fix(wf10): fixing more of the add/add problems

Closes #10861

robot/e2e/wf10_batch.robot

@@ -93,10 +93,18 @@ Write Action Config
     RETURN    ${yaml_path}
 
 Clean Workspace Template Files
-    [Documentation]    Remove template files from the workspace that the LLM
-    ...                may regenerate during formatting, to prevent add/add
-    ...                merge conflicts during plan apply.
+    [Documentation]    Remove template files from the workspace and monorepo
+    ...                that the LLM may regenerate during formatting, to prevent
+    ...                add/add merge conflicts during plan apply.
+    ...
+    ...                CleverAgents copies workspace template files into project
+    ...                directories during ``project create``, so this keyword
+    ...                must run **after** project registration and **before**
+    ...                plan launch.  It also runs ``git clean -fd`` in the
+    ...                monorepo to remove any untracked files that were copied.
+    [Arguments]    ${target_dir}=${SUITE_HOME}
     @{conflicting}=    Create List
+    ...    .flake8
     ...    .pre-commit-config.yaml
     ...    pyproject.toml
     ...    requirements-dev.txt
@@ -105,9 +113,13 @@ Clean Workspace Template Files
     ...    setup.cfg
     ...    tox.ini
     FOR    ${file}    IN    @{conflicting}
-        ${path}=    Set Variable    ${SUITE_HOME}${/}${file}
+        ${path}=    Set Variable    ${target_dir}${/}${file}
         Run Keyword And Ignore Error    Remove File    ${path}
     END
+    # Also run git clean to remove any untracked files/directories that
+    # the workspace template may have deposited in the monorepo.
+    ${git_clean}=    Run Process    git    clean    -fd    cwd=${target_dir}    timeout=60s    on_timeout=kill
+    Log    git clean in ${target_dir}: rc=${git_clean.rc}    level=DEBUG
 
 Write Broken Action Config
     [Documentation]    Write a deliberately broken action YAML that uses a non-existent
@@ -301,6 +313,10 @@ Workflow 10 Full-Auto Batch Formatting
     # --- Step 3: Register resources and projects for all packages ---
     Register Package Resources And Projects    ${monorepo}    ${branch}    @{PACKAGE_NAMES}
 
+    # Clean workspace template files that were copied into the monorepo
+    # during project creation, to prevent add/add merge conflicts during apply.
+    Clean Workspace Template Files    ${monorepo}
+
     # --- Step 4: Create plans — healthy + broken ---
     # 4a: Launch plans for healthy packages with the good action
     @{plan_ids}=    Launch Batch Plans    @{PACKAGE_NAMES}