agent-bios 0.15.0 → 0.16.0

package/compose/corpus_session.py

@@ -0,0 +1,726 @@
+"""Per-call corpus delivery and durable host-session bindings.
+
+Native homes stay native. The only files this module writes are private activation
+records and pins; no global instructions, auth, or discovery registration is copied.
+"""
+from __future__ import annotations
+
+import hashlib
+import json
+import os
+import pathlib
+import queue
+import re
+import subprocess
+import sys
+import threading
+import time
+import uuid
+import unicodedata
+
+
+class SessionError(RuntimeError):
+    pass
+
+
+def _global_instruction_choice(host, include_global_instructions):
+    if type(include_global_instructions) is not bool:
+        raise SessionError('include_global_instructions must be a boolean')
+    if not include_global_instructions and host != 'claude':
+        raise SessionError(
+            'excluding global instruction files is not supported by the current Codex adapter; '
+            'keep global instructions included. The native CLI has no selective source control, '
+            'and the OS-level workaround interferes with its execution sandbox'
+        )
+    return include_global_instructions
+
+
+def _claude_global_instruction_patterns(env, cwd, check_paths=True):
+    """Match Claude's user-scope lookup without redirecting its configuration home."""
+    configured = env.get('CLAUDE_CONFIG_DIR')
+    if configured is None:
+        home = env.get('HOME')
+        if home is None:
+            import pwd
+            home = pwd.getpwuid(os.getuid()).pw_dir
+        if not isinstance(home, str) or not home or not pathlib.Path(home).is_absolute():
+            raise SessionError('global instruction exclusion requires an absolute native home; keep inclusion enabled')
+        configured = str(pathlib.Path(home) / '.claude')
+    if not isinstance(configured, str) or not configured or not pathlib.Path(configured).is_absolute():
+        raise SessionError(
+            'global instruction exclusion does not support an empty or relative CLAUDE_CONFIG_DIR; '
+            'keep inclusion enabled without changing the existing login/configuration identity'
+        )
+    path = pathlib.Path(os.path.normpath(unicodedata.normalize('NFC', configured))) / 'CLAUDE.md'
+    # Claude's exclusion API uses globs and adds resolved-path variants. Restrict
+    # the adapter to literal, unambiguous roots so it cannot exclude project files.
+    if any(char in str(path) for char in '*?[]{}()!+@|\\'):
+        raise SessionError('global instruction exclusion does not support glob metacharacters in the config path; keep inclusion enabled')
+    rules = path.parent / 'rules'
+    if check_paths:
+        if any(part.is_symlink() for part in (path, *path.parents)):
+            raise SessionError('global instruction exclusion does not support a symlinked global instruction path; keep inclusion enabled')
+        if rules.is_symlink() or (rules.is_dir() and any(member.is_symlink() for member in rules.rglob('*'))):
+            raise SessionError('global instruction exclusion does not support symlinked user rules; keep inclusion enabled')
+        directory = pathlib.Path(cwd).resolve()
+        parents = (directory, *directory.parents)
+        project_root = next((parent for parent in parents if (parent / '.git').exists()), directory)
+        for parent in parents:
+            for relative in ('CLAUDE.md', 'CLAUDE.local.md', '.claude/CLAUDE.md'):
+                project = parent / relative
+                if project == path:
+                    if directory.is_relative_to(path.parent) or path.is_relative_to(project_root):
+                        raise SessionError(f'global instructions also belong to this project: {path}; keep inclusion enabled')
+                elif project.is_file() and (
+                    (path.is_file() and project.samefile(path)) or project.resolve().is_relative_to(rules)
+                ):
+                    raise SessionError(f'global and project instructions refer to the same file: {project}; keep inclusion enabled')
+    # User rules are a separate native instruction source, not imports of CLAUDE.md.
+    return [str(path), str(rules) + '/**']
+
+
+def _claude_exclusion_version(command, cwd, env):
+    try:
+        result = subprocess.run([command, '--version'], cwd=cwd, env=env, input='',
+                                capture_output=True, text=True, timeout=10)
+    except (OSError, subprocess.TimeoutExpired) as exc:
+        raise SessionError('could not verify Claude support for global instruction exclusion; keep inclusion enabled') from exc
+    version = re.match(r'^(\d+)\.(\d+)\.(\d+)(?:\s|$)', result.stdout.strip())
+    if result.returncode or version is None or tuple(map(int, version.groups())) < (2, 1, 263):
+        raise SessionError('global instruction exclusion requires Claude Code 2.1.263 or newer; keep inclusion enabled')
+
+
+def _settings_values(argv):
+    if not isinstance(argv, (list, tuple)) or not all(isinstance(token, str) for token in argv):
+        raise SessionError('global instruction exclusion requires a valid argument list')
+    options = argv[:argv.index('--')] if '--' in argv else argv
+    values = []
+    for index, token in enumerate(options):
+        if token == '--settings':
+            values.append(options[index + 1] if index + 1 < len(options) else None)
+        elif token.startswith('--settings='):
+            values.append(token.split('=', 1)[1])
+    return values
+
+
+def _record_instruction_choice(record, env, check_paths=True):
+    include = _global_instruction_choice(record['host'], record.get('include_global_instructions', True))
+    if not include:
+        values = _settings_values(record['argv'])
+        expected = {'claudeMdExcludes': _claude_global_instruction_patterns(env, record['cwd'], check_paths)}
+        try:
+            valid = len(values) == 1 and json.loads(values[0]) == expected
+        except (TypeError, ValueError):
+            valid = False
+        if not valid:
+            raise SessionError('session pin does not carry its declared global instruction exclusion; start a new session')
+    return include
+
+
+def atomic_json(path, data):
+    path = pathlib.Path(path)
+    if path.parent.is_symlink():
+        raise SessionError(f"refusing symlink directory: {path.parent}")
+    path.parent.mkdir(parents=True, exist_ok=True, mode=0o700)
+    if path.is_symlink():
+        raise SessionError(f"refusing symlink: {path}")
+    tmp = path.with_name(path.name + '.' + uuid.uuid4().hex + '.tmp')
+    try:
+        with open(tmp, 'x', encoding='utf-8') as out:
+            os.chmod(tmp, 0o600)
+            json.dump(data, out, ensure_ascii=False, indent=2)
+            out.write('\n')
+            out.flush()
+            os.fsync(out.fileno())
+        os.replace(tmp, path)
+        fd = os.open(path.parent, os.O_RDONLY)
+        try:
+            os.fsync(fd)
+        finally:
+            os.close(fd)
+    finally:
+        tmp.unlink(missing_ok=True)
+
+
+class CodexServer:
+    """One owned stdio server. No turn/start or model generation is used."""
+
+    def __init__(self, command, config_args=(), cwd=None, env=None):
+        self.command, self.config_args, self.cwd, self.env = command, config_args, cwd, env
+        self.sequence = 0
+        self.events = queue.Queue()
+
+    def __enter__(self):
+        self.proc = subprocess.Popen(
+            [self.command, *self.config_args, 'app-server', '--stdio'],
+            stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL,
+            cwd=self.cwd, env=self.env, text=True, encoding='utf-8',
+        )
+        self.reader = threading.Thread(target=self._read, daemon=True)
+        self.reader.start()
+        try:
+            self.call('initialize', {'clientInfo': {'name': 'agent-bios', 'version': '1'},
+                                     'capabilities': {'experimentalApi': True}})
+            self.proc.stdin.write('{"method":"initialized"}\n')
+            self.proc.stdin.flush()
+            return self
+        except BaseException:
+            self.__exit__(None, None, None)
+            raise
+
+    def _read(self):
+        try:
+            for line in self.proc.stdout:
+                try:
+                    self.events.put(json.loads(line))
+                except ValueError:
+                    self.events.put({'transport_error': 'invalid app-server JSON'})
+        finally:
+            self.events.put({'transport_error': 'app-server closed before its response'})
+
+    def call(self, method, params, timeout=45):
+        self.sequence += 1
+        request_id = self.sequence
+        self.proc.stdin.write(json.dumps({'id': request_id, 'method': method, 'params': params}) + '\n')
+        self.proc.stdin.flush()
+        deadline = time.monotonic() + timeout
+        while time.monotonic() < deadline:
+            try:
+                message = self.events.get(timeout=max(0.01, deadline - time.monotonic()))
+            except queue.Empty as exc:
+                raise SessionError(f"app-server timed out: {method}") from exc
+            if 'transport_error' in message:
+                raise SessionError(message['transport_error'])
+            if message.get('id') != request_id:
+                continue
+            if 'error' in message:
+                raise SessionError(f"app-server {method}: {message['error'].get('message', 'refused')}")
+            return message['result']
+        raise SessionError(f"app-server timed out: {method}")
+
+    def __exit__(self, *unused):
+        if self.proc.stdin:
+            self.proc.stdin.close()
+        try:
+            self.proc.wait(timeout=5)
+        except subprocess.TimeoutExpired:
+            self.proc.terminate()
+            try:
+                self.proc.wait(timeout=5)
+            except subprocess.TimeoutExpired:
+                self.proc.kill()
+                self.proc.wait(timeout=5)
+        if self.proc.stdout:
+            self.proc.stdout.close()
+        self.reader.join(timeout=2)
+
+
+def config_flags(argv, exclude_developer=False):
+    result = []
+    index = 0
+    while index < len(argv):
+        token = argv[index]
+        if token in ('-c', '--config'):
+            if index + 1 >= len(argv):
+                raise SessionError(f"missing value for {token}")
+            value = argv[index + 1]
+            if not (exclude_developer and value.split('=', 1)[0] == 'developer_instructions'):
+                result += ['-c', value]
+            index += 2
+            continue
+        if token.startswith('--config='):
+            value = token[len('--config='):]
+            if not (exclude_developer and value.split('=', 1)[0] == 'developer_instructions'):
+                result += ['-c', value]
+        if token in ('-p', '--profile') and index + 1 < len(argv):
+            result += ['--profile', argv[index + 1]]
+            index += 1
+        if token.startswith('--profile='):
+            result += ['--profile', token.split('=', 1)[1]]
+        index += 1
+    return result
+
+
+def named_profile(argv):
+    """Return the one native profile requested by a Codex argv, if any.
+
+    Profiles are a top-level Codex runtime feature.  The app-server used below
+    for ``config/read`` deliberately has no profile input, so treating a
+    profile as ``-c profile=...`` either changes its meaning or makes the
+    server reject the request.  Keep this parser narrow and fail before a host
+    process is started rather than silently reading the base configuration.
+    """
+    profile = None
+    index = 0
+    while index < len(argv):
+        token = argv[index]
+        if token in ('-p', '--profile'):
+            if index + 1 >= len(argv):
+                raise SessionError(f'missing value for {token}')
+            value = argv[index + 1]
+            index += 2
+        elif token.startswith('--profile='):
+            value = token.split('=', 1)[1]
+            index += 1
+        else:
+            index += 1
+            continue
+        if not value:
+            raise SessionError('invalid empty Codex profile')
+        if profile is not None and profile != value:
+            raise SessionError('multiple Codex profiles are not supported')
+        profile = value
+    return profile
+
+
+def replace_developer(argv, text):
+    result, index = [], 0
+    while index < len(argv):
+        token = argv[index]
+        if token in ('-c', '--config') and index + 1 < len(argv):
+            if argv[index + 1].split('=', 1)[0] == 'developer_instructions':
+                index += 2
+                continue
+        if token.startswith('--config=developer_instructions='):
+            index += 1
+            continue
+        result.append(token)
+        index += 1
+    return [*result, '-c', 'developer_instructions=' + json.dumps(text)]
+
+
+def instruction_value(argv, host):
+    argv = list(argv[:argv.index('--')]) if '--' in argv else argv
+    if host == 'claude':
+        values = [argv[i + 1] for i, a in enumerate(argv[:-1]) if a == '--append-system-prompt']
+        return '\n\n'.join(values)
+    for i, a in enumerate(argv[:-1]):
+        if a in ('-c', '--config') and argv[i + 1].startswith('developer_instructions='):
+            return json.loads(argv[i + 1].split('=', 1)[1])
+    return ''
+
+
+def _claude_plugin_paths(snapshot):
+    assets = snapshot.get('assets') or {}
+    if not isinstance(assets, dict) or set(assets) - {'claude_plugins'}:
+        raise SessionError('invalid native snapshot assets')
+    values = assets.get('claude_plugins', [])
+    if not isinstance(values, list) or not all(isinstance(value, str) for value in values):
+        raise SessionError('invalid native plugin paths')
+    if not values:
+        return []
+    root = pathlib.Path(snapshot['path']).resolve()
+    result = []
+    for value in values:
+        relative = pathlib.PurePosixPath(value)
+        if relative.is_absolute() or '..' in relative.parts or relative.as_posix() != value:
+            raise SessionError('native plugin is outside the pinned snapshot')
+        path = root / relative
+        if not path.resolve().is_relative_to(root) or path == root:
+            raise SessionError('native plugin is outside the pinned snapshot')
+        result.append(str(path))
+    if len(result) != len(set(result)):
+        raise SessionError('duplicate native plugin')
+    return result
+
+
+def validate_claude_plugins(command, snapshot, cwd, env):
+    """Native validation is manifest-only; assert actual carriers separately."""
+    for raw in _claude_plugin_paths(snapshot):
+        root = pathlib.Path(raw)
+        agents = list((root / 'agents').glob('*.md'))
+        hooks = root / 'hooks/hooks.json'
+        if bool(agents) == hooks.is_file():
+            raise SessionError('native item plugin must have one agent or hook carrier')
+        if agents and len(agents) != 1:
+            raise SessionError('native item plugin has unexpected agents')
+        completed = subprocess.run([command, 'plugin', 'validate', '--json', str(root)],
+                                   cwd=cwd, env=env, input='', capture_output=True, text=True, timeout=30)
+        try:
+            result = json.loads(completed.stdout)
+        except ValueError as exc:
+            raise SessionError('Claude must support plugin validate --json for native corpus activation') from exc
+        manifest = result.get('manifest') if isinstance(result, dict) else None
+        if completed.returncode or not isinstance(result, dict) or result.get('success') is not True or not isinstance(manifest, dict) or manifest.get('errors') != []:
+            raise SessionError(f'Claude rejected native corpus plugin {root.name}: {completed.stdout[-1500:]}')
+        for warning in manifest.get('warnings', []):
+            print(f"agent-bios: native plugin warning: {warning.get('message', warning)}", file=sys.stderr)
+
+
+def _verified_launch_snapshot(state_root, snapshot):
+    from corpus_store import verify_snapshot
+    ref = snapshot.get('content_ref')
+    if not isinstance(ref, str) or not re.fullmatch('[0-9a-f]{64}', ref):
+        raise SessionError('invalid corpus content ref')
+    root = pathlib.Path(state_root) / 'sessions/snapshots' / ref
+    if pathlib.Path(snapshot.get('path', '')).resolve() != root.resolve():
+        raise SessionError('activation snapshot is not owned by this private store')
+    verified = verify_snapshot(root, ref)
+    return {**verified['output'], 'path': str(root), 'content_ref': ref,
+            'assets': verified['output'].get('assets', {})}
+
+
+def compose_argv(command, argv, host, snapshot, cwd=None, env=None, include_global_instructions=True):
+    """Preserve native instructions before the selected corpus and launch contract."""
+    _global_instruction_choice(host, include_global_instructions)
+    native_env = dict(os.environ if env is None else env)
+    native_cwd = pathlib.Path(cwd or pathlib.Path.cwd()).resolve()
+    exclusion = []
+    if not include_global_instructions:
+        if _settings_values(argv):
+            raise SessionError(
+                'global instruction exclusion cannot be combined with an existing --settings argument: '
+                'Claude would replace it; keep inclusion enabled to preserve those settings'
+            )
+        patterns = _claude_global_instruction_patterns(native_env, native_cwd)
+        _claude_exclusion_version(command, native_cwd, native_env)
+        exclusion = ['--settings', json.dumps({'claudeMdExcludes': patterns}, ensure_ascii=False)]
+    content = snapshot['instruction_text']
+    contract = instruction_value(argv, host)
+    if host == 'codex':
+        profile = named_profile(argv)
+        if profile is not None:
+            raise SessionError(
+                f'named Codex profile {profile!r} cannot be used with private corpus activation: '
+                'the native app-server config/read route does not accept --profile, so its '
+                'effective developer instructions cannot be read without rebuilding native '
+                'profile semantics'
+            )
+        with CodexServer(command, config_flags(argv, exclude_developer=True), cwd, env) as server:
+            config = server.call('config/read', {'cwd': str(cwd or pathlib.Path.cwd()), 'includeLayers': False})
+        native = config.get('config', {}).get('developer_instructions') or ''
+        if not isinstance(native, str):
+            raise SessionError('effective developer_instructions is not text')
+        return replace_developer(argv, '\n\n'.join(x for x in (native, content, contract) if x))
+    boundary = argv.index('--') if '--' in argv else len(argv)
+    options, tail = argv[:boundary], argv[boundary:]
+    result, index = [], 0
+    while index < len(options):
+        if options[index] == '--append-system-prompt':
+            index += 2
+        else:
+            result.append(options[index])
+            index += 1
+    for path in _claude_plugin_paths(snapshot):
+        result += ['--plugin-dir', path]
+    return [*result, *exclusion, '--append-system-prompt', '\n\n'.join(x for x in (content, contract) if x), *tail]
+
+
+def session_paths(state_root):
+    root = pathlib.Path(state_root)
+    for relative in ('', 'runtime', 'runtime/activations', 'sessions', 'sessions/pins',
+                     'sessions/pins/codex', 'sessions/pins/claude', 'sessions/snapshots'):
+        if (root / relative).is_symlink():
+            raise SessionError(f'refusing symlink state directory: {root / relative}')
+    return root / 'runtime' / 'activations', root / 'sessions' / 'pins'
+
+
+def validate_session_id(value):
+    if not isinstance(value, str) or not re.fullmatch(r'[A-Za-z0-9][A-Za-z0-9_-]{3,127}', value):
+        raise SessionError('invalid host session id')
+    return value
+
+
+def native_home(host, env, cwd=None):
+    key, default = ('CODEX_HOME', '.codex') if host == 'codex' else ('CLAUDE_CONFIG_DIR', '.claude')
+    base = pathlib.Path(cwd or pathlib.Path.cwd())
+    configured = env.get(key)
+    if configured:
+        path = pathlib.Path(configured)
+    else:
+        home = pathlib.Path(env.get('HOME', str(pathlib.Path.home())))
+        path = home / default
+    if not path.is_absolute():
+        path = base / path
+    return path.resolve()
+
+
+def environment_provenance(host, env):
+    """Capture only the native-home representation, never credential contents."""
+    if host not in ('codex', 'claude'):
+        raise SessionError('unknown host')
+    key = 'CODEX_HOME' if host == 'codex' else 'CLAUDE_CONFIG_DIR'
+    value = env.get(key)
+    if key in env and not isinstance(value, str):
+        raise SessionError(f'invalid {key} environment value')
+    variables = {key: {'state': 'set', 'value': value} if key in env else {'state': 'unset'}}
+    # HOME affects a native default when the host variable is absent or empty.
+    if value in (None, ''):
+        home = env.get('HOME')
+        if 'HOME' in env and not isinstance(home, str):
+            raise SessionError('invalid HOME environment value')
+        variables['HOME'] = {'state': 'set', 'value': home} if 'HOME' in env else {'state': 'unset'}
+    return {'schema_version': 1, 'variables': variables}
+
+
+def restore_environment(record, env):
+    """Restore an exact captured set/unset native-home representation."""
+    host = record.get('host')
+    key = 'CODEX_HOME' if host == 'codex' else 'CLAUDE_CONFIG_DIR' if host == 'claude' else None
+    provenance = record.get('environment')
+    if key is None or not isinstance(provenance, dict) or set(provenance) != {'schema_version', 'variables'} or type(provenance.get('schema_version')) is not int or provenance['schema_version'] != 1:
+        raise SessionError('pin lacks environment provenance; start a new activated session or run an explicit future migration')
+    variables = provenance.get('variables')
+    if not isinstance(variables, dict) or key not in variables:
+        raise SessionError('pin has invalid environment provenance; start a new activated session or run an explicit future migration')
+    host_entry = variables[key]
+    if not isinstance(host_entry, dict):
+        raise SessionError('pin has invalid native-home environment entry')
+    needs_home = host_entry.get('state') == 'unset' or host_entry.get('value') == ''
+    if set(variables) != ({key, 'HOME'} if needs_home else {key}):
+        raise SessionError('pin has incomplete or unknown native-home environment entries')
+    restored = dict(env)
+    for name in (key, 'HOME'):
+        if name not in variables:
+            continue
+        entry = variables[name]
+        if not isinstance(entry, dict) or set(entry) - {'state', 'value'} or entry.get('state') not in {'set', 'unset'}:
+            raise SessionError('pin has invalid environment provenance; start a new activated session or run an explicit future migration')
+        if entry['state'] == 'unset':
+            if 'value' in entry:
+                raise SessionError('pin has invalid environment provenance; start a new activated session or run an explicit future migration')
+            restored.pop(name, None)
+        elif not isinstance(entry.get('value'), str):
+            raise SessionError('pin has invalid environment provenance; start a new activated session or run an explicit future migration')
+        else:
+            restored[name] = entry['value']
+    return restored
+
+
+def prepare(state_root, host, snapshot, argv, cwd=None, env=None, include_global_instructions=True):
+    if host not in ('codex', 'claude'):
+        raise SessionError('unknown host')
+    _global_instruction_choice(host, include_global_instructions)
+    intents, _ = session_paths(state_root)
+    cwd = pathlib.Path(cwd or pathlib.Path.cwd()).resolve()
+    intent_id = uuid.uuid4().hex
+    record = {'schema_version': 1, 'intent_id': intent_id, 'state': 'PREPARED',
+              'host': host, 'content_ref': snapshot['content_ref'], 'snapshot_path': str(snapshot['path']),
+              'config_home': str(native_home(host, os.environ if env is None else env, cwd)),
+              'environment': environment_provenance(host, os.environ if env is None else env),
+              'include_global_instructions': include_global_instructions,
+              'argv': list(argv), 'cwd': str(cwd or pathlib.Path.cwd()), 'created': time.time()}
+    _record_instruction_choice(record, dict(os.environ if env is None else env))
+    atomic_json(intents / intent_id / 'journal.json', record)
+    return record
+
+
+def recorded_cwd(record):
+    value = record.get('cwd')
+    if not isinstance(value, str) or not pathlib.Path(value).is_absolute():
+        raise SessionError('session pin lacks an absolute working directory; start a new activated session')
+    try:
+        canonical = str(pathlib.Path(value).resolve())
+    except (OSError, RuntimeError, ValueError) as exc:
+        raise SessionError('session working directory cannot be resolved') from exc
+    if canonical != value:
+        raise SessionError('session working directory is no longer canonical; start a new activated session')
+    return value
+
+
+def observe_and_pin(state_root, record, host_id, evidence):
+    if not isinstance(record.get('intent_id'), str) or not re.fullmatch('[0-9a-f]{32}', record['intent_id']):
+        raise SessionError('invalid activation journal identity')
+    recorded_cwd(record)
+    native_env = restore_environment(record, {})
+    _record_instruction_choice(record, native_env, check_paths=False)
+    host_id = validate_session_id(host_id)
+    intents, pins = session_paths(state_root)
+    pin_path = pins / record['host'] / f'{host_id}.json'
+    if pin_path.exists():
+        existing = read_pin(state_root, record['host'], host_id)
+        if existing['intent_id'] != record['intent_id'] or existing['content_ref'] != record['content_ref']:
+            raise SessionError('host session already belongs to a different corpus activation')
+    record.update(state='HOST_OBSERVED', session_id=host_id, evidence=evidence)
+    atomic_json(intents / record['intent_id'] / 'journal.json', record)
+    atomic_json(pin_path, record)
+    record['state'] = 'PINNED'
+    atomic_json(intents / record['intent_id'] / 'journal.json', record)
+    return record
+
+
+def read_pin(state_root, host, session_id):
+    if host not in ('codex', 'claude'):
+        raise SessionError('unknown host')
+    session_id = validate_session_id(session_id)
+    _, pins = session_paths(state_root)
+    path = pins / host / f'{session_id}.json'
+    if path.is_symlink() or not path.is_file():
+        raise SessionError(f'no corpus pin for {host} session {session_id}')
+    record = json.loads(path.read_text())
+    if record.get('host') != host or record.get('session_id') != session_id:
+        raise SessionError('session pin identity mismatch')
+    recorded_cwd(record)
+    native_env = restore_environment(record, {})
+    _record_instruction_choice(record, native_env, check_paths=False)
+    snapshot = pathlib.Path(record['snapshot_path'])
+    allowed = (pathlib.Path(state_root) / 'sessions' / 'snapshots').resolve()
+    if not snapshot.resolve().is_relative_to(allowed) or snapshot.is_symlink():
+        raise SessionError('session pin names an unowned snapshot')
+    if not snapshot.is_dir():
+        raise SessionError('pinned corpus snapshot missing; recover it before resuming')
+    from corpus_store import verify_snapshot
+    verify_snapshot(snapshot, record['content_ref'])
+    return record
+
+
+def claude_evidence(record, env):
+    requested = record.get('requested_session_id')
+    if not requested:
+        return None
+    validate_session_id(requested)
+    home = native_home('claude', restore_environment(record, env), recorded_cwd(record))
+    from corpus_store import _reject_symlink_path
+    _reject_symlink_path(home / 'projects')
+    for trace in (home / 'projects').glob(f'*/{requested}.jsonl'):
+        _reject_symlink_path(trace.parent)
+        _reject_symlink_path(trace)
+        with trace.open(encoding='utf-8') as source:
+            for line in source:
+                try:
+                    event = json.loads(line)
+                except ValueError:
+                    continue
+                if isinstance(event, dict) and event.get('sessionId') == requested:
+                    if event.get('cwd') and pathlib.Path(event['cwd']).resolve() != pathlib.Path(record['cwd']).resolve():
+                        continue
+                    return {'method': 'native-session-log', 'path': str(trace)}
+    return None
+
+
+def recover_activations(state_root, command=None, host=None, env=None):
+    """Reconcile exact recorded ids against host evidence; retain unresolved intents."""
+    env = dict(os.environ if env is None else env)
+    intents, _ = session_paths(state_root)
+    result = {'pinned': [], 'pending': []}
+    for path in sorted(intents.glob('*/journal.json')):
+        if path.is_symlink() or path.parent.is_symlink():
+            raise SessionError('symlink activation journal')
+        record = json.loads(path.read_text())
+        if not isinstance(record, dict) or record.get('intent_id') != path.parent.name or not re.fullmatch('[0-9a-f]{32}', path.parent.name):
+            raise SessionError('activation journal identity does not match its owned directory')
+        if record.get('state') in ('PREPARED', 'HOST_OBSERVED'):
+            try:
+                recorded_cwd(record)
+                native_env = restore_environment(record, env)
+                _record_instruction_choice(record, native_env, check_paths=False)
+            except SessionError as exc:
+                print(f"agent-bios: activation {record.get('intent_id', path.parent.name)} remains pending: {exc}", file=sys.stderr)
+                result['pending'].append(record.get('intent_id', path.parent.name))
+                continue
+        if record.get('state') == 'HOST_OBSERVED':
+            observe_and_pin(state_root, record, record['session_id'], record['evidence'])
+            result['pinned'].append(record['session_id'])
+        elif record.get('state') == 'PREPARED':
+            evidence = None
+            requested = record.get('requested_session_id')
+            if requested and record['host'] == 'claude':
+                try:
+                    evidence = claude_evidence(record, env)
+                except SessionError as exc:
+                    print(f"agent-bios: activation {record.get('intent_id', '?')} remains pending: {exc}", file=sys.stderr)
+            elif requested and record['host'] == 'codex' and host == 'codex' and command:
+                validate_session_id(requested)
+                try:
+                    native_env = restore_environment(record, env)
+                    with CodexServer(command, config_flags(record['argv']), record['cwd'], native_env) as server:
+                        observed = server.call('thread/read', {'threadId': requested, 'includeTurns': False})
+                    if observed.get('thread', {}).get('id') == requested:
+                        evidence = {'method': 'recovered-thread/read'}
+                except SessionError as exc:
+                    print(f"agent-bios: activation {record['intent_id']} remains pending: {exc}", file=sys.stderr)
+            if evidence:
+                observe_and_pin(state_root, record, requested, evidence)
+                result['pinned'].append(requested)
+            else:
+                result['pending'].append(record['intent_id'])
+    return result
+
+
+def create_codex_session(command, argv, state_root, record, cwd, env):
+    with CodexServer(command, config_flags(argv), cwd, env) as server:
+        params = {'cwd': str(cwd), 'developerInstructions': instruction_value(argv, 'codex'),
+                  'ephemeral': False, 'experimentalRawEvents': False}
+        for index, token in enumerate(argv[:-1]):
+            if token in ('--model', '-m'):
+                params['model'] = argv[index + 1]
+        result = server.call('thread/start', params)
+        thread = result['thread']
+        host_id = validate_session_id(thread['id'])
+        # thread/start alone may return an id before persisting a resumable thread.
+        # Retain the exact id in PREPARED before recording a small developer item;
+        # inject_items persists history without generating a model turn.
+        record['requested_session_id'] = host_id
+        intents, _ = session_paths(state_root)
+        atomic_json(intents / record['intent_id'] / 'journal.json', record)
+        server.call('thread/inject_items', {'threadId': host_id, 'items': [
+            {'type': 'message', 'role': 'developer', 'content': [
+                {'type': 'input_text', 'text': f"agent-bios session snapshot: {record['content_ref']}"}]}]})
+    with CodexServer(command, config_flags(argv), cwd, env) as server:
+        persisted = server.call('thread/read', {'threadId': host_id, 'includeTurns': False})
+        if persisted.get('thread', {}).get('id') != host_id:
+            raise SessionError('host did not persist the requested corpus session')
+    observe_and_pin(state_root, record, host_id,
+                    {'method': 'thread/start+inject_items+read', 'thread_path': thread.get('path')})
+    return host_id
+
+
+def launch(command, argv, state_root, host, snapshot, cwd=None, env=None, resume_id=None,
+           include_global_instructions=True):
+    """Start a pinned native session, returning its exit status."""
+    cwd = pathlib.Path(cwd or pathlib.Path.cwd()).resolve()
+    env = dict(os.environ if env is None else env)
+    if resume_id and include_global_instructions is not True:
+        raise SessionError('resume uses its recorded global instruction choice; omit the override or start a new session')
+    if not resume_id:
+        _global_instruction_choice(host, include_global_instructions)
+    recovered = recover_activations(state_root, command, host, env)
+    if recovered['pending']:
+        print(f"agent-bios: {len(recovered['pending'])} activation(s) lack host evidence; their snapshots remain retained.", file=sys.stderr)
+    if resume_id:
+        record = read_pin(state_root, host, resume_id)
+        env = restore_environment(record, env)
+        if not _record_instruction_choice(record, env):
+            _claude_exclusion_version(command, record['cwd'], env)
+        if host == 'claude':
+            pinned = _verified_launch_snapshot(state_root, {'path': record['snapshot_path'], 'content_ref': record['content_ref']})
+            validate_claude_plugins(command, pinned, record['cwd'], env)
+        argv = record['argv']
+        native = ['resume', resume_id, *argv] if host == 'codex' else ['--resume', resume_id, *argv]
+        return subprocess.call([command, *native], cwd=record['cwd'], env=env)
+    snapshot = _verified_launch_snapshot(state_root, snapshot)
+    argv = compose_argv(command, argv, host, snapshot, cwd, env, include_global_instructions)
+    if host == 'claude':
+        validate_claude_plugins(command, snapshot, cwd, env)
+    record = prepare(state_root, host, snapshot, argv, cwd, env, include_global_instructions)
+    if host == 'codex':
+        # Create the durable thread before opening the native resume UI. The returned
+        # id comes from the real host and is pinned before any user turn is possible.
+        create_codex_session(command, argv, state_root, record, cwd, env)
+        native = ['resume', record['session_id'], *argv]
+        return subprocess.call([command, *native], cwd=cwd, env=env)
+    requested_id = str(uuid.uuid4())
+    record['requested_session_id'] = requested_id
+    intents, _ = session_paths(state_root)
+    atomic_json(intents / record['intent_id'] / 'journal.json', record)
+    native = ['--session-id', requested_id, *argv]
+    child = subprocess.Popen([command, *native], cwd=cwd, env=env)
+    try:
+        while True:
+            if record['state'] == 'PREPARED':
+                evidence = claude_evidence(record, env)
+                if evidence:
+                    observe_and_pin(state_root, record, requested_id, evidence)
+            if child.poll() is not None:
+                if record['state'] != 'PINNED':
+                    print(f"agent-bios: no host session evidence; activation {record['intent_id']} retained for recovery.", file=sys.stderr)
+                return child.returncode
+            time.sleep(0.15)
+    finally:
+        if child.poll() is None:
+            child.terminate()
+            try:
+                child.wait(timeout=5)
+            except subprocess.TimeoutExpired:
+                child.kill()
+                child.wait(timeout=5)