
+    deletes, and renames when the current local filesystem still matches that
+    base.
+  - `[x]` Ambiguous three-way changes remain durable conflicts instead of being
+    overwritten.
 
 - `[x]` Conflict handling.
   Acceptance criteria: