cyvest 4.4.0__py3-none-any.whl

cyvest/investigation.py

@@ -0,0 +1,1644 @@
+"""
+Investigation core - central state management for cybersecurity investigations.
+
+Handles all object storage, merging, scoring, and statistics in a unified way.
+Provides automatic merge-on-create for all object types.
+"""
+
+from __future__ import annotations
+
+from copy import deepcopy
+from datetime import datetime, timezone
+from decimal import Decimal
+from typing import TYPE_CHECKING, Any, Literal
+
+from logurich import logger
+
+from cyvest.level_score_rules import recalculate_level_for_score
+from cyvest.levels import Level, normalize_level
+from cyvest.model import (
+    AuditEvent,
+    Check,
+    Container,
+    Enrichment,
+    InvestigationWhitelist,
+    Observable,
+    ObservableLink,
+    ObservableType,
+    Relationship,
+    Taxonomy,
+    ThreatIntel,
+)
+from cyvest.model_enums import PropagationMode, RelationshipDirection, RelationshipType
+from cyvest.score import ScoreEngine, ScoreMode
+from cyvest.stats import InvestigationStats
+from cyvest.ulid import generate_ulid
+
+if TYPE_CHECKING:
+    from cyvest.model_schema import StatisticsSchema
+
+
+class Investigation:
+    """
+    Core investigation state and operations.
+
+    Manages all investigation objects (observables, checks, threat intel, etc.),
+    handles automatic merging on creation, score propagation, and statistics tracking.
+    """
+
+    _MODEL_METADATA_RULES: dict[str, dict[str, set[str]]] = {
+        "observable": {
+            "fields": {"comment", "extra", "internal", "whitelisted"},
+            "dict_fields": {"extra"},
+        },
+        "check": {
+            "fields": {"comment", "extra", "description"},
+            "dict_fields": {"extra"},
+        },
+        "threat_intel": {
+            "fields": {"comment", "extra", "level", "taxonomies"},
+            "dict_fields": {"extra"},
+        },
+        "enrichment": {
+            "fields": {"context", "data"},
+            "dict_fields": {"data"},
+        },
+        "container": {
+            "fields": {"description"},
+            "dict_fields": set(),
+        },
+    }
+
+    def __init__(
+        self,
+        root_data: Any = None,
+        root_type: ObservableType | Literal["file", "artifact"] = ObservableType.FILE,
+        score_mode_obs: ScoreMode | Literal["max", "sum"] = ScoreMode.MAX,
+        *,
+        investigation_id: str | None = None,
+        investigation_name: str | None = None,
+    ) -> None:
+        """
+        Initialize a new investigation.
+
+        Args:
+            root_data: Data stored on the root observable (optional)
+            root_type: Root observable type (ObservableType.FILE or ObservableType.ARTIFACT)
+            score_mode_obs: Observable score calculation mode (MAX or SUM)
+            investigation_name: Optional human-readable investigation name
+        """
+        self.investigation_id = investigation_id or generate_ulid()
+        self.investigation_name = investigation_name
+        self._audit_log: list[AuditEvent] = []
+        self._audit_enabled = True
+
+        # Record investigation start as the first event
+        self._record_event(
+            event_type="INVESTIGATION_STARTED",
+            object_type="investigation",
+            object_key=self.investigation_id,
+        )
+
+        # Object collections
+        self._observables: dict[str, Observable] = {}
+        self._checks: dict[str, Check] = {}
+        self._threat_intels: dict[str, ThreatIntel] = {}
+        self._enrichments: dict[str, Enrichment] = {}
+        self._containers: dict[str, Container] = {}
+
+        # Internal components
+        normalized_score_mode_obs = ScoreMode.normalize(score_mode_obs)
+        self._score_engine = ScoreEngine(score_mode_obs=normalized_score_mode_obs, sink=self)
+        self._stats = InvestigationStats()
+        self._whitelists: dict[str, InvestigationWhitelist] = {}
+
+        # Create root observable
+        obj_type = ObservableType.normalize_root_type(root_type)
+
+        self._root_observable = Observable(
+            obs_type=obj_type,
+            value="root",
+            internal=False,
+            whitelisted=False,
+            comment="Root observable for investigation",
+            extra=root_data,
+            score=Decimal("0"),
+            level=Level.INFO,
+        )
+        self._observables[self._root_observable.key] = self._root_observable
+        self._score_engine.register_observable(self._root_observable)
+        self._stats.register_observable(self._root_observable)
+        self._record_event(
+            event_type="OBSERVABLE_CREATED",
+            object_type="observable",
+            object_key=self._root_observable.key,
+        )
+
+    def _record_event(
+        self,
+        *,
+        event_type: str,
+        object_type: str | None = None,
+        object_key: str | None = None,
+        reason: str | None = None,
+        actor: str | None = None,
+        tool: str | None = None,
+        details: dict[str, Any] | None = None,
+        timestamp: datetime | None = None,
+    ) -> AuditEvent | None:
+        if not self._audit_enabled:
+            return None
+
+        event = AuditEvent(
+            event_id=generate_ulid(),
+            timestamp=timestamp or datetime.now(timezone.utc),
+            event_type=event_type,
+            actor=actor,
+            reason=reason,
+            tool=tool,
+            object_type=object_type,
+            object_key=object_key,
+            details=deepcopy(details) if details else {},
+        )
+        self._audit_log.append(event)
+        return event
+
+    @property
+    def started_at(self) -> datetime:
+        """Return the investigation start time from the first event in the audit log."""
+        for event in self._audit_log:
+            if event.event_type == "INVESTIGATION_STARTED":
+                return event.timestamp
+        # Fallback if no INVESTIGATION_STARTED event (shouldn't happen)
+        return datetime.now(timezone.utc)
+
+    def _add_threat_intel_to_observable(self, observable: Observable, ti: ThreatIntel) -> None:
+        if any(existing.key == ti.key for existing in observable.threat_intels):
+            return
+        observable.threat_intels.append(ti)
+
+    def _add_relationship_internal(
+        self,
+        source_obs: Observable,
+        target_key: str,
+        relationship_type: RelationshipType | str,
+        direction: RelationshipDirection | str | None = None,
+    ) -> None:
+        rel = Relationship(target_key=target_key, relationship_type=relationship_type, direction=direction)
+        rel_tuple = (rel.target_key, rel.relationship_type, rel.direction)
+        existing_rels = {(r.target_key, r.relationship_type, r.direction) for r in source_obs.relationships}
+        if rel_tuple not in existing_rels:
+            source_obs.relationships.append(rel)
+
+    def _add_check_observable_link(self, check: Check, link: ObservableLink) -> bool:
+        existing: dict[tuple[str, PropagationMode], int] = {}
+        for idx, existing_link in enumerate(check.observable_links):
+            existing[(existing_link.observable_key, existing_link.propagation_mode)] = idx
+        link_tuple = (link.observable_key, link.propagation_mode)
+        if link_tuple in existing:
+            return False
+
+        check.observable_links.append(link)
+        return True
+
+    def _container_add_check(self, container: Container, check: Check) -> None:
+        if any(existing.key == check.key for existing in container.checks):
+            return
+        container.checks.append(check)
+
+    def _container_add_sub_container(self, parent: Container, child: Container) -> None:
+        parent.sub_containers[child.key] = child
+
+    def _infer_object_type(self, obj: Any) -> str | None:
+        if isinstance(obj, Observable):
+            return "observable"
+        if isinstance(obj, Check):
+            return "check"
+        if isinstance(obj, ThreatIntel):
+            return "threat_intel"
+        if isinstance(obj, Enrichment):
+            return "enrichment"
+        if isinstance(obj, Container):
+            return "container"
+        return None
+
+    def apply_score_change(
+        self,
+        obj: Any,
+        new_score: Decimal,
+        *,
+        reason: str = "",
+        event_type: str = "SCORE_CHANGED",
+        contributing_investigation_ids: set[str] | None = None,
+    ) -> bool:
+        """Apply a score change and emit an audit event."""
+        if not isinstance(new_score, Decimal):
+            new_score = Decimal(str(new_score))
+
+        old_score = obj.score
+        old_level = obj.level
+        new_level = recalculate_level_for_score(old_level, new_score)
+
+        if new_score == old_score and new_level == old_level:
+            return False
+
+        obj.score = new_score
+        obj.level = new_level
+
+        if event_type == "SCORE_RECALCULATED":
+            # Skip audit log entry for recalculated scores.
+            return True
+
+        details = {
+            "old_score": float(old_score),
+            "new_score": float(new_score),
+            "old_level": old_level.value,
+            "new_level": new_level.value,
+        }
+        if contributing_investigation_ids:
+            details["contributing_investigation_ids"] = sorted(contributing_investigation_ids)
+
+        self._record_event(
+            event_type=event_type,
+            object_type=self._infer_object_type(obj),
+            object_key=getattr(obj, "key", None),
+            reason=reason,
+            details=details,
+        )
+        return True
+
+    def apply_level_change(
+        self,
+        obj: Any,
+        level: Level | str,
+        *,
+        reason: str = "",
+        event_type: str = "LEVEL_UPDATED",
+    ) -> bool:
+        """Apply a level change and emit an audit event."""
+        new_level = normalize_level(level)
+        old_level = obj.level
+        if new_level == old_level:
+            return False
+
+        obj.level = new_level
+        self._record_event(
+            event_type=event_type,
+            object_type=self._infer_object_type(obj),
+            object_key=getattr(obj, "key", None),
+            reason=reason,
+            details={
+                "old_level": old_level.value,
+                "new_level": new_level.value,
+                "score": float(obj.score),
+            },
+        )
+        return True
+
+    def _sync_check_links_for_observable(self, observable_key: str) -> None:
+        obs = self._observables.get(observable_key)
+        if not obs:
+            return
+        check_keys = self._score_engine.get_check_links_for_observable(observable_key)
+        obs._check_links = check_keys
+
+    def _refresh_check_links(self) -> None:
+        for observable_key in self._observables:
+            self._sync_check_links_for_observable(observable_key)
+
+    def get_audit_log(self) -> list[AuditEvent]:
+        """Return a deep copy of the audit log."""
+        return [event.model_copy(deep=True) for event in self._audit_log]
+
+    def get_audit_events(
+        self,
+        *,
+        object_type: str | None = None,
+        object_key: str | None = None,
+        event_type: str | None = None,
+    ) -> list[AuditEvent]:
+        """Filter audit events by optional object type/key and event type."""
+        events = self._audit_log
+        if object_type is not None:
+            events = [event for event in events if event.object_type == object_type]
+        if object_key is not None:
+            events = [event for event in events if event.object_key == object_key]
+        if event_type is not None:
+            events = [event for event in events if event.event_type == event_type]
+        return [event.model_copy(deep=True) for event in events]
+
+    def set_investigation_name(self, name: str | None, *, reason: str | None = None) -> None:
+        """Set or clear the human-readable investigation name."""
+        name = str(name).strip() if name is not None else None
+        if name == self.investigation_name:
+            return
+        old_name = self.investigation_name
+        self.investigation_name = name
+        self._record_event(
+            event_type="INVESTIGATION_NAME_UPDATED",
+            object_type="investigation",
+            object_key=self.investigation_id,
+            reason=reason,
+            details={"old_name": old_name, "new_name": name},
+        )
+
+    # Private merge methods
+
+    def _merge_observable(self, existing: Observable, incoming: Observable) -> tuple[Observable, list]:
+        """
+        Merge an incoming observable into an existing observable.
+
+        Strategy:
+        - Update score (take maximum)
+        - Update level (take maximum)
+        - Update extra (merge dicts)
+        - Concatenate comments
+        - Merge threat intels
+        - Merge relationships (defer if target missing)
+        - Preserve provenance metadata
+
+        Args:
+            existing: The existing observable
+            incoming: The incoming observable to merge
+
+        Returns:
+            Tuple of (merged observable, deferred relationships)
+        """
+        # Normal merge logic for scores and levels (SAFE level protection in Observable.update_score)
+        # Take the higher score
+        if incoming.score > existing.score:
+            self.apply_score_change(
+                existing,
+                incoming.score,
+                reason=f"Merged from {incoming.key}",
+            )
+
+        # Take the higher level
+        if incoming.level > existing.level:
+            self.apply_level_change(existing, incoming.level, reason=f"Merged from {incoming.key}")
+
+        # Update extra (merge dictionaries)
+        if existing.extra:
+            existing.extra.update(incoming.extra)
+        elif incoming.extra:
+            existing.extra = dict(incoming.extra)
+
+        # Concatenate comments
+        if incoming.comment:
+            if existing.comment:
+                existing.comment += "\n\n" + incoming.comment
+            else:
+                existing.comment = incoming.comment
+
+        # Merge whitelisted status (if either is whitelisted, result is whitelisted)
+        existing.whitelisted = existing.whitelisted or incoming.whitelisted
+
+        # Merge internal status (if either is external, result is external)
+        existing.internal = existing.internal and incoming.internal
+
+        # Merge threat intels (avoid duplicates by key)
+        existing_ti_keys = {ti.key for ti in existing.threat_intels}
+        for ti in incoming.threat_intels:
+            if ti.key not in existing_ti_keys:
+                self._add_threat_intel_to_observable(existing, ti)
+                existing_ti_keys.add(ti.key)
+
+        # Merge relationships (defer if target not yet available)
+        deferred_relationships = []
+        for rel in incoming.relationships:
+            if rel.target_key in self._observables:
+                # Target exists - add relationship immediately
+                self._add_relationship_internal(existing, rel.target_key, rel.relationship_type, rel.direction)
+            else:
+                # Target doesn't exist yet - defer for Pass 2 of merge_investigation()
+                deferred_relationships.append((existing.key, rel))
+
+        return existing, deferred_relationships
+
+    def _merge_check(self, existing: Check, incoming: Check) -> Check:
+        """
+        Merge an incoming check into an existing check.
+
+        Strategy:
+        - Update score (take maximum)
+        - Update level (take maximum)
+        - Update extra (merge dicts)
+        - Concatenate comments
+        - Merge observable links (tuple-based deduplication, provenance-preserving)
+
+        Args:
+            existing: The existing check
+            incoming: The incoming check to merge
+
+        Returns:
+            The merged check (existing is modified in place)
+        """
+        if not incoming.origin_investigation_id:
+            incoming.origin_investigation_id = self.investigation_id
+        if not existing.origin_investigation_id:
+            existing.origin_investigation_id = incoming.origin_investigation_id
+
+        # Take the higher score
+        if incoming.score > existing.score:
+            self.apply_score_change(
+                existing,
+                incoming.score,
+                reason=f"Merged from {incoming.key}",
+            )
+
+        # Take the higher level
+        if incoming.level > existing.level:
+            self.apply_level_change(existing, incoming.level, reason=f"Merged from {incoming.key}")
+
+        # Update extra (merge dictionaries)
+        existing.extra.update(incoming.extra)
+
+        # Concatenate comments
+        if incoming.comment:
+            if existing.comment:
+                existing.comment += "\n\n" + incoming.comment
+            else:
+                existing.comment = incoming.comment
+
+        existing_by_tuple: dict[tuple[str, PropagationMode], int] = {}
+        for idx, existing_link in enumerate(existing.observable_links):
+            existing_by_tuple[(existing_link.observable_key, existing_link.propagation_mode)] = idx
+        for incoming_link in incoming.observable_links:
+            link_tuple = (incoming_link.observable_key, incoming_link.propagation_mode)
+            existing_idx = existing_by_tuple.get(link_tuple)
+            if existing_idx is None:
+                existing.observable_links.append(incoming_link)
+                existing_by_tuple[link_tuple] = len(existing.observable_links) - 1
+                continue
+
+        return existing
+
+    def _merge_threat_intel(self, existing: ThreatIntel, incoming: ThreatIntel) -> ThreatIntel:
+        """
+        Merge an incoming threat intel into an existing threat intel.
+
+        Strategy:
+        - Update score (take maximum)
+        - Update level (take maximum)
+        - Update extra (merge dicts)
+        - Concatenate comments
+        - Merge taxonomies
+
+        Args:
+            existing: The existing threat intel
+            incoming: The incoming threat intel to merge
+
+        Returns:
+            The merged threat intel (existing is modified in place)
+        """
+        # Take the higher score
+        if incoming.score > existing.score:
+            self.apply_score_change(
+                existing,
+                incoming.score,
+                reason=f"Merged from {incoming.key}",
+            )
+
+        # Take the higher level
+        if incoming.level > existing.level:
+            self.apply_level_change(existing, incoming.level, reason=f"Merged from {incoming.key}")
+
+        # Update extra (merge dictionaries)
+        existing.extra.update(incoming.extra)
+
+        # Concatenate comments
+        if incoming.comment:
+            if existing.comment:
+                existing.comment += "\n\n" + incoming.comment
+            else:
+                existing.comment = incoming.comment
+
+        # Merge taxonomies (ensure unique names)
+        existing_by_name: dict[str, int] = {taxonomy.name: idx for idx, taxonomy in enumerate(existing.taxonomies)}
+        for taxonomy in incoming.taxonomies:
+            existing_idx = existing_by_name.get(taxonomy.name)
+            if existing_idx is None:
+                existing.taxonomies.append(taxonomy)
+                existing_by_name[taxonomy.name] = len(existing.taxonomies) - 1
+            else:
+                existing.taxonomies[existing_idx] = taxonomy
+
+        return existing
+
+    def _merge_enrichment(self, existing: Enrichment, incoming: Enrichment) -> Enrichment:
+        """
+        Merge an incoming enrichment into an existing enrichment.
+
+        Strategy:
+        - Deep merge data structure (merge dictionaries recursively)
+
+        Args:
+            existing: The existing enrichment
+            incoming: The incoming enrichment to merge
+
+        Returns:
+            The merged enrichment (existing is modified in place)
+        """
+
+        def deep_merge(base: dict, update: dict) -> dict:
+            """Recursively merge dictionaries."""
+            for key, value in update.items():
+                if key in base and isinstance(base[key], dict) and isinstance(value, dict):
+                    deep_merge(base[key], value)
+                else:
+                    base[key] = value
+            return base
+
+        # Deep merge data structures
+        if isinstance(existing.data, dict) and isinstance(incoming.data, dict):
+            deep_merge(existing.data, incoming.data)
+        else:
+            existing.data = deepcopy(incoming.data)
+
+        # Update context if incoming has one
+        if incoming.context:
+            existing.context = incoming.context
+
+        return existing
+
+    def _merge_container(self, existing: Container, incoming: Container) -> Container:
+        """
+        Merge an incoming container into an existing container.
+
+        Strategy:
+        - Merge checks (dict-based lookup for efficiency)
+        - Merge sub-containers recursively
+
+        Args:
+            existing: The existing container
+            incoming: The incoming container to merge
+
+        Returns:
+            The merged container (existing is modified in place)
+        """
+        # Update description if incoming has one
+        if incoming.description:
+            existing.description = incoming.description
+
+        # Merge checks using dict-based lookup (more efficient)
+        existing_checks_dict = {check.key: check for check in existing.checks}
+
+        for incoming_check in incoming.checks:
+            if incoming_check.key in existing_checks_dict:
+                # Merge existing check
+                self._merge_check(existing_checks_dict[incoming_check.key], incoming_check)
+            else:
+                # Add new check
+                self._container_add_check(existing, incoming_check)
+
+        # Merge sub-containers recursively
+        for sub_key, incoming_sub in incoming.sub_containers.items():
+            if sub_key in existing.sub_containers:
+                # Merge existing sub-container
+                self._merge_container(existing.sub_containers[sub_key], incoming_sub)
+            else:
+                # Add new sub-container
+                self._container_add_sub_container(existing, incoming_sub)
+
+        return existing
+
+    # Public add methods with merge-on-create
+
+    def add_observable(self, obs: Observable) -> tuple[Observable, list]:
+        """
+        Add or merge an observable.
+
+        Args:
+            obs: Observable to add or merge
+
+        Returns:
+            Tuple of (resulting observable, deferred relationships)
+        """
+        if obs.key in self._observables:
+            r = self._merge_observable(self._observables[obs.key], obs)
+            self._score_engine.recalculate_all()
+            return r
+
+        # Register new observable
+        self._observables[obs.key] = obs
+        self._score_engine.register_observable(obs)
+        self._stats.register_observable(obs)
+        self._sync_check_links_for_observable(obs.key)
+        self._record_event(
+            event_type="OBSERVABLE_CREATED",
+            object_type="observable",
+            object_key=obs.key,
+        )
+        return obs, []
+
+    def add_check(self, check: Check) -> Check:
+        """
+        Add or merge a check.
+
+        Args:
+            check: Check to add or merge
+
+        Returns:
+            The resulting check (either new or merged)
+        """
+        if check.key in self._checks:
+            r = self._merge_check(self._checks[check.key], check)
+            self._score_engine.rebuild_link_index()
+            self._score_engine.recalculate_all()
+            for link in r.observable_links:
+                self._sync_check_links_for_observable(link.observable_key)
+            return r
+
+        if not getattr(check, "origin_investigation_id", None):
+            check.origin_investigation_id = self.investigation_id
+
+        # Register new check
+        self._checks[check.key] = check
+        self._score_engine.register_check(check)
+        self._stats.register_check(check)
+        for link in check.observable_links:
+            self._sync_check_links_for_observable(link.observable_key)
+        self._record_event(
+            event_type="CHECK_CREATED",
+            object_type="check",
+            object_key=check.key,
+        )
+        return check
+
+    def add_threat_intel(self, ti: ThreatIntel, observable: Observable) -> ThreatIntel:
+        """
+        Add or merge threat intel and link to observable.
+
+        Args:
+            ti: Threat intel to add or merge
+            observable: Observable to link to
+
+        Returns:
+            The resulting threat intel (either new or merged)
+        """
+        if ti.key in self._threat_intels:
+            merged_ti = self._merge_threat_intel(self._threat_intels[ti.key], ti)
+            # Propagate score to observable
+            self._score_engine.propagate_threat_intel_to_observable(merged_ti, observable)
+            self._record_event(
+                event_type="THREAT_INTEL_ATTACHED",
+                object_type="observable",
+                object_key=observable.key,
+                details={
+                    "threat_intel_key": merged_ti.key,
+                    "source": merged_ti.source,
+                    "score": merged_ti.score,
+                    "level": merged_ti.level,
+                },
+            )
+            return merged_ti
+
+        # Register new threat intel
+        self._threat_intels[ti.key] = ti
+        self._stats.register_threat_intel(ti)
+
+        # Add to observable
+        self._add_threat_intel_to_observable(observable, ti)
+
+        # Propagate score
+        self._score_engine.propagate_threat_intel_to_observable(ti, observable)
+
+        self._record_event(
+            event_type="THREAT_INTEL_ATTACHED",
+            object_type="observable",
+            object_key=observable.key,
+            details={
+                "threat_intel_key": ti.key,
+                "source": ti.source,
+                "score": ti.score,
+                "level": ti.level,
+            },
+        )
+        return ti
+
+    def add_threat_intel_taxonomy(self, threat_intel_key: str, taxonomy: Taxonomy) -> ThreatIntel:
+        """
+        Add or replace a taxonomy entry on a threat intel by name.
+
+        Args:
+            threat_intel_key: Threat intel key
+            taxonomy: Taxonomy entry to add or replace
+
+        Returns:
+            The updated threat intel
+        """
+        ti = self._threat_intels.get(threat_intel_key)
+        if ti is None:
+            raise KeyError(f"threat_intel '{threat_intel_key}' not found in investigation.")
+
+        updated_taxonomies = list(ti.taxonomies)
+        replaced = False
+        for idx, existing in enumerate(updated_taxonomies):
+            if existing.name == taxonomy.name:
+                updated_taxonomies[idx] = taxonomy
+                replaced = True
+                break
+
+        if not replaced:
+            updated_taxonomies.append(taxonomy)
+
+        return self.update_model_metadata("threat_intel", threat_intel_key, {"taxonomies": updated_taxonomies})
+
+    def remove_threat_intel_taxonomy(self, threat_intel_key: str, name: str) -> ThreatIntel:
+        """
+        Remove a taxonomy entry from a threat intel by name.
+
+        Args:
+            threat_intel_key: Threat intel key
+            name: Taxonomy name to remove
+
+        Returns:
+            The updated threat intel
+        """
+        ti = self._threat_intels.get(threat_intel_key)
+        if ti is None:
+            raise KeyError(f"threat_intel '{threat_intel_key}' not found in investigation.")
+
+        updated_taxonomies = [taxonomy for taxonomy in ti.taxonomies if taxonomy.name != name]
+        if len(updated_taxonomies) == len(ti.taxonomies):
+            return ti
+
+        return self.update_model_metadata("threat_intel", threat_intel_key, {"taxonomies": updated_taxonomies})
+
+    def add_enrichment(self, enrichment: Enrichment) -> Enrichment:
+        """
+        Add or merge enrichment.
+
+        Args:
+            enrichment: Enrichment to add or merge
+
+        Returns:
+            The resulting enrichment (either new or merged)
+        """
+        if enrichment.key in self._enrichments:
+            return self._merge_enrichment(self._enrichments[enrichment.key], enrichment)
+
+        # Register new enrichment
+        self._enrichments[enrichment.key] = enrichment
+        self._record_event(
+            event_type="ENRICHMENT_CREATED",
+            object_type="enrichment",
+            object_key=enrichment.key,
+        )
+        return enrichment
+
+    def add_container(self, container: Container) -> Container:
+        """
+        Add or merge container.
+
+        Args:
+            container: Container to add or merge
+
+        Returns:
+            The resulting container (either new or merged)
+        """
+        if container.key in self._containers:
+            r = self._merge_container(self._containers[container.key], container)
+            self._score_engine.recalculate_all()
+            return r
+
+        # Register new container
+        self._containers[container.key] = container
+        self._stats.register_container(container)
+        self._record_event(
+            event_type="CONTAINER_CREATED",
+            object_type="container",
+            object_key=container.key,
+        )
+        return container
+
+    # Relationship and linking methods
+
+    def add_relationship(
+        self,
+        source: Observable | str,
+        target: Observable | str,
+        relationship_type: RelationshipType | str,
+        direction: RelationshipDirection | str | None = None,
+    ) -> Observable:
+        """
+        Add a relationship between observables.
+
+        Args:
+            source: Source observable or its key
+            target: Target observable or its key
+            relationship_type: Type of relationship
+            direction: Direction of the relationship (None = use semantic default)
+
+        Returns:
+            The source observable
+
+        Raises:
+            KeyError: If the source or target observable does not exist
+        """
+
+        # Extract keys from Observable objects if needed
+        source_key = source.key if isinstance(source, Observable) else source
+        target_key = target.key if isinstance(target, Observable) else target
+
+        # Check if target is a copy from shared context (anti-pattern)
+        if isinstance(target, Observable) and getattr(target, "_from_shared_context", False):
+            obs_type_name = target.obs_type.name
+            raise ValueError(
+                f"Cannot use observable from shared_context.observable_get() directly in relationships.\n"
+                f"Observable '{target_key}' is a read-only copy not registered in this investigation.\n\n"
+                f"Incorrect pattern:\n"
+                f"  source.relate_to(shared_context.observable_get(...), RelationshipType.{relationship_type})\n\n"
+                f"Correct pattern (and use reconcile or merge):\n"
+                f"  # Use cy.observable() to create/get observable in local investigation\n"
+                f"  source.relate_to(\n"
+                f"      cy.observable(ObservableType.{obs_type_name}, '{target.value}'),\n"
+                f"      RelationshipType.{relationship_type}\n"
+                f"  )"
+            )
+
+        # Validate both source and target exist
+        source_obs = self._observables.get(source_key)
+        target_obs = self._observables.get(target_key)
+
+        if not source_obs:
+            raise KeyError(f"observable '{source_key}' not found in investigation.")
+
+        if not target_obs:
+            raise KeyError(f"observable '{target_key}' not found in investigation.")
+
+        # Add relationship using internal method
+        self._add_relationship_internal(source_obs, target_key, relationship_type, direction)
+
+        self._record_event(
+            event_type="RELATIONSHIP_CREATED",
+            object_type="observable",
+            object_key=source_obs.key,
+            details={
+                "target_key": target_key,
+                "relationship_type": relationship_type,
+                "direction": direction,
+            },
+        )
+
+        # Recalculate scores after adding relationship
+        self._score_engine.recalculate_all()
+
+        return source_obs
+
+    def link_check_observable(
+        self,
+        check_key: str,
+        observable_key: str,
+        propagation_mode: PropagationMode | str = PropagationMode.LOCAL_ONLY,
+    ) -> Check:
+        """
+        Link an observable to a check.
+
+        Args:
+            check_key: Key of the check
+            observable_key: Key of the observable
+            propagation_mode: Propagation behavior for this link
+
+        Returns:
+            The check
+
+        Raises:
+            KeyError: If the check or observable does not exist
+        """
+        check = self._checks.get(check_key)
+        observable = self._observables.get(observable_key)
+
+        if check is None:
+            raise KeyError(f"check '{check_key}' not found in investigation.")
+        if observable is None:
+            raise KeyError(f"observable '{observable_key}' not found in investigation.")
+
+        if check and observable:
+            propagation_mode = PropagationMode(propagation_mode)
+            link = ObservableLink(
+                observable_key=observable_key,
+                propagation_mode=propagation_mode,
+            )
+            created = self._add_check_observable_link(check, link)
+            if created:
+                self._score_engine.register_check_observable_link(check_key=check.key, observable_key=observable_key)
+                self._sync_check_links_for_observable(observable_key)
+                self._record_event(
+                    event_type="CHECK_LINKED_TO_OBSERVABLE",
+                    object_type="check",
+                    object_key=check.key,
+                    details={
+                        "observable_key": observable_key,
+                        "propagation_mode": propagation_mode.value,
+                    },
+                )
+                is_effective = (
+                    propagation_mode == PropagationMode.GLOBAL or self.investigation_id == check.origin_investigation_id
+                )
+                if is_effective and check.level == Level.NONE:
+                    self.apply_level_change(check, Level.INFO, reason="Effective link added")
+
+            self._score_engine._propagate_observable_to_checks(observable_key)
+
+        return check
+
+    def add_check_to_container(self, container_key: str, check_key: str) -> Container:
+        """
+        Add a check to a container.
+
+        Args:
+            container_key: Key of the container
+            check_key: Key of the check
+
+        Returns:
+            The container
+
+        Raises:
+            KeyError: If the container or check does not exist
+        """
+        container = self._containers.get(container_key)
+        check = self._checks.get(check_key)
+
+        if container is None:
+            raise KeyError(f"container '{container_key}' not found in investigation.")
+        if check is None:
+            raise KeyError(f"check '{check_key}' not found in investigation.")
+
+        if container and check:
+            self._container_add_check(container, check)
+            self._record_event(
+                event_type="CONTAINER_CHECK_ADDED",
+                object_type="container",
+                object_key=container.key,
+                details={"check_key": check.key},
+            )
+
+        return container
+
+    def add_sub_container(self, parent_key: str, child_key: str) -> Container:
+        """
+        Add a sub-container to a container.
+
+        Args:
+            parent_key: Key of the parent container
+            child_key: Key of the child container
+
+        Returns:
+            The parent container
+
+        Raises:
+            KeyError: If the parent or child container does not exist
+        """
+        parent = self._containers.get(parent_key)
+        child = self._containers.get(child_key)
+
+        if parent is None:
+            raise KeyError(f"container '{parent_key}' not found in investigation.")
+        if child is None:
+            raise KeyError(f"container '{child_key}' not found in investigation.")
+
+        if parent and child:
+            self._container_add_sub_container(parent, child)
+            self._record_event(
+                event_type="CONTAINER_SUBCONTAINER_ADDED",
+                object_type="container",
+                object_key=parent.key,
+                details={"child_container_key": child.key},
+            )
+
+        return parent
+
+    # Query methods
+
+    def get_observable(self, key: str) -> Observable | None:
+        """Get observable by full key string."""
+        return self._observables.get(key)
+
+    def get_check(self, key: str) -> Check | None:
+        """Get check by full key string."""
+        return self._checks.get(key)
+
+    def get_container(self, key: str) -> Container | None:
+        """Get a container by key."""
+        return self._containers.get(key)
+
+    def get_enrichment(self, key: str) -> Enrichment | None:
+        """Get an enrichment by key."""
+        return self._enrichments.get(key)
+
+    def get_threat_intel(self, key: str) -> ThreatIntel | None:
+        """Get a threat intel by key."""
+        return self._threat_intels.get(key)
+
+    @staticmethod
+    def _normalize_taxonomies(value: Any) -> list[Taxonomy]:
+        if value is None:
+            return []
+        if not isinstance(value, list):
+            raise TypeError("taxonomies must be a list of taxonomy objects.")
+        taxonomies = [Taxonomy.model_validate(item) for item in value]
+        seen: set[str] = set()
+        duplicates: set[str] = set()
+        for taxonomy in taxonomies:
+            if taxonomy.name in seen:
+                duplicates.add(taxonomy.name)
+            seen.add(taxonomy.name)
+        if duplicates:
+            dupes = ", ".join(sorted(duplicates))
+            raise ValueError(f"Duplicate taxonomy name(s): {dupes}")
+        return taxonomies
+
+    def get_root(self) -> Observable:
+        """Get the root observable."""
+        return self._root_observable
+
+    def update_model_metadata(
+        self,
+        model_type: Literal["observable", "check", "threat_intel", "enrichment", "container"],
+        key: str,
+        updates: dict[str, Any],
+        *,
+        dict_merge: dict[str, bool] | None = None,
+    ):
+        """
+        Update mutable metadata fields for a stored model instance.
+
+        Args:
+            model_type: Model family to update.
+            key: Key of the target object.
+            updates: Mapping of field names to new values. ``None`` values are ignored.
+            dict_merge: Optional overrides for dict fields (True=merge, False=replace).
+
+        Returns:
+            The updated model instance.
+
+        Raises:
+            KeyError: If the key cannot be found.
+            ValueError: If an unsupported field is requested.
+            TypeError: If a dict field receives a non-dict value.
+        """
+        store_lookup: dict[str, dict[str, Any]] = {
+            "observable": self._observables,
+            "check": self._checks,
+            "threat_intel": self._threat_intels,
+            "enrichment": self._enrichments,
+            "container": self._containers,
+        }
+        store = store_lookup[model_type]
+        target = store.get(key)
+        if target is None:
+            raise KeyError(f"{model_type} '{key}' not found in investigation.")
+
+        if not updates:
+            return target
+
+        rules = self._MODEL_METADATA_RULES[model_type]
+        allowed_fields = rules["fields"]
+        dict_fields = rules["dict_fields"]
+
+        changes: dict[str, dict[str, Any]] = {}
+
+        for field, value in updates.items():
+            if field not in allowed_fields:
+                raise ValueError(f"Field '{field}' is not mutable on {model_type}.")
+            if value is None:
+                continue
+            old_value = deepcopy(getattr(target, field, None))
+            if field == "level":
+                value = normalize_level(value)
+            if model_type == "threat_intel" and field == "taxonomies":
+                value = self._normalize_taxonomies(value)
+            if field in dict_fields:
+                if not isinstance(value, dict):
+                    raise TypeError(f"Field '{field}' on {model_type} expects a dict value.")
+                merge = dict_merge.get(field, True) if dict_merge else True
+                if merge:
+                    current_value = getattr(target, field, None)
+                    if current_value is None:
+                        setattr(target, field, deepcopy(value))
+                    else:
+                        current_value.update(value)
+                else:
+                    setattr(target, field, deepcopy(value))
+            else:
+                setattr(target, field, value)
+            new_value = deepcopy(getattr(target, field, None))
+            if old_value != new_value:
+                changes[field] = {"old": old_value, "new": new_value}
+
+        if changes:
+            self._record_event(
+                event_type="METADATA_UPDATED",
+                object_type=model_type,
+                object_key=key,
+                details={"changes": changes},
+            )
+        return target
+
+    def get_all_observables(self) -> dict[str, Observable]:
+        """Get all observables."""
+        return self._observables.copy()
+
+    def get_all_checks(self) -> dict[str, Check]:
+        """Get all checks."""
+        return self._checks.copy()
+
+    def get_all_threat_intels(self) -> dict[str, ThreatIntel]:
+        """Get all threat intels."""
+        return self._threat_intels.copy()
+
+    def get_all_enrichments(self) -> dict[str, Enrichment]:
+        """Get all enrichments."""
+        return self._enrichments.copy()
+
+    def get_all_containers(self) -> dict[str, Container]:
+        """Get all containers."""
+        return self._containers.copy()
+
+    # Scoring and statistics
+
+    def get_global_score(self) -> Decimal:
+        """Get the global investigation score."""
+        return self._score_engine.get_global_score()
+
+    def get_global_level(self) -> Level:
+        """Get the global investigation level."""
+        return self._score_engine.get_global_level()
+
+    def is_whitelisted(self) -> bool:
+        """Return whether the investigation has any whitelist entries."""
+        return bool(self._whitelists)
+
+    def add_whitelist(self, identifier: str, name: str, justification: str | None = None) -> InvestigationWhitelist:
+        """
+        Add or update a whitelist entry.
+
+        Args:
+            identifier: Unique identifier for this whitelist entry.
+            name: Human-readable name for the whitelist entry.
+            justification: Optional markdown justification.
+
+        Returns:
+            The stored whitelist entry.
+        """
+        identifier = str(identifier).strip()
+        name = str(name).strip()
+        if not identifier:
+            raise ValueError("Whitelist identifier must be provided.")
+        if not name:
+            raise ValueError("Whitelist name must be provided.")
+        if justification is not None:
+            justification = str(justification)
+
+        entry = InvestigationWhitelist(identifier=identifier, name=name, justification=justification)
+        self._whitelists[identifier] = entry
+        self._record_event(
+            event_type="WHITELIST_APPLIED",
+            object_type="investigation",
+            object_key=self.investigation_id,
+            details={
+                "identifier": identifier,
+                "name": name,
+                "justification": justification,
+            },
+        )
+        return entry
+
+    def remove_whitelist(self, identifier: str) -> bool:
+        """
+        Remove a whitelist entry by identifier.
+
+        Returns:
+            True if removed, False if it did not exist.
+        """
+        removed = self._whitelists.pop(identifier, None)
+        if removed:
+            self._record_event(
+                event_type="WHITELIST_REMOVED",
+                object_type="investigation",
+                object_key=self.investigation_id,
+                details={"identifier": identifier},
+            )
+        return removed is not None
+
+    def clear_whitelists(self) -> None:
+        """Remove all whitelist entries."""
+        if not self._whitelists:
+            return
+        removed = list(self._whitelists.keys())
+        self._whitelists.clear()
+        self._record_event(
+            event_type="WHITELIST_CLEARED",
+            object_type="investigation",
+            object_key=self.investigation_id,
+            details={"identifiers": removed},
+        )
+
+    def get_whitelists(self) -> list[InvestigationWhitelist]:
+        """Return a copy of all whitelist entries."""
+        return [w.model_copy(deep=True) for w in self._whitelists.values()]
+
+    def get_statistics(self) -> StatisticsSchema:
+        """Get comprehensive investigation statistics."""
+        return self._stats.get_summary()
+
+    def finalize_relationships(self) -> None:
+        """
+        Finalize observable relationships by linking orphans to root.
+
+        Detects orphan sub-graphs (connected components not linked to root) and links
+        the most appropriate starting node of each sub-graph to root.
+        """
+        root_key = self._root_observable.key
+
+        # Build adjacency lists for graph traversal
+        graph = {key: set() for key in self._observables.keys()}
+        incoming = {key: set() for key in self._observables.keys()}
+
+        for obs_key, obs in self._observables.items():
+            for rel in obs.relationships:
+                if rel.target_key in self._observables:
+                    graph[obs_key].add(rel.target_key)
+                    incoming[rel.target_key].add(obs_key)
+
+        # Find all connected components using BFS
+        visited = set()
+        components = []
+
+        def bfs(start_key: str) -> set[str]:
+            """Breadth-first search to find connected component."""
+            component = set()
+            queue = [start_key]
+            component.add(start_key)
+
+            while queue:
+                current = queue.pop(0)
+                # Check both outgoing and incoming edges for connectivity
+                neighbors = graph[current] | incoming[current]
+                for neighbor in neighbors:
+                    if neighbor not in component:
+                        component.add(neighbor)
+                        queue.append(neighbor)
+
+            return component
+
+        # Find all connected components
+        for obs_key in self._observables.keys():
+            if obs_key not in visited:
+                component = bfs(obs_key)
+                visited.update(component)
+                components.append(component)
+
+        # Process each component that doesn't include root
+        for component in components:
+            if root_key in component:
+                continue  # This component is already connected to root
+
+            # Find the best starting node in this orphan sub-graph
+            # Prioritize nodes with:
+            # 1. No incoming edges (true source nodes)
+            # 2. Most outgoing edges (central nodes)
+            best_node = None
+            best_score = (-1, -1)  # (negative incoming count, outgoing count)
+
+            for node_key in component:
+                incoming_count = len(incoming[node_key] & component)
+                outgoing_count = len(graph[node_key] & component)
+                score = (-incoming_count, outgoing_count)
+
+                if score > best_score:
+                    best_score = score
+                    best_node = node_key
+
+            # Link the best starting node to root
+            if best_node:
+                self._add_relationship_internal(self._root_observable, best_node, RelationshipType.RELATED_TO)
+                self._record_event(
+                    event_type="RELATIONSHIP_CREATED",
+                    object_type="observable",
+                    object_key=self._root_observable.key,
+                    reason="Finalize relationships",
+                    details={
+                        "target_key": best_node,
+                        "relationship_type": RelationshipType.RELATED_TO.value,
+                        "direction": RelationshipType.RELATED_TO.get_default_direction().value,
+                    },
+                )
+        self._score_engine.recalculate_all()
+
+    # Investigation merging
+
+    def merge_investigation(self, other: Investigation) -> None:
+        """
+        Merge another investigation into this one.
+
+        Uses a two-pass approach to handle relationship dependencies:
+        - Pass 1: Merge all observables, collecting deferred relationships
+        - Pass 2: Add deferred relationships now that all observables exist
+
+        Args:
+            other: The investigation to merge
+        """
+
+        def _diff_fields(before: dict[str, Any], after: dict[str, Any]) -> list[str]:
+            return [field for field, value in before.items() if value != after.get(field)]
+
+        def _snapshot_observable(obs: Observable) -> dict[str, Any]:
+            relationships = [
+                (
+                    rel.target_key,
+                    rel.relationship_type_name,
+                    rel.direction.value,
+                )
+                for rel in obs.relationships
+            ]
+            return {
+                "score": obs.score,
+                "level": obs.level,
+                "comment": obs.comment,
+                "extra": deepcopy(obs.extra),
+                "internal": obs.internal,
+                "whitelisted": obs.whitelisted,
+                "threat_intels": sorted(ti.key for ti in obs.threat_intels),
+                "relationships": sorted(relationships),
+            }
+
+        def _snapshot_check(check: Check) -> dict[str, Any]:
+            links = [
+                (
+                    link.observable_key,
+                    link.propagation_mode.value,
+                )
+                for link in check.observable_links
+            ]
+            return {
+                "score": check.score,
+                "level": check.level,
+                "comment": check.comment,
+                "description": check.description,
+                "extra": deepcopy(check.extra),
+                "origin_investigation_id": check.origin_investigation_id,
+                "observable_links": sorted(links),
+            }
+
+        def _snapshot_threat_intel(ti: ThreatIntel) -> dict[str, Any]:
+            return {
+                "score": ti.score,
+                "level": ti.level,
+                "comment": ti.comment,
+                "extra": deepcopy(ti.extra),
+                "taxonomies": deepcopy(ti.taxonomies),
+            }
+
+        def _snapshot_enrichment(enrichment: Enrichment) -> dict[str, Any]:
+            return {
+                "context": enrichment.context,
+                "data": deepcopy(enrichment.data),
+            }
+
+        def _snapshot_container(container: Container) -> dict[str, Any]:
+            return {
+                "description": container.description,
+                "checks": sorted(check.key for check in container.checks),
+                "sub_containers": sorted(container.sub_containers.keys()),
+            }
+
+        merge_summary: list[dict[str, Any]] = []
+
+        (
+            incoming_observables,
+            incoming_threat_intels,
+            incoming_checks,
+            incoming_enrichments,
+            incoming_containers,
+        ) = self._clone_for_merge(other)
+
+        # PASS 1: Merge observables and collect deferred relationships
+        all_deferred_relationships = []
+        for obs in incoming_observables.values():
+            existing = self._observables.get(obs.key)
+            before = _snapshot_observable(existing) if existing else None
+            _, deferred = self.add_observable(obs)
+            all_deferred_relationships.extend(deferred)
+            if existing:
+                after = _snapshot_observable(existing)
+                changed_fields = _diff_fields(before, after) if before else []
+                action = "merged" if changed_fields else "skipped"
+                merge_summary.append(
+                    {
+                        "object_type": "observable",
+                        "object_key": obs.key,
+                        "action": action,
+                        "changed_fields": changed_fields,
+                    }
+                )
+            else:
+                merge_summary.append(
+                    {
+                        "object_type": "observable",
+                        "object_key": obs.key,
+                        "action": "created",
+                        "changed_fields": [],
+                    }
+                )
+
+        # PASS 2: Process deferred relationships now that all observables exist
+        for source_key, rel in all_deferred_relationships:
+            source_obs = self._observables.get(source_key)
+            if source_obs and rel.target_key in self._observables:
+                # Both source and target exist - add relationship
+                self._add_relationship_internal(source_obs, rel.target_key, rel.relationship_type, rel.direction)
+            else:
+                # Genuine error - target still doesn't exist after Pass 2
+                logger.critical(
+                    "Relationship target '{}' not found after merge completion for observable '{}'. "
+                    "This indicates corrupted data or a bug in the merge logic.",
+                    rel.target_key,
+                    source_key,
+                )
+
+        # Merge threat intels (need to link to observables)
+        for ti in incoming_threat_intels.values():
+            existing_ti = self._threat_intels.get(ti.key)
+            before = _snapshot_threat_intel(existing_ti) if existing_ti else None
+            # Find the observable this TI belongs to
+            observable = self._observables.get(ti.observable_key)
+            if observable:
+                self.add_threat_intel(ti, observable)
+            if existing_ti:
+                after = _snapshot_threat_intel(existing_ti)
+                changed_fields = _diff_fields(before, after) if before else []
+                action = "merged" if changed_fields else "skipped"
+            else:
+                changed_fields = []
+                action = "created"
+            merge_summary.append(
+                {
+                    "object_type": "threat_intel",
+                    "object_key": ti.key,
+                    "action": action,
+                    "changed_fields": changed_fields,
+                }
+            )
+
+        # Merge checks
+        for check in incoming_checks.values():
+            existing_check = self._checks.get(check.key)
+            before = _snapshot_check(existing_check) if existing_check else None
+            self.add_check(check)
+            if existing_check:
+                after = _snapshot_check(existing_check)
+                changed_fields = _diff_fields(before, after) if before else []
+                action = "merged" if changed_fields else "skipped"
+            else:
+                changed_fields = []
+                action = "created"
+            merge_summary.append(
+                {
+                    "object_type": "check",
+                    "object_key": check.key,
+                    "action": action,
+                    "changed_fields": changed_fields,
+                }
+            )
+
+        # Merge enrichments
+        for enrichment in incoming_enrichments.values():
+            existing_enrichment = self._enrichments.get(enrichment.key)
+            before = _snapshot_enrichment(existing_enrichment) if existing_enrichment else None
+            self.add_enrichment(enrichment)
+            if existing_enrichment:
+                after = _snapshot_enrichment(existing_enrichment)
+                changed_fields = _diff_fields(before, after) if before else []
+                action = "merged" if changed_fields else "skipped"
+            else:
+                changed_fields = []
+                action = "created"
+            merge_summary.append(
+                {
+                    "object_type": "enrichment",
+                    "object_key": enrichment.key,
+                    "action": action,
+                    "changed_fields": changed_fields,
+                }
+            )
+
+        # Merge containers
+        for container in incoming_containers.values():
+            existing_container = self._containers.get(container.key)
+            before = _snapshot_container(existing_container) if existing_container else None
+            self.add_container(container)
+            if existing_container:
+                after = _snapshot_container(existing_container)
+                changed_fields = _diff_fields(before, after) if before else []
+                action = "merged" if changed_fields else "skipped"
+            else:
+                changed_fields = []
+                action = "created"
+            merge_summary.append(
+                {
+                    "object_type": "container",
+                    "object_key": container.key,
+                    "action": action,
+                    "changed_fields": changed_fields,
+                }
+            )
+
+        # Merge whitelists (other investigation overrides on identifier conflicts)
+        for entry in other.get_whitelists():
+            self.add_whitelist(entry.identifier, entry.name, entry.justification)
+
+        # Rebuild link index after merges
+        self._score_engine.rebuild_link_index()
+        self._refresh_check_links()
+
+        # Final score recalculation
+        self._score_engine.recalculate_all()
+
+        self._record_event(
+            event_type="INVESTIGATION_MERGED",
+            object_type="investigation",
+            object_key=self.investigation_id,
+            details={
+                "from_investigation_id": other.investigation_id,
+                "into_investigation_id": self.investigation_id,
+                "from_investigation_name": other.investigation_name,
+                "into_investigation_name": self.investigation_name,
+                "object_changes": merge_summary,
+            },
+        )
+
+    def _clone_for_merge(
+        self, other: Investigation
+    ) -> tuple[
+        dict[str, Observable],
+        dict[str, ThreatIntel],
+        dict[str, Check],
+        dict[str, Enrichment],
+        dict[str, Container],
+    ]:
+        """Clone incoming models while preserving shared object references."""
+        incoming_threat_intels = {key: ti.model_copy(deep=True) for key, ti in other._threat_intels.items()}
+        incoming_checks = {key: check.model_copy(deep=True) for key, check in other._checks.items()}
+        incoming_enrichments = {key: enrichment.model_copy(deep=True) for key, enrichment in other._enrichments.items()}
+
+        orphan_threat_intels: dict[str, ThreatIntel] = {}
+
+        def _copy_threat_intel(ti: ThreatIntel) -> ThreatIntel:
+            if ti.key in incoming_threat_intels:
+                return incoming_threat_intels[ti.key]
+            existing = orphan_threat_intels.get(ti.key)
+            if existing:
+                return existing
+            copied = ti.model_copy(deep=True)
+            orphan_threat_intels[ti.key] = copied
+            return copied
+
+        incoming_observables: dict[str, Observable] = {}
+        for obs in other._observables.values():
+            copied_obs = obs.model_copy(deep=True)
+            if obs.threat_intels:
+                copied_obs.threat_intels = [_copy_threat_intel(ti) for ti in obs.threat_intels]
+            incoming_observables[obs.key] = copied_obs
+
+        orphan_checks: dict[str, Check] = {}
+
+        def _copy_check(check: Check) -> Check:
+            if check.key in incoming_checks:
+                return incoming_checks[check.key]
+            existing = orphan_checks.get(check.key)
+            if existing:
+                return existing
+            copied = check.model_copy(deep=True)
+            orphan_checks[check.key] = copied
+            return copied
+
+        incoming_containers: dict[str, Container] = {}
+
+        def _copy_container(container: Container) -> Container:
+            existing = incoming_containers.get(container.key)
+            if existing:
+                return existing
+            copied = Container(
+                path=container.path,
+                description=container.description,
+                checks=[_copy_check(check) for check in container.checks],
+                sub_containers={},
+                key=container.key,
+            )
+            incoming_containers[container.key] = copied
+            for sub_key, sub in container.sub_containers.items():
+                copied.sub_containers[sub_key] = _copy_container(sub)
+            return copied
+
+        for container in other._containers.values():
+            _copy_container(container)
+
+        return (
+            incoming_observables,
+            incoming_threat_intels,
+            incoming_checks,
+            incoming_enrichments,
+            incoming_containers,
+        )