monoco-toolkit 0.3.11__py3-none-any.whl → 0.3.12__py3-none-any.whl

monoco/features/issue/core.py

@@ -46,6 +46,30 @@ def get_issue_dir(issue_type: str, issues_root: Path) -> Path:
     return issues_root / folder
 
 
+def _parse_isolation_ref(ref: str) -> str:
+    """
+    Parse isolation ref and strip any 'branch:' or 'worktree:' prefix.
+    
+    The isolation.ref field may contain prefixes like 'branch:feat/xxx' or 'worktree:xxx'
+    for display/logging purposes, but git commands need the raw branch name.
+    
+    Args:
+        ref: The isolation ref string, may contain prefix
+        
+    Returns:
+        The clean branch name without prefix
+    """
+    if not ref:
+        return ref
+    
+    # Strip known prefixes
+    for prefix in ("branch:", "worktree:"):
+        if ref.startswith(prefix):
+            return ref[len(prefix):]
+    
+    return ref
+
+
 def _get_slug(title: str) -> str:
     slug = title.lower()
     # Replace non-word characters (including punctuation, spaces) with hyphens
@@ -466,6 +490,227 @@ def find_issue_path(issues_root: Path, issue_id: str, include_archived: bool = T
     return None
 
 
+def find_issue_path_across_branches(
+    issues_root: Path, 
+    issue_id: str, 
+    project_root: Optional[Path] = None,
+    include_archived: bool = True
+) -> Tuple[Optional[Path], Optional[str]]:
+    """
+    Find issue path across all local git branches.
+    
+    Implements the "Golden Path" logic:
+    - If issue found in exactly one branch -> return it silently
+    - If issue found in multiple branches -> raise error (conflict)
+    - If issue not found in any branch -> return None
+    
+    Args:
+        issues_root: Root directory of issues
+        issue_id: Issue ID to find
+        project_root: Project root (defaults to issues_root.parent)
+        include_archived: Whether to search in archived directory
+        
+    Returns:
+        Tuple of (file_path, branch_name) or (None, None) if not found
+        
+    Raises:
+        RuntimeError: If issue found in multiple branches (conflict)
+    """
+    # First, try to find in current working tree
+    local_path = find_issue_path(issues_root, issue_id, include_archived)
+    
+    # Determine project root
+    if project_root is None:
+        project_root = issues_root.parent
+    
+    # If not a git repo, just return local result
+    if not git.is_git_repo(project_root):
+        return (local_path, None) if local_path else (None, None)
+    
+    # Get current branch
+    current_branch = git.get_current_branch(project_root)
+    
+    # Search in all branches to detect conflicts (FIX-0006)
+    # If found locally, we still check other branches to detect potential duplicate files (conflict)
+    if local_path:
+        # Get relative path for git checking
+        try:
+            rel_path = local_path.relative_to(project_root)
+        except ValueError:
+            # If path is outside project root, we can't search other branches anyway
+            return local_path, current_branch
+            
+        conflicting_branches = _find_branches_with_file(project_root, str(rel_path), current_branch)
+        
+        # SPECIAL CASE (FIX-0006): During 'issue close' or similar operations,
+        # it is expected that the file exists in the feature branch (isolation branch)
+        # and now in the target branch (e.g. main). This is NOT a conflict.
+        if conflicting_branches:
+            # Try to parse metadata to see if these "conflicts" are actually the isolation branch
+            try:
+                meta = parse_issue(local_path)
+                if meta and meta.isolation:
+                    iso_type = getattr(meta.isolation, "type", None)
+                    iso_ref = getattr(meta.isolation, "ref", None)
+                    
+                    source_branch = None
+                    if iso_type == "branch":
+                        source_branch = iso_ref
+                    elif iso_ref and iso_ref.startswith("branch:"):
+                        source_branch = iso_ref[7:]
+                    
+                    if source_branch:
+                        # Filter out the source branch from conflicts
+                        conflicting_branches = [b for b in conflicting_branches if b != source_branch]
+            except Exception:
+                # If parsing fails, stick with raw conflicts to be safe
+                pass
+
+        if conflicting_branches:
+             raise RuntimeError(
+                f"Issue {issue_id} found in multiple branches: {current_branch}, {', '.join(conflicting_branches)}. "
+                f"Please resolve the conflict by merging branches or deleting duplicate issue files."
+            )
+        return local_path, current_branch
+        
+    # Not found locally, search in all branches
+    return _search_issue_in_branches(issues_root, issue_id, project_root, include_archived)
+
+
+def _find_branches_with_file(project_root: Path, rel_path: str, exclude_branch: str) -> List[str]:
+    """
+    Find all branches (except excluded) that contain the given file path.
+    
+    Args:
+        project_root: Project root path
+        rel_path: Relative path from project root
+        exclude_branch: Branch to exclude from search
+        
+    Returns:
+        List of branch names containing the file
+    """
+    branches_with_file = []
+    
+    # Get all local branches
+    code, stdout, _ = git._run_git(["branch", "--format=%(refname:short)"], project_root)
+    if code != 0:
+        return []
+    
+    all_branches = [b.strip() for b in stdout.splitlines() if b.strip()]
+    
+    for branch in all_branches:
+        if branch == exclude_branch:
+            continue
+            
+        # Check if file exists in this branch
+        code, _, _ = git._run_git(["show", f"{branch}:{rel_path}"], project_root)
+        if code == 0:
+            branches_with_file.append(branch)
+    
+    return branches_with_file
+
+
+def _search_issue_in_branches(
+    issues_root: Path,
+    issue_id: str,
+    project_root: Path,
+    include_archived: bool = True
+) -> Tuple[Optional[Path], Optional[str]]:
+    """
+    Search for an issue file across all branches.
+    
+    Returns:
+        Tuple of (file_path, branch_name) or (None, None)
+        
+    Raises:
+        RuntimeError: If issue found in multiple branches
+    """
+    parsed = IssueID(issue_id)
+    
+    if not parsed.is_local:
+        # For workspace issues, just use standard find
+        path = find_issue_path(issues_root, issue_id, include_archived)
+        return (path, None) if path else (None, None)
+    
+    # Get issue type from prefix
+    try:
+        prefix = parsed.local_id.split("-")[0].upper()
+    except IndexError:
+        return None, None
+    
+    reverse_prefix_map = get_reverse_prefix_map(issues_root)
+    issue_type = reverse_prefix_map.get(prefix)
+    if not issue_type:
+        return None, None
+    
+    # Build possible paths to search
+    base_dir = get_issue_dir(issue_type, issues_root)
+    rel_base = base_dir.relative_to(project_root)
+    
+    status_dirs = ["open", "backlog", "closed"]
+    if include_archived:
+        status_dirs.append("archived")
+    
+    # Search pattern: Issues/{Type}/{status}/{issue_id}-*.md
+    found_in_branches: List[Tuple[str, str]] = []  # (branch, file_path)
+    
+    # Get all local branches
+    code, stdout, _ = git._run_git(["branch", "--format=%(refname:short)"], project_root)
+    if code != 0:
+        return None, None
+    
+    all_branches = [b.strip() for b in stdout.splitlines() if b.strip()]
+    
+    for branch in all_branches:
+        # List files in each status directory for this branch
+        for status_dir in status_dirs:
+            dir_path = f"{rel_base}/{status_dir}"
+            
+            # List all files in this directory on the branch
+            code, stdout, _ = git._run_git(
+                ["ls-tree", "-r", "--name-only", branch, dir_path], 
+                project_root
+            )
+            
+            if code != 0 or not stdout.strip():
+                continue
+            
+            # Find matching issue file (Handling quoted paths from git ls-tree)
+            pattern = f"{parsed.local_id}-"
+            for line in stdout.splitlines():
+                line = line.strip()
+                # Git quotes non-ASCII paths: "Issues/Chores/...md"
+                if line.startswith('"') and line.endswith('"'):
+                    line = line[1:-1]
+                
+                if pattern in line and line.endswith(".md"):
+                    found_in_branches.append((branch, line))
+    
+    if not found_in_branches:
+        return None, None
+    
+    if len(found_in_branches) > 1:
+        # Found in multiple branches - conflict
+        branches = [b for b, _ in found_in_branches]
+        raise RuntimeError(
+            f"Issue {issue_id} found in multiple branches: {', '.join(branches)}. "
+            f"Please resolve the conflict by merging branches or deleting duplicate issue files."
+        )
+    
+    # Golden path: exactly one match
+    branch, file_path = found_in_branches[0]
+    
+    # Checkout the file to working tree
+    try:
+        git.git_checkout_files(project_root, branch, [file_path])
+        full_path = project_root / file_path
+        return full_path, branch
+    except Exception:
+        # If checkout fails, return the path anyway - caller can handle
+        full_path = project_root / file_path
+        return full_path, branch
+
+
 def update_issue(
     issues_root: Path,
     issue_id: str,
@@ -899,7 +1144,7 @@ def prune_issue_resources(
         return []
 
     if issue.isolation.type == IsolationType.BRANCH:
-        branch = issue.isolation.ref
+        branch = _parse_isolation_ref(issue.isolation.ref)
         current = git.get_current_branch(project_root)
         if current == branch:
             raise RuntimeError(
@@ -925,7 +1170,7 @@ def prune_issue_resources(
             # Also delete the branch associated?
             # Worktree create makes a branch. When removing worktree, branch remains.
             # Usually we want to remove the branch too if it was created for this issue.
-            branch = issue.isolation.ref
+            branch = _parse_isolation_ref(issue.isolation.ref)
             if branch and git.branch_exists(project_root, branch):
                 # We can't delete branch if it is checked out in the worktree we just removed?
                 # git worktree remove unlocks the branch.
@@ -983,7 +1228,7 @@ def sync_issue_files(issues_root: Path, issue_id: str, project_root: Path) -> Li
     target_ref = None
 
     if issue.isolation and issue.isolation.ref:
-        target_ref = issue.isolation.ref
+        target_ref = _parse_isolation_ref(issue.isolation.ref)
         if target_ref == "current":
              target_ref = git.get_current_branch(project_root)
     else:
@@ -1061,7 +1306,7 @@ def merge_issue_changes(
     # If not there, we try heuristic.
     source_ref = None
     if issue.isolation and issue.isolation.ref:
-        source_ref = issue.isolation.ref
+        source_ref = _parse_isolation_ref(issue.isolation.ref)
     else:
         # Heuristic: Search for branch by convention
         # We can't use 'current' here safely if we are on main,

monoco/features/spike/commands.py

@@ -81,13 +81,15 @@ def remove_repo(
     target_path = spikes_dir / name
     deleted = False
     if target_path.exists():
-        if force or typer.confirm(
-            f"Do you want to delete the directory {target_path}?", default=False
-        ):
+        if force:
             core.remove_repo_dir(spikes_dir, name)
             deleted = True
         else:
             deleted = False
+            if not OutputManager.is_agent_mode():
+                from rich.console import Console
+                console = Console()
+                console.print(f"[yellow]Skipping physical deletion of {target_path}. Use --force to delete.[/yellow]")
 
     OutputManager.print(
         {"status": "removed", "name": name, "directory_deleted": deleted}

{monoco_toolkit-0.3.11.dist-info → monoco_toolkit-0.3.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monoco-toolkit
-Version: 0.3.11
+Version: 0.3.12
 Summary: Agent Native Toolkit for Monoco - Task Management & Kanban for AI Agents
 Project-URL: Homepage, https://monoco.io
 Project-URL: Repository, https://github.com/IndenScale/Monoco

{monoco_toolkit-0.3.11.dist-info → monoco_toolkit-0.3.12.dist-info}/RECORD

@@ -4,10 +4,10 @@ monoco/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 monoco/cli/project.py,sha256=FqLaDD3hiWxa0_TKzxEF7PYH9RPsvmLyjO3NYVckgGs,2737
 monoco/cli/workspace.py,sha256=vcUHjSarRZk8k3SNjtLSVD2VUPhBIUyx5J1OPtGa7-Q,1541
 monoco/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-monoco/core/config.py,sha256=tmbfQd64CCOHfFTFf2zrUvCd9jvk25X6-UaksTkpaIY,16872
+monoco/core/config.py,sha256=lY0A4iUqwmzSwNAbYjKZ1O6cTw4GKBJXpP1lmQDo9VI,16850
 monoco/core/execution.py,sha256=7522s7uVWiNdMKtWlIb8JHzbAcJgLVuxUFp_6VmhWNQ,1801
 monoco/core/feature.py,sha256=bcK0C1CaQgNLcdMF0RuniaaQRCYSA-0JdOpQz9W_1xM,1968
-monoco/core/git.py,sha256=C0wq8z9XOVmIOW2K583rPPsHRB6eHT0TRH1qLSzqOyo,9170
+monoco/core/git.py,sha256=yKrkF8i9RPHlidu6lgTDnao9C99uHJyO0Xo2ADaLWqg,9696
 monoco/core/githooks.py,sha256=QY4c74LIYDtcjtWYax1PrK5CtVNKYTfVVVBOj-SCulo,1826
 monoco/core/injection.py,sha256=BCMbppPqBH_1XVT7is0UgemstSDnb98E1Df1sdE6JKY,8391
 monoco/core/integrations.py,sha256=V_PgRfJt1X9rAuq0EkILaJufqbwqilyBQmH2-RV4D3U,7917
@@ -26,9 +26,18 @@ monoco/core/workspace.py,sha256=H_PHD5A0HZFq841u1JtLoFjkXdQg9D6x6I7QcFtJge4,3000
 monoco/core/artifacts/__init__.py,sha256=emmW_RHKZbJ4ED-oPx6Eoci34f4NKCXTuBohQmQ5gcU,406
 monoco/core/artifacts/manager.py,sha256=WinaVMrXWVm56CRYtSEz6O2JWZZ1A7xWiEnR8O7ppHc,19543
 monoco/core/artifacts/models.py,sha256=fk_iS3kkUFEwf7O8YKO2sVVHaNS8JaGQRoHsJceSBLw,5241
+monoco/core/automation/__init__.py,sha256=Ou1lxTkhl6FR4fCB5AEZRpOe3TN7pZz4jkXIlfCkMw8,1218
+monoco/core/automation/config.py,sha256=nRlUhZGj9901ELdgJtDH8i8SfJFDvSuAXdXpaLHSp5g,10777
+monoco/core/automation/field_watcher.py,sha256=HCy8w9VXiA-UQZzBULet3d52z4APIEqGhICO26WOvk0,9459
+monoco/core/automation/handlers.py,sha256=hroCeKN1kpyKdTXU7KOCttGCIMxmWfyPIUmG_pRa2p8,24226
+monoco/core/executor/__init__.py,sha256=5Yp3iwxHzf8_ttYQejgv6-jTDqAKH2qORUlBN3ib7LU,1140
+monoco/core/executor/agent_action.py,sha256=yjlooGZ5NiLdnzO11huLXD_qPOMiS-YlTqaqb3sHft8,8360
+monoco/core/executor/git_action.py,sha256=DEGcdgaTnzkKBNb8DaIrNQCzbyRVMYLhoXamyFZigkc,9558
+monoco/core/executor/im_action.py,sha256=Zk6PDlKwhUMe7jsI0IpldGI6uuy2oPq_AucqaYFQo78,10185
+monoco/core/executor/pytest_action.py,sha256=IirSUus_fsqGcHeVnIxZ9ECFLItLiVoDdYh6po34KWU,6676
 monoco/core/hooks/__init__.py,sha256=8dWjDSwJG9JdghWBxgk7zH1U1FlJCiRo66mfbWcDK3M,437
 monoco/core/hooks/base.py,sha256=GQ59E_VX8RmtWezyg5sMFqmKRDsD7PJflcAb2TTy8S8,3276
-monoco/core/hooks/context.py,sha256=A0xwwU6JcsBH3t4h9jlodAdEMuajU8QeW_3bSMTWfPY,4005
+monoco/core/hooks/context.py,sha256=i6G4zjiDdvPlRzJTDQgV56Mo14zQGKDL5Cibv_3p3vE,6011
 monoco/core/hooks/registry.py,sha256=O_IO1c7R9NbHk3F-xtLowQQkzPBs6qM1Xii398ZfbNU,7100
 monoco/core/hooks/builtin/__init__.py,sha256=R_e04bOLnBKy7pX5QVBkDjgUNeQ82o1IHq--CKgIX_I,177
 monoco/core/hooks/builtin/git_cleanup.py,sha256=crtUv2RJoeo1qOAgLulr6Q0_M-oFTLDNq3Uku1pl3QU,9701
@@ -41,29 +50,41 @@ monoco/core/resource/__init__.py,sha256=CZvZHdtyfgrAehCjoAUuVAJ-XGaLqN7DcGE2SEKH
 monoco/core/resource/finder.py,sha256=izX-jTw0juajXbcAuk7MtCXD7Os0pzLXBgTxL-nxwe0,4329
 monoco/core/resource/manager.py,sha256=ZRDyvZFvcFPhD9jzmE3jYbZHCIRkheqcR6INxTke6_Y,3484
 monoco/core/resource/models.py,sha256=mJffVMZ8PpWety-yHhierfmgPst_e1mRqgLWfrUrk4g,934
+monoco/core/router/__init__.py,sha256=5jZ76GBR3dKTkbLhpwUeQwGqh1naSl9QamEgYKVrYcU,1289
+monoco/core/router/action.py,sha256=QcsfQ1WV01OOclVGj7hDO5olknPaG85Yawtg-50vmZ0,10192
+monoco/core/router/router.py,sha256=qNHak6cEKgbddgJH62uEx-zVNuUhDWqVXocgPlQHsgs,12756
+monoco/core/scheduler/__init__.py,sha256=J7qv72y0FK4HFXAS50oAO0j71FHfHp6D_1JuFXS-TA0,1533
+monoco/core/scheduler/base.py,sha256=7ywbKRK6o5OtEWKk4y3Q4-SI85ZMyVId4JsCJ0ohWGQ,4265
+monoco/core/scheduler/engines.py,sha256=d4D50kN-n31eiCpUdNfTAFfwI2SIT0YaZ6xg_s0YJfQ,4643
+monoco/core/scheduler/events.py,sha256=XpN93gXp_u4J7ayr4ubOur6Z-RG4ajkRtWoVX7PAB0U,5694
+monoco/core/scheduler/local.py,sha256=fjAKGOm0MawJFfBuCsl_oAUbpbR0idIOWf56Pee-Gk0,12633
+monoco/core/watcher/__init__.py,sha256=L2i39bMZmCTNWcSHFCRmRNc79VBQ5Pm0MjNjR0jTUFE,1408
+monoco/core/watcher/base.py,sha256=J9jZsIGB6lmctdT2UQ5XTfaPAVSaHZ2AmR9M-No4Ab8,11837
+monoco/core/watcher/dropzone.py,sha256=CGI21wozuxA7-b_qj_PpiYwXgkH-UXPSjClZcxrURmo,4903
+monoco/core/watcher/issue.py,sha256=eAKSznb-ihU4Ij6X6QU2uLhPUcHfr3E6C4CjZarMXaU,10229
+monoco/core/watcher/memo.py,sha256=HDZ3wJpMsLW5p5MWm3HQmFQKFsG7kGHoyMmHdAtDcf0,6405
+monoco/core/watcher/task.py,sha256=0bwPfZn7WSbjqhPQshEdRjIMc7UuBkMN6Vku-n5jea8,7254
 monoco/daemon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 monoco/daemon/app.py,sha256=SqE-IVawsZsgncCk5L4y2i5Hb2P2lBvpdmQIznVf2GY,17994
 monoco/daemon/commands.py,sha256=Af0zvS4xuJFyST8LiX9J82gkR4nRNLQERKp2biHHs-k,1490
+monoco/daemon/events.py,sha256=5TgCfHAoN8uE8LpKbJfbe5Am55Zfz1cwDlw6drcC0dY,750
 monoco/daemon/mailroom_service.py,sha256=w5hFnT1fJODAs_HZN8A8Bu65bUZic2pEyr-hYdSM14k,6811
 monoco/daemon/models.py,sha256=O4NEsjrO22yOJCYFz9LH2SR9CFS57CA1SGNbjiHlxXQ,1053
 monoco/daemon/reproduce_stats.py,sha256=LghJ8o1jTeDpA1zVPI2vF0okGU3h4esEI1thNa6shKI,1196
-monoco/daemon/scheduler.py,sha256=AQGn8nbq8Abtx4J32F7u0p5dN5928TrBtnUL6HW1gGY,10786
-monoco/daemon/services.py,sha256=prGePP9F7nGtrUTWYaypmWgT17l_sX7Wc5N5xAJsp6I,12091
+monoco/daemon/scheduler.py,sha256=mD3OstIWjGto8pZsGfJ1jsQPYHc-MgCKZbJX1_GVH7I,7219
+monoco/daemon/services.py,sha256=UGGTxg_tHeNKiwxbqN8apWqp-cx56jLypU9xj_zcJbg,4201
 monoco/daemon/stats.py,sha256=XTtuFWx68O1OA44SmN0BGVa6sswts2ExmkiavUzCYiA,4800
 monoco/daemon/triggers.py,sha256=sBsXLfvI7_d3bUPzaDit1YQBypLBFJFv3l-DEIoKpbA,1815
 monoco/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-monoco/features/agent/__init__.py,sha256=nZ8DXHy0F6jvU6jvUUfKmLXxojYuErtmjCniY832qLQ,576
+monoco/features/agent/__init__.py,sha256=CybgqfTSOuO2QUP_JXyIeY2nbxm-9-Cc5OIAX01q78o,1025
 monoco/features/agent/adapter.py,sha256=T3lS2UjR5KFWwnCurUhsvM4_Xu5sdp3MJvuRkExecTU,1476
-monoco/features/agent/apoptosis.py,sha256=d2q9RsGZXFAfTGGbOhmj9rAjy9-YswGolDs0-eknPmM,1524
-monoco/features/agent/cli.py,sha256=HorUNabexlsVipVs4iizt8z0S5hPT_z8J6lcoYrDt8Y,9670
+monoco/features/agent/cli.py,sha256=fbVwbem1Ymfw6T--Kz2ATxYGutnQECUemFDlQtnzXwc,10624
 monoco/features/agent/config.py,sha256=nBjwZsod8DI5O4MdD_N9TED87V8dxpK8m-KJAzAsc8c,3296
 monoco/features/agent/defaults.py,sha256=lw3-UIE6ZA8yR5iqczBKYtwu06pHRuuDOy4GPnmDWwU,390
-monoco/features/agent/engines.py,sha256=d4D50kN-n31eiCpUdNfTAFfwI2SIT0YaZ6xg_s0YJfQ,4643
+monoco/features/agent/engines.py,sha256=ETZ2k6dYnprjtCA4ZiSW2099emRDx-GESbtdLoAMcxA,820
 monoco/features/agent/flow_skills.py,sha256=9YQZvhebS_J2oERsGMfWd6WjDKkAWGzlJ0guIrYgsMw,9079
-monoco/features/agent/manager.py,sha256=A0r81kvTXGQlK7h9vJkG9cj56Jm3TdWODfuNYsnloso,4566
 monoco/features/agent/models.py,sha256=WP1i0slVdJxQfGmmxabKOLGU5qc75QXJFvkin-5sxw0,856
-monoco/features/agent/session.py,sha256=A1APoF5rrQAyv6LHtldpQHeN2J6n9sZC-AwS3TSbJ_4,6144
-monoco/features/agent/worker.py,sha256=wCJZQCJQ6ssQmXBb6TOttZamRRnXocjUla9r5w9wy50,5742
+monoco/features/agent/worker.py,sha256=ILX6EhA_NeV3QUbuhBo8AVli0rpMYJTWwlFAjG6M_QU,5755
 monoco/features/agent/resources/atoms/atom-code-dev.yaml,sha256=a4zbewWZ4bKNdA8tIIKdXt-s5Gd_M2_IU25qLpDkPlk,1790
 monoco/features/agent/resources/atoms/atom-issue-lifecycle.yaml,sha256=OEDzvMqTB3CtI8ci_z6I-ZapxD6XkJFhXIAPNpQdQac,2417
 monoco/features/agent/resources/atoms/atom-knowledge.yaml,sha256=hTkbUzycgtXPBGpAoVcHIi_P7WVson6zu9Kp79iU5HU,1735
@@ -115,8 +136,8 @@ monoco/features/i18n/resources/zh/AGENTS.md,sha256=lKkwLLCADRH7UDq9no4eQY2sRfJrb
 monoco/features/i18n/resources/zh/skills/monoco_atom_i18n/SKILL.md,sha256=3ajNeaaPlqWCnNDIiWiiQHTuHMzUScWqD27PE-YBVrM,1915
 monoco/features/i18n/resources/zh/skills/monoco_workflow_i18n_scan/SKILL.md,sha256=mBZbONW9aiIyXcSyj0ZdE0tNT9MhO8-ydtEkmrhCsmM,2759
 monoco/features/issue/adapter.py,sha256=puCyGKI-S5o2wcJy8fNinIqh2pCyO2auK2pATT67B8k,1769
-monoco/features/issue/commands.py,sha256=akSDFnsLRdyQH1vj8fxc57Z-CmOBKtIluHxM3zZRNMU,61148
-monoco/features/issue/core.py,sha256=qWPiUhuNvmA38Ur2dSNcK-j7zOZAXRXvv2W1PSweB3o,64612
+monoco/features/issue/commands.py,sha256=nKCU6-NQzLuACdKD_nu00ujd-15lhaYfA9YPoQ10ZmY,63540
+monoco/features/issue/core.py,sha256=4bDJpd7eF4459PjFvn84wk-Mse77Mez1CB98xuDcwCY,73602
 monoco/features/issue/criticality.py,sha256=Bw0xH0vpx8z59bL-WQjfy4a5zmjXNM0f-aWBzQ5JZCA,18931
 monoco/features/issue/domain_commands.py,sha256=eatSF_uZp4nGpVr2PIgb00MWfEBm0OnyAd4JvUJEAAA,1535
 monoco/features/issue/domain_service.py,sha256=bEs_WXOWmotgIR-lGwyWekF4nonvjsgrK1YG3pyVfwk,2564
@@ -166,7 +187,7 @@ monoco/features/memo/resources/zh/AGENTS.md,sha256=AFlzvhGxAk77np-E8XLb-tkWJCo0b
 monoco/features/memo/resources/zh/skills/monoco_atom_memo/SKILL.md,sha256=XjJw6qYd99_EQcnwE9RPHjRIsgCf8R-_FHAIEQLyBno,2174
 monoco/features/memo/resources/zh/skills/monoco_workflow_note_processing/SKILL.md,sha256=CfmGNy11n4uDeapQ2qB4e9lH-4D_TO-AyAhsrjKRf6g,4297
 monoco/features/spike/adapter.py,sha256=DqwhFuHdBCy_gpgOuMJ7faccMJKJGVdjxTDecIZPsI8,1571
-monoco/features/spike/commands.py,sha256=EuJ7trDaobIe7ae7pJ-ftpo_cO8-19R_fAZZCh2JcMg,3871
+monoco/features/spike/commands.py,sha256=r5gvqVp6oSjYq5HOA7a99_cVjjzn9GWeZ3hBaT2j7_c,4016
 monoco/features/spike/core.py,sha256=OuNWXQ-cBttP2oIF0B5iy0aEUH2MUMyGANG8ayEmjPo,4120
 monoco/features/spike/resources/en/AGENTS.md,sha256=NG3CMnlDk_0J8hnRUcueAM9lgIQr_dZ42R_31-LC48E,306
 monoco/features/spike/resources/en/skills/monoco_atom_spike/SKILL.md,sha256=JwEAEZesYbbFi1UVPPv_yCGhY-W56uTNUGmOrsn6_3I,1942
@@ -174,8 +195,8 @@ monoco/features/spike/resources/en/skills/monoco_workflow_research/SKILL.md,sha2
 monoco/features/spike/resources/zh/AGENTS.md,sha256=5RHNl7fc3RdYYTFH483ojJl_arGPKkyYziOuGgFbqqg,290
 monoco/features/spike/resources/zh/skills/monoco_atom_spike/SKILL.md,sha256=sgnRtrGsrW2jQnjYkq-PjyjtNTKSgmsuaKOCoqFWK1A,1741
 monoco/features/spike/resources/zh/skills/monoco_workflow_research/SKILL.md,sha256=qDqHHIPTMDZ_bmgiApP8hCvSPP-b1UeW40fsSAGBdEE,3344
-monoco_toolkit-0.3.11.dist-info/METADATA,sha256=hqdzXIfWZ_tTdtJHy6bmSo21NQlanv1zUOSAZDT5M1A,4909
-monoco_toolkit-0.3.11.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-monoco_toolkit-0.3.11.dist-info/entry_points.txt,sha256=iYj7FWYBdtClU15-Du1skqD0s6SFSIhJvxJ29VWp8ng,43
-monoco_toolkit-0.3.11.dist-info/licenses/LICENSE,sha256=ACAGGjV6aod4eIlVUTx1q9PZbnZGN5bBwkSs9RHj83s,1071
-monoco_toolkit-0.3.11.dist-info/RECORD,,
+monoco_toolkit-0.3.12.dist-info/METADATA,sha256=e2D_EGe8NFCKan53cAQKb8HdI8mgpXmR0JBuHbodnOY,4909
+monoco_toolkit-0.3.12.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+monoco_toolkit-0.3.12.dist-info/entry_points.txt,sha256=iYj7FWYBdtClU15-Du1skqD0s6SFSIhJvxJ29VWp8ng,43
+monoco_toolkit-0.3.12.dist-info/licenses/LICENSE,sha256=ACAGGjV6aod4eIlVUTx1q9PZbnZGN5bBwkSs9RHj83s,1071
+monoco_toolkit-0.3.12.dist-info/RECORD,,

monoco/features/agent/apoptosis.py

@@ -1,44 +0,0 @@
-from .manager import SessionManager
-from .models import RoleTemplate
-
-class ApoptosisManager:
-    """
-    Manages the controlled shutdown (Apoptosis) and investigation (Autopsy) 
-    of failed agent sessions.
-    """
-    
-    def __init__(self, session_manager: SessionManager):
-        self.session_manager = session_manager
-        
-    def trigger_apoptosis(self, session_id: str, failure_reason: str = "Unknown") -> None:
-        """
-        Trigger the apoptosis process for a given session.
-        1. Mark session as crashed.
-        2. Spin up a Coroner agent to diagnose.
-        """
-        session = self.session_manager.get_session(session_id)
-        if not session:
-            return
-            
-        # 1. Mark as crashed
-        session.model.status = "crashed"
-        
-        # 2. Start Coroner
-        self._perform_autopsy(session, failure_reason)
-        
-    def _perform_autopsy(self, victim_session, failure_reason: str):
-        coroner_role = RoleTemplate(
-            name="Coroner",
-            description="Investigates cause of death for failed agents.",
-            trigger="system.crash",
-            goal=f"Determine why the previous agent failed. Reason: {failure_reason}",
-            system_prompt="You are the Coroner. Analyze the logs.",
-            engine="gemini"
-        )
-        
-        coroner_session = self.session_manager.create_session(
-            issue_id=victim_session.model.issue_id,
-            role=coroner_role
-        )
-        
-        coroner_session.start()

monoco/features/agent/manager.py

@@ -1,127 +0,0 @@
-from typing import Dict, List, Optional
-import uuid
-from pathlib import Path
-
-from .models import RoleTemplate
-from .worker import Worker
-from .session import Session, RuntimeSession
-from monoco.core.hooks import HookRegistry, get_registry
-from monoco.core.config import find_monoco_root, MonocoConfig
-
-
-class SessionManager:
-    """
-    Manages the lifecycle of sessions.
-    Responsible for creating, tracking, and retrieving sessions.
-    """
-
-    def __init__(
-        self,
-        project_root: Optional[Path] = None,
-        hook_registry: Optional[HookRegistry] = None,
-        config: Optional[MonocoConfig] = None,
-    ):
-        # In-memory storage for now. In prod, this might be a DB or file-backed.
-        self._sessions: Dict[str, RuntimeSession] = {}
-        self.project_root = project_root or find_monoco_root()
-        self.config = config
-
-        self.sessions_dir = self.project_root / ".monoco" / "sessions"
-        self.sessions_dir.mkdir(parents=True, exist_ok=True)
-
-        # Initialize hook registry
-        self.hook_registry = hook_registry or get_registry()
-
-        # Load hooks from config if available
-        self._load_hooks_from_config()
-
-        # Load persisted sessions
-        self._load_sessions()
-
-    def _load_sessions(self):
-        """Load sessions from disk."""
-        import json
-
-        for session_file in self.sessions_dir.glob("*.json"):
-            try:
-                data = json.loads(session_file.read_text())
-                session_model = Session(**data)
-                # Rehydrate as Observer
-                runtime = RuntimeSession(
-                    session_model,
-                    worker=None,  # No worker for loaded sessions initially (Observer mode)
-                    hook_registry=self.hook_registry,
-                    project_root=self.project_root,
-                    save_callback=self._save_session,
-                )
-                self._sessions[session_model.id] = runtime
-                # Check status immediately to see if it's still running
-                runtime.refresh_status()
-            except Exception as e:
-                print(f"Failed to load session {session_file}: {e}")
-
-    def _save_session(self, session: Session):
-        """Save session to disk."""
-        file_path = self.sessions_dir / f"{session.id}.json"
-        file_path.write_text(session.model_dump_json(indent=2))
-
-    def _load_hooks_from_config(self) -> None:
-        """Load and register hooks from configuration."""
-        if self.config is None:
-            try:
-                from monoco.core.config import get_config
-
-                self.config = get_config(str(self.project_root))
-            except Exception:
-                return
-
-        # Load hooks from config
-        if self.config and hasattr(self.config, "session_hooks"):
-            hooks_config = self.config.session_hooks
-            if hooks_config:
-                self.hook_registry.load_from_config(hooks_config, self.project_root)
-
-    def create_session(self, issue_id: str, role: RoleTemplate) -> RuntimeSession:
-        session_id = str(uuid.uuid4())
-        branch_name = (
-            f"agent/{issue_id}/{session_id[:8]}"  # Simple branch naming strategy
-        )
-
-        session_model = Session(
-            id=session_id,
-            issue_id=issue_id,
-            role_name=role.name,
-            branch_name=branch_name,
-        )
-
-        # Get timeout from config
-        timeout = 900
-        if self.config and hasattr(self.config, "agent"):
-            timeout = self.config.agent.timeout_seconds
-
-        worker = Worker(role, issue_id, timeout=timeout)
-        runtime = RuntimeSession(
-            session_model,
-            worker,
-            hook_registry=self.hook_registry,
-            project_root=self.project_root,
-            save_callback=self._save_session,
-        )
-        self._sessions[session_id] = runtime
-        self._save_session(session_model)
-        return runtime
-
-    def get_session(self, session_id: str) -> Optional[RuntimeSession]:
-        return self._sessions.get(session_id)
-
-    def list_sessions(self, issue_id: Optional[str] = None) -> List[RuntimeSession]:
-        if issue_id:
-            return [s for s in self._sessions.values() if s.model.issue_id == issue_id]
-        return list(self._sessions.values())
-
-    def terminate_session(self, session_id: str):
-        session = self.get_session(session_id)
-        if session:
-            session.terminate()
-            # We keep the record for history
-            # del self._sessions[session_id]