diff --git a/TODO_process_tracking.md b/TODO_process_tracking.md
index 321897a4..0b3e3e14 100644
--- a/TODO_process_tracking.md
+++ b/TODO_process_tracking.md
@@ -578,119 +578,445 @@ class Process(ModelWithHealthStats):
 
 ---
 
-## Phase 2: Hook System Changes
+## Phase 2: Hook System Changes (Detailed)
 
-### 2.1 Update `run_hook()` to Create Process Records
+This section provides a line-by-line mapping of current code to required changes.
 
-**File:** `archivebox/hooks.py`
+### 2.1 Current Architecture Overview
 
-Current implementation creates `subprocess.Popen` directly. Refactor to:
+**Current Flow:**
+```
+ArchiveResult.run() [core/models.py:2463]
+    └── run_hook() [hooks.py:238]
+            └── subprocess.Popen() [hooks.py:381]
+                    └── writes: stdout.log, stderr.log, hook.pid, cmd.sh
+```
 
-1. Accept an optional `parent_process` parameter
-2. Create a `Process` record for the hook script
-3. Create a separate `Process` record for the binary (if hook reports one)
+**Target Flow:**
+```
+ArchiveResult.run()
+    └── run_hook(parent_process=self.process)  # Pass existing Process FK
+            └── hook_process = Process.objects.create(parent=parent_process, type=HOOK)
+            └── hook_process.launch(background=is_bg)  # Uses Process methods
+                    └── writes: stdout.log, stderr.log via Process.stdout_file/stderr_file
+                    └── Process handles PID file internally
+            └── parse JSONL for {"type": "Process"} records → create child binary Processes
+```
 
+### 2.2 Changes to `hooks.py`
+
+#### 2.2.1 Update `run_hook()` Signature and Body
+
+**File:** `archivebox/hooks.py` lines 238-483
+
+**CURRENT CODE (lines 374-398):**
+```python
+# Set up output files for ALL hooks (useful for debugging)
+stdout_file = output_dir / 'stdout.log'
+stderr_file = output_dir / 'stderr.log'
+pid_file = output_dir / 'hook.pid'
+cmd_file = output_dir / 'cmd.sh'
+
+try:
+    # Write command script for validation
+    from archivebox.misc.process_utils import write_cmd_file
+    write_cmd_file(cmd_file, cmd)
+
+    # Open log files for writing
+    with open(stdout_file, 'w') as out, open(stderr_file, 'w') as err:
+        process = subprocess.Popen(
+            cmd,
+            cwd=str(output_dir),
+            stdout=out,
+            stderr=err,
+            env=env,
+        )
+
+        # Write PID with mtime set to process start time for validation
+        from archivebox.misc.process_utils import write_pid_file_with_mtime
+        process_start_time = time.time()
+        write_pid_file_with_mtime(pid_file, process.pid, process_start_time)
+
+        if is_background:
+            # Background hook - return None immediately, don't wait
+            return None
+```
+
+**NEW CODE:**
 ```python
 def run_hook(
     script: Path,
     output_dir: Path,
     config: Dict[str, Any],
     timeout: Optional[int] = None,
-    parent_process: Optional['Process'] = None,  # NEW
+    parent_process: Optional['Process'] = None,  # NEW: from ArchiveResult.process
     **kwargs: Any
 ) -> HookResult:
-    """
-    Execute a hook script with the given arguments.
-
-    Now creates Process records for tracking:
-    - One Process for the hook script itself
-    - Child Process records for any binaries the hook reports running
-    """
     from archivebox.machine.models import Process, Machine
 
-    # ... existing setup code ...
+    # ... existing setup (lines 270-372) ...
 
-    # Create Process record for this hook
+    # Create Process record for this hook execution
+    # Parent is the ArchiveResult's Process (passed from ArchiveResult.run())
     hook_process = Process.objects.create(
         machine=Machine.current(),
         parent=parent_process,
         process_type=Process.TypeChoices.HOOK,
         cmd=cmd,
         pwd=str(output_dir),
-        env=env,  # Store sanitized env
+        env={k: v for k, v in env.items() if k not in os.environ},  # Only store non-default env
         timeout=timeout,
         status=Process.StatusChoices.QUEUED,
     )
 
-    # Launch the hook
-    hook_process.launch(background=is_background_hook)
+    # Use Process.launch() which handles:
+    # - subprocess.Popen
+    # - PID file with mtime validation
+    # - cmd.sh script
+    # - stdout/stderr capture
+    # - status transitions
+    if is_background:
+        hook_process.launch(background=True)
+        # Return None for background hooks (existing behavior)
+        # HookResult not returned - caller uses hook_process.id to track
+        return None
+    else:
+        hook_process.launch(background=False)  # Blocks until completion
 
-    # ... rest of processing ...
+    # Read output from Process (instead of files directly)
+    stdout = hook_process.stdout
+    stderr = hook_process.stderr
+    returncode = hook_process.exit_code
+
+    # ... existing JSONL parsing (lines 427-448) ...
+
+    # NEW: Create child Process records for binaries reported in JSONL
+    for record in records:
+        if record.get('type') == 'Process':
+            Process.objects.create(
+                machine=hook_process.machine,
+                parent=hook_process,
+                process_type=Process.TypeChoices.BINARY,
+                cmd=record.get('cmd', []),
+                pwd=record.get('pwd', str(output_dir)),
+                pid=record.get('pid'),
+                exit_code=record.get('exit_code'),
+                started_at=parse_ts(record.get('started_at')),
+                ended_at=parse_ts(record.get('ended_at')),
+                status=Process.StatusChoices.EXITED,
+            )
 
     return HookResult(
+        returncode=returncode,
+        stdout=stdout,
+        stderr=stderr,
         # ... existing fields ...
-        process_id=str(hook_process.id),  # NEW: include process ID
+        process_id=str(hook_process.id),  # NEW
     )
 ```
 
-### 2.2 Update HookResult TypedDict
+#### 2.2.2 Update `process_is_alive()` to Use Process Model
 
+**CURRENT CODE (lines 1238-1256):**
 ```python
-class HookResult(TypedDict, total=False):
-    """Raw result from run_hook()."""
-    returncode: int
-    stdout: str
-    stderr: str
-    output_json: Optional[Dict[str, Any]]
-    output_files: List[str]
-    duration_ms: int
-    hook: str
-    plugin: str
-    hook_name: str
-    records: List[Dict[str, Any]]
-    process_id: str  # NEW: ID of the hook Process record
+def process_is_alive(pid_file: Path) -> bool:
+    """Check if process in PID file is still running."""
+    if not pid_file.exists():
+        return False
+    try:
+        pid = int(pid_file.read_text().strip())
+        os.kill(pid, 0)
+        return True
+    except (OSError, ValueError):
+        return False
 ```
 
-### 2.3 Handle Binary Process Records from Hook Output
-
-Hooks can output JSONL records describing binaries they run. Parse these and create child `Process` records:
-
+**NEW CODE:**
 ```python
-def process_hook_binary_records(
-    hook_process: 'Process',
-    records: List[Dict[str, Any]]
-) -> List['Process']:
+def process_is_alive(pid_file_or_process: 'Path | Process') -> bool:
     """
-    Create child Process records for binaries reported by hook.
+    Check if process is still running.
 
-    Hooks output JSONL like:
-        {"type": "Process", "cmd": ["wget", "-p", "..."], "exit_code": 0}
+    Accepts either:
+    - Path to hook.pid file (legacy)
+    - Process model instance (new)
     """
     from archivebox.machine.models import Process
 
-    binary_processes = []
+    if isinstance(pid_file_or_process, Process):
+        return pid_file_or_process.is_alive()
 
-    for record in records:
-        if record.get('type') != 'Process':
+    # Legacy path-based check (for backwards compatibility)
+    pid_file = pid_file_or_process
+    if not pid_file.exists():
+        return False
+
+    # Try to find matching Process record
+    try:
+        pid = int(pid_file.read_text().strip())
+        process = Process.objects.get_by_pid(pid)
+        if process:
+            return process.is_alive()
+    except (ValueError, Process.DoesNotExist):
+        pass
+
+    # Fallback to OS check
+    from archivebox.misc.process_utils import validate_pid_file
+    return validate_pid_file(pid_file)
+```
+
+#### 2.2.3 Update `kill_process()` to Use Process Model
+
+**CURRENT CODE (lines 1259-1282):**
+```python
+def kill_process(pid_file: Path, sig: int = signal.SIGTERM, validate: bool = True):
+    """Kill process in PID file with optional validation."""
+    from archivebox.misc.process_utils import safe_kill_process
+
+    if validate:
+        cmd_file = pid_file.parent / 'cmd.sh'
+        safe_kill_process(pid_file, cmd_file, signal_num=sig)
+    else:
+        # Legacy behavior
+        ...
+```
+
+**NEW CODE:**
+```python
+def kill_process(
+    pid_file_or_process: 'Path | Process',
+    sig: int = signal.SIGTERM,
+    validate: bool = True
+):
+    """
+    Kill process with optional validation.
+
+    Accepts either:
+    - Path to hook.pid file (legacy)
+    - Process model instance (new)
+    """
+    from archivebox.machine.models import Process
+
+    if isinstance(pid_file_or_process, Process):
+        pid_file_or_process.kill(signal_num=sig)
+        return
+
+    # Legacy path-based kill
+    pid_file = pid_file_or_process
+
+    # Try to find matching Process record first
+    try:
+        pid = int(pid_file.read_text().strip())
+        process = Process.objects.get_by_pid(pid)
+        if process:
+            process.kill(signal_num=sig)
+            return
+    except (ValueError, Process.DoesNotExist, FileNotFoundError):
+        pass
+
+    # Fallback to file-based kill
+    if validate:
+        from archivebox.misc.process_utils import safe_kill_process
+        cmd_file = pid_file.parent / 'cmd.sh'
+        safe_kill_process(pid_file, cmd_file, signal_num=sig)
+```
+
+### 2.3 Changes to `core/models.py` - ArchiveResult
+
+#### 2.3.1 Update `ArchiveResult.run()` to Pass Parent Process
+
+**File:** `archivebox/core/models.py` lines 2463-2565
+
+**CURRENT CODE (lines 2527-2535):**
+```python
+result = run_hook(
+    hook,
+    output_dir=plugin_dir,
+    config=config,
+    url=self.snapshot.url,
+    snapshot_id=str(self.snapshot.id),
+    crawl_id=str(self.snapshot.crawl.id),
+    depth=self.snapshot.depth,
+)
+```
+
+**NEW CODE:**
+```python
+result = run_hook(
+    hook,
+    output_dir=plugin_dir,
+    config=config,
+    parent_process=self.process,  # NEW: Pass our Process as parent for hook's Process
+    url=self.snapshot.url,
+    snapshot_id=str(self.snapshot.id),
+    crawl_id=str(self.snapshot.crawl.id),
+    depth=self.snapshot.depth,
+)
+```
+
+#### 2.3.2 Update `ArchiveResult.update_from_output()` to Use Process
+
+**File:** `archivebox/core/models.py` lines 2568-2700
+
+**CURRENT CODE (lines 2598-2600):**
+```python
+# Read and parse JSONL output from stdout.log
+stdout_file = plugin_dir / 'stdout.log'
+stdout = stdout_file.read_text() if stdout_file.exists() else ''
+```
+
+**NEW CODE:**
+```python
+# Read output from Process record (populated by Process.launch())
+if self.process_id:
+    # Process already has stdout/stderr from launch()
+    stdout = self.process.stdout
+    stderr = self.process.stderr
+else:
+    # Fallback to file-based read (legacy)
+    stdout_file = plugin_dir / 'stdout.log'
+    stdout = stdout_file.read_text() if stdout_file.exists() else ''
+```
+
+### 2.4 Changes to `core/models.py` - Snapshot
+
+#### 2.4.1 Update `Snapshot.cleanup()` to Use Process Model
+
+**File:** `archivebox/core/models.py` lines 1381-1401
+
+**CURRENT CODE:**
+```python
+def cleanup(self):
+    from archivebox.hooks import kill_process
+
+    if not self.OUTPUT_DIR.exists():
+        return
+
+    # Find all .pid files in this snapshot's output directory
+    for pid_file in self.OUTPUT_DIR.glob('**/*.pid'):
+        kill_process(pid_file, validate=True)
+
+    # Update all STARTED ArchiveResults from filesystem
+    results = self.archiveresult_set.filter(status=ArchiveResult.StatusChoices.STARTED)
+    for ar in results:
+        ar.update_from_output()
+```
+
+**NEW CODE:**
+```python
+def cleanup(self):
+    """
+    Clean up background ArchiveResult hooks.
+
+    Uses Process model to find and kill running hooks.
+    Falls back to PID file scanning for legacy compatibility.
+    """
+    from archivebox.machine.models import Process
+
+    # Kill running hook Processes for this snapshot's ArchiveResults
+    for ar in self.archiveresult_set.filter(status=ArchiveResult.StatusChoices.STARTED):
+        if ar.process_id:
+            # Get hook Processes that are children of this AR's Process
+            hook_processes = Process.objects.filter(
+                parent=ar.process,
+                process_type=Process.TypeChoices.HOOK,
+                status=Process.StatusChoices.RUNNING,
+            )
+            for hook_proc in hook_processes:
+                hook_proc.kill()
+
+        # Also kill any child binary processes
+        if ar.process_id:
+            for child in ar.process.children.filter(status=Process.StatusChoices.RUNNING):
+                child.kill()
+
+    # Legacy fallback: scan for .pid files not tracked in DB
+    if self.OUTPUT_DIR.exists():
+        from archivebox.hooks import kill_process
+        for pid_file in self.OUTPUT_DIR.glob('**/*.pid'):
+            kill_process(pid_file, validate=True)
+
+    # Update all STARTED ArchiveResults from filesystem/Process
+    for ar in self.archiveresult_set.filter(status=ArchiveResult.StatusChoices.STARTED):
+        ar.update_from_output()
+```
+
+#### 2.4.2 Update `Snapshot.has_running_background_hooks()` to Use Process Model
+
+**CURRENT CODE (lines 1403-1420):**
+```python
+def has_running_background_hooks(self) -> bool:
+    from archivebox.hooks import process_is_alive
+
+    if not self.OUTPUT_DIR.exists():
+        return False
+
+    for plugin_dir in self.OUTPUT_DIR.iterdir():
+        if not plugin_dir.is_dir():
             continue
+        pid_file = plugin_dir / 'hook.pid'
+        if process_is_alive(pid_file):
+            return True
 
-        binary_process = Process.objects.create(
-            machine=hook_process.machine,
-            parent=hook_process,
-            process_type=Process.TypeChoices.BINARY,
-            cmd=record.get('cmd', []),
-            pwd=record.get('pwd', hook_process.pwd),
-            pid=record.get('pid'),
-            exit_code=record.get('exit_code'),
-            stdout=record.get('stdout', ''),
-            stderr=record.get('stderr', ''),
-            started_at=parse_datetime(record.get('started_at')),
-            ended_at=parse_datetime(record.get('ended_at')),
-            status=Process.StatusChoices.EXITED,
-        )
-        binary_processes.append(binary_process)
+    return False
+```
 
-    return binary_processes
+**NEW CODE:**
+```python
+def has_running_background_hooks(self) -> bool:
+    """
+    Check if any ArchiveResult background hooks are still running.
+
+    Uses Process model for tracking, falls back to PID file check.
+    """
+    from archivebox.machine.models import Process
+
+    # Check via Process model (preferred)
+    for ar in self.archiveresult_set.filter(status=ArchiveResult.StatusChoices.STARTED):
+        if ar.process_id:
+            # Check if hook Process children are running
+            running_hooks = Process.objects.filter(
+                parent=ar.process,
+                process_type=Process.TypeChoices.HOOK,
+                status=Process.StatusChoices.RUNNING,
+            ).exists()
+            if running_hooks:
+                return True
+
+            # Also check the AR's own process
+            if ar.process.is_alive():
+                return True
+
+    # Legacy fallback: check PID files
+    if self.OUTPUT_DIR.exists():
+        from archivebox.hooks import process_is_alive
+        for plugin_dir in self.OUTPUT_DIR.iterdir():
+            if plugin_dir.is_dir():
+                pid_file = plugin_dir / 'hook.pid'
+                if process_is_alive(pid_file):
+                    return True
+
+    return False
+```
+
+### 2.5 Hook JSONL Output Contract Update
+
+Hooks should now output `{"type": "Process", ...}` records for any binaries they run:
+
+```jsonl
+{"type": "ArchiveResult", "status": "succeeded", "output_str": "Downloaded page"}
+{"type": "Process", "cmd": ["/usr/bin/wget", "-p", "https://example.com"], "pid": 12345, "exit_code": 0, "started_at": "2024-01-15T10:30:00Z", "ended_at": "2024-01-15T10:30:05Z"}
+{"type": "Process", "cmd": ["/usr/bin/curl", "-O", "image.png"], "pid": 12346, "exit_code": 0}
+```
+
+This allows full tracking of the process hierarchy:
+```
+Process(archivebox add, type=CLI)
+    └── Process(orchestrator, type=ORCHESTRATOR)
+            └── Process(archiveresult_worker, type=WORKER)
+                    └── Process(on_Snapshot__50_wget.py, type=HOOK)  # ArchiveResult.process
+                            └── Process(wget -p ..., type=BINARY)   # from JSONL
+                            └── Process(curl -O ..., type=BINARY)   # from JSONL
 ```
 
 ---