apsimo 1.4.4__tar.gz → 1.4.6__tar.gz

{apsimo-1.4.4 → apsimo-1.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsimo
-Version: 1.4.4
+Version: 1.4.6
 Summary: Persistent identity, memory and autonomy for AI agents
 License-Expression: MIT
 Requires-Python: >=3.11
@@ -28,7 +28,7 @@ Requires-Dist: pandas>=2.0; extra == "vectors"
 Requires-Dist: pyarrow>=15.0; extra == "vectors"
 Requires-Dist: lancedb>=0.10; extra == "vectors"
 Provides-Extra: hermes
-Requires-Dist: apsimo-hermes<2,>=1.4.4; extra == "hermes"
+Requires-Dist: apsimo-hermes<2,>=1.4.6; extra == "hermes"
 Provides-Extra: mcp
 Requires-Dist: mcp[cli]<2,>=1.0; extra == "mcp"
 Provides-Extra: lancedb

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/api/routers/host.py

@@ -2516,7 +2516,7 @@ async def context_assemble(
 
     # --- Memory: authorized candidates, one selection and one budget ---
     if _canonical_person_allowed and query_text:
-        from apsimo.intelligence.graph.recall import source_candidates
+        from apsimo.memory.recall import source_candidates
         beliefs, quotations, source_hits, semantic_media = [], [], [], []
         source_ledger = None
         if not _canonical_only and _graph is not None:
@@ -2581,7 +2581,7 @@ async def context_assemble(
                     contact_tz, body.context.timezone or ("UTC" if _canonical_only else None)))
             if source_ledger is not None:
                 from apsimo.beliefs.source_projection import SourceClaimProjection
-                from apsimo.intelligence.graph.selection import current_work_query
+                from apsimo.memory.selection import current_work_query
                 beliefs, quotations = SourceClaimProjection(source_ledger).prepare_context(
                     beliefs, source_hits, contact_id=body.context.contact_id,
                     session_id=body.context.session_id, time_query=time_query,
@@ -2598,7 +2598,7 @@ async def context_assemble(
                     # The projected view preserves envelope and current-source
                     # checks. A fact needs query overlap before any fail-open
                     # reranker path; confidence alone never makes it relevant.
-                    from apsimo.intelligence.graph.recall import contact_fact_candidates
+                    from apsimo.memory.recall import contact_fact_candidates
                     fact_result = _tom_context_facts.list_facts(
                         contact_id=body.context.contact_id, limit=512)
                     facts = fact_result if isinstance(fact_result, list) else fact_result.get('facts', [])
@@ -2623,7 +2623,7 @@ async def context_assemble(
                 from apsimo.turns.source_annotations import current_candidates
                 retained = current_candidates(source_ledger, selected, **annotation_scope)
                 if len(retained) != len(selected):
-                    from apsimo.intelligence.graph.recall import pack_memory_context
+                    from apsimo.memory.recall import pack_memory_context
                     selected, body_text = pack_memory_context(retained, limit=5,
                         max_chars=max(0, min(max_chars, 24000)))
             if body_text:
@@ -11284,7 +11284,7 @@ async def enriched_context(
             and (_p8_runtime is None or _enriched_p8_viewer is not None):
         async def _shared_facts():
             try:
-                from apsimo.intelligence.graph.recall import contact_fact_candidates, pack_memory_context
+                from apsimo.memory.recall import contact_fact_candidates, pack_memory_context
                 from apsimo.turns.source_annotations import expand, current_candidates
                 store = _p8_runtime.facts_store if _p8_runtime is not None else _facts_store
                 view = (_p8_runtime.projected_facts_view(_enriched_p8_viewer,
@@ -11725,8 +11725,8 @@ def _memory_context_selector():
     """Keep one selector per active reranker, also usable without graph storage."""
     global _context_recall_selector
     if _context_recall_selector is None or _context_recall_selector[0] is not _reranker:
-        from apsimo.intelligence.graph.selection import RecallSelector
-        from apsimo.intelligence.graph.recall import provider_calibration_metadata
+        from apsimo.memory.selection import RecallSelector
+        from apsimo.memory.recall import provider_calibration_metadata
         provider = _reranker
         selector = RecallSelector(
             provider.rerank if provider is not None else None,

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/api/schemas/host.py

@@ -102,7 +102,7 @@ class MemoryReadRequest(BaseModel):
     source_id: Optional[str] = Field(default=None, min_length=1, max_length=256)
     source_version: Optional[str] = Field(default=None, pattern='^[0-9a-f]{64}$')
     session_id: Optional[str] = Field(default=None, min_length=1, max_length=256)
-    source_view: Literal['source', 'assertions', 'image', 'document', 'video'] = 'source'
+    source_view: Literal['source', 'assertions', 'observations', 'image', 'document', 'video'] = 'source'
     asset_hash: Optional[str] = Field(default=None, pattern='^[0-9a-f]{64}$')
     page: Optional[int] = Field(default=None, ge=1, strict=True)
     requested_ms: Optional[int] = Field(default=None, ge=0, le=30000, strict=True)

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/beliefs/source_projection.py

@@ -470,7 +470,7 @@ class SourceClaimProjection:
         Unknown, corrected, changed, multiple-input and cross-scope provenance
         remains recallable. This transient hint never changes stored history.
         """
-        from apsimo.intelligence.graph.selection import current_work_query
+        from apsimo.memory.selection import current_work_query
         from apsimo.turns.idempotency import canonical_turn_digest, source_message_hash
         if message.get('role') != 'assistant' or source['scope'] != 'person':
             return False
@@ -521,7 +521,7 @@ class SourceClaimProjection:
         """
         from apsimo.turns.idempotency import source_message_hash
         from apsimo.turns.audio import source_text
-        from apsimo.intelligence.graph.recall import source_candidates
+        from apsimo.memory.recall import source_candidates
         turn_ids = list(dict.fromkeys(
             [row["turn_id"] for row in source_hits] + [str(row["source_uri"])[5:] for row in beliefs
              if str(row.get("source_uri") or "").startswith("turn:")]))

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/channels/phone_gateways.py

@@ -1,7 +1,7 @@
 """Shared phone gateway resolution.
 
 Replaces the three hardcoded _PHONE_GATEWAYS tuples scattered across
-contacts/store.py, identity/resolver.py, and contacts/world_bridge.py.
+contacts/store.py and identity/resolver.py.
 
 Reads from the channel store when available; falls back to a built-in
 set so the system works before any channels are registered.

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/cli.py

@@ -43,6 +43,7 @@ def main() -> None:
     init_p.add_argument("--quiet-hours", help="Optional local follow-up quiet window, HH:MM-HH:MM; grants no outreach permission")
     init_p.add_argument("--whatsapp-read-receipts", choices=["on", "off"], help="Set this Hermes profile's read receipts for accepted WhatsApp messages; omission preserves its setting")
     init_p.add_argument("--preferences-only", action="store_true", help="Update only an existing Hermes config preference; skip instance and model setup")
+    init_p.add_argument("--skills-only", action="store_true", help="Install or explicitly refresh owned bundled skills in one Hermes profile; no instance or model setup")
     init_p.add_argument("--preview", action="store_true", help="With --preferences-only, show changed preference paths without writing")
     init_p.add_argument("--model-url", help="One local OpenAI-compatible API root")
     init_p.add_argument("--model", help="Model identifier at that endpoint")
@@ -313,7 +314,7 @@ def main() -> None:
         code = run_init(root_dir=args.dir, args=args)
         if code != 0:
             sys.exit(code)
-        if args.preferences_only:
+        if args.preferences_only or args.skills_only:
             return
 
         # Initialize Apsimo identity if not already done

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/contacts/importer.py

@@ -132,11 +132,9 @@ class SQLiteContactImporter(ContactImporter):
         self,
         store: SQLiteContactStore,
         config: Optional[ContactsConfig] = None,
-        bridge = None,  # Optional[WorldModelContactBridge]
     ) -> None:
         self._store = store
         self._config = config or ContactsConfig()
-        self._bridge = bridge
 
     async def import_raw(self, records: List[RawContactRecord], source: str) -> BatchImportResult:
         result = BatchImportResult(source=source, total=len(records))
@@ -186,9 +184,6 @@ class SQLiteContactImporter(ContactImporter):
                         contact_id=existing_id,
                         merged_into_id=existing_id,
                     ))
-                    # Absorb any discovered contacts with overlapping handles
-                    if self._bridge:
-                        await self._absorb_discovered_for(existing_id, norm_phones, norm_emails)
                 elif candidates and candidates[0][0] >= proposal_threshold:
                     # Below auto-merge but above proposal threshold — create and propose
                     contact = await self._store.create(
@@ -209,8 +204,6 @@ class SQLiteContactImporter(ContactImporter):
                         outcome=ImportOutcome.CREATED,
                         contact_id=contact.contact_id,
                     ))
-                    if self._bridge:
-                        await self._absorb_discovered_for(contact.contact_id, norm_phones, norm_emails)
                 else:
                     # No match — create new contact
                     contact = await self._store.create(
@@ -230,8 +223,6 @@ class SQLiteContactImporter(ContactImporter):
                         outcome=ImportOutcome.CREATED,
                         contact_id=contact.contact_id,
                     ))
-                    if self._bridge:
-                        await self._absorb_discovered_for(contact.contact_id, norm_phones, norm_emails)
             except Exception as exc:
                 logger.warning(
                     "Failed to import record (name_hash=%s): %s",
@@ -245,26 +236,6 @@ class SQLiteContactImporter(ContactImporter):
                 ))
         return result
 
-    async def _absorb_discovered_for(
-        self,
-        curated_contact_id: str,
-        norm_phones: List[str],
-        norm_emails: List[str],
-    ) -> None:
-        """Find discovered contacts with overlapping handles and absorb them."""
-        if not self._bridge:
-            return
-        for phone in norm_phones:
-            discovered = await self._store.find_discovered_by_handle("imessage", phone)
-            if discovered:
-                await self._bridge.absorb_discovered_contact(curated_contact_id, discovered)
-                return
-        for email in norm_emails:
-            discovered = await self._store.find_discovered_by_handle("email", email)
-            if discovered:
-                await self._bridge.absorb_discovered_contact(curated_contact_id, discovered)
-                return
-
     async def import_from_macos_contacts(self) -> BatchImportResult:
         from .importers.macos_contacts import MacOSContactsImporter
         importer = MacOSContactsImporter(normalize_phones=self._config.import_cfg.normalize_phones)

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/contacts/store.py

@@ -258,10 +258,9 @@ class ContactStore(ABC):
 class SQLiteContactStore(ContactStore):
     """SQLite-backed implementation of ContactStore."""
 
-    def __init__(self, config: Optional[ContactsConfig] = None, graph=None) -> None:
+    def __init__(self, config: Optional[ContactsConfig] = None) -> None:
         self._config = config or ContactsConfig()
         self._db: Optional[aiosqlite.Connection] = None
-        self._graph = graph  # Optional ColonyGraph for score sync
 
     async def connect(self) -> None:
         path = self._config.sqlite_path
@@ -529,28 +528,6 @@ class SQLiteContactStore(ContactStore):
             return None
         return Contact.from_row(dict(row))
 
-    async def find_discovered_by_handle(
-        self, gateway: str, address: str
-    ) -> Optional[Contact]:
-        """Find a discovered (world_model) contact that owns a given handle."""
-        db = self._require_db()
-        norm = _normalize_email(address) if gateway == "email" else _normalize_phone(address) if gateway in ("imessage", "sms", "signal") else address
-        async with db.execute(
-            """
-            SELECT c.* FROM contacts c
-            JOIN contact_handles h ON h.contact_id = c.contact_id
-            WHERE c.import_source = 'world_model'
-              AND c.deleted_at IS NULL
-              AND h.gateway = ? AND h.address = ?
-            LIMIT 1
-            """,
-            (gateway, norm),
-        ) as cur:
-            row = await cur.fetchone()
-        if row is None:
-            return None
-        return Contact.from_row(dict(row))
-
     # ── Write ops ─────────────────────────────────────────────────────────────
 
     async def create(
@@ -1121,16 +1098,6 @@ class SQLiteContactStore(ContactStore):
             (score, _now_iso(), contact_id),
         )
         await db.commit()
-        # Sync to graph if linked
-        if self._graph is not None:
-            try:
-                contact = await self.get(contact_id)
-                if contact and contact.person_node_id:
-                    await self._graph.update_person(
-                        contact.person_node_id, score=score,
-                    )
-            except Exception as exc:
-                logger.debug("Score sync to graph failed for %s: %s", contact_id, exc)
 
     async def update_interaction_allowed(
         self, contact_id: str, allowed: bool, performed_by: str = "operator"

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/intelligence/graph/client.py

@@ -1260,7 +1260,7 @@ class ColonyGraph:
                             memories.append(mem)
 
                 if hybrid:
-                    from .recall import fuse_candidates
+                    from apsimo.memory.recall import fuse_candidates
                     candidate_limit = min(max(limit * 5, limit), max(100, limit))
                     lexical = await self._recall_lexical(
                         query, candidate_limit, min_strength, min_confidence,
@@ -1394,7 +1394,7 @@ class ColonyGraph:
         content reaches Python/reranking. A missing/populating index degrades
         to the existing vector/keyword path.
         """
-        from .recall import FULLTEXT_INDEX, lexical_query
+        from .queries import FULLTEXT_INDEX, lexical_query
         search_text = lexical_query(query)
         if not search_text:
             return []
@@ -1468,7 +1468,7 @@ class ColonyGraph:
         self, query, memories, limit, *, strength_ranking=False,
     ):
         # The same selector is used for mixed source/belief turn context.
-        from .selection import RecallSelector
+        from apsimo.memory.selection import RecallSelector
         selector = getattr(self, "_recall_selector", None)
         if selector is None:
             selector = self._recall_selector = RecallSelector(

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/intelligence/graph/queries.py

@@ -7,6 +7,16 @@ and makes it easy to test / review / optimise in one place.
 Parameters are referenced with ``$param`` syntax for Neo4j driver binding.
 """
 
+FULLTEXT_INDEX = "memory_content_fulltext"
+
+
+def lexical_query(text: str, max_terms: int = 16) -> str:
+    """Literal words/identifiers, not caller-supplied Lucene operators."""
+    from apsimo.memory.recall import lexical_terms
+
+    return " OR ".join(f'"{word}"' for word in lexical_terms(text, max_terms))
+
+
 # ──────────────────────────────────────────────────────────────────────
 # Memory operations
 # ──────────────────────────────────────────────────────────────────────

apsimo-1.4.6/apsimo/memory/__init__.py

@@ -0,0 +1 @@
+"""Shared evidence selection and rendering for Apsimo memory."""

{apsimo-1.4.4/apsimo/intelligence/graph → apsimo-1.4.6/apsimo/memory}/recall.py

@@ -1,4 +1,4 @@
-"""Small retrieval helpers shared by the existing graph/vector recall path."""
+"""Shared source candidates, rank fusion and bounded memory rendering."""
 from __future__ import annotations
 
 import re
@@ -7,7 +7,6 @@ import json
 import os
 from typing import Any
 
-FULLTEXT_INDEX = "memory_content_fulltext"
 _WORDS = re.compile(r"[^\W_]+(?:[-.][^\W_]+)*", re.UNICODE)
 _STOP = frozenset("a an and are as at be by do does for from how i in is it me of on or that the this to was what when where which who with you".split())
 
@@ -209,11 +208,6 @@ def lexical_terms(text: str, max_terms: int = 16) -> list[str]:
     return list(words)[:max_terms]
 
 
-def lexical_query(text: str, max_terms: int = 16) -> str:
-    """Literal words/identifiers, not caller-supplied Lucene operators."""
-    return " OR ".join(f'"{word}"' for word in lexical_terms(text, max_terms))
-
-
 def contact_fact_candidates(query: str, facts: list[dict[str, Any]], *, limit: int = 25) -> list[dict[str, Any]]:
     """Lexical candidates from an authorized, current source-linked fact view.
 

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/qualification/memory_cases.py

@@ -13,7 +13,7 @@ from .records import CaseSpec
 
 def _recollect(projection, query, *, contact, session, now, max_chars):
     from apsimo.beliefs.source_time import interpret_time_query
-    from apsimo.intelligence.graph.recall import pack_memory_context
+    from apsimo.memory.recall import pack_memory_context
     from apsimo.turns.source_annotations import expand, current_candidates
     ledger = projection.ledger
     hits = ledger.search_sources(query, contact_id=contact, session_id=session, limit=10)

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/server.py

@@ -1433,6 +1433,19 @@ def _scheduler_health_check(autonomy_loop) -> dict:
             "autonomy_running": bool(getattr(autonomy_loop, "_running", False))}
 
 
+async def _initialize_contacts_store():
+    """Open the canonical contact store without graph backfill or pruning."""
+    from apsimo.contacts.config import ContactsConfig
+    from apsimo.contacts.store import SQLiteContactStore
+
+    config = ContactsConfig.from_env()
+    store = SQLiteContactStore(config=config)
+    await store.connect()
+    set_contacts_store(store)
+    logger.info("ContactsStore initialized (path=%s)", config.sqlite_path)
+    return store
+
+
 @asynccontextmanager
 async def lifespan(app: FastAPI):
     """Initialize subsystems on startup, tear down on shutdown."""
@@ -1861,7 +1874,7 @@ async def lifespan(app: FastAPI):
             # set_embed_fn wiring above). Registration alone changes
             # nothing: use is gated by COLONY_RECALL_RERANK (default off).
             if graph is not None and hasattr(graph, "set_rerank_fn"):
-                from apsimo.intelligence.graph.recall import provider_calibration_metadata
+                from apsimo.memory.recall import provider_calibration_metadata
                 def recall_calibration_metadata():
                     return provider_calibration_metadata(reranker_provider)
                 graph.set_rerank_fn(
@@ -2526,36 +2539,10 @@ async def lifespan(app: FastAPI):
     # --- 8. Contacts ---
     contacts_store = None
     try:
-        from apsimo.contacts.config import ContactsConfig
-        from apsimo.contacts.store import SQLiteContactStore
-        contacts_config = ContactsConfig.from_env()
-        contacts_store = SQLiteContactStore(config=contacts_config, graph=graph)
-        await contacts_store.connect()
-        set_contacts_store(contacts_store)
-        logger.info("ContactsStore initialized (path=%s)", contacts_config.sqlite_path)
+        contacts_store = await _initialize_contacts_store()
     except Exception as exc:
         logger.warning("ContactsStore init failed: %s", exc)
 
-    # --- 8b. Contact-World Model Bridge ---
-    if contacts_store is not None and graph is not None:
-        try:
-            from apsimo.contacts.world_bridge import WorldModelContactBridge
-            bridge = WorldModelContactBridge(graph=graph, store=contacts_store)
-            # Backfill all substantive Person nodes on startup
-            backfill_stats = await bridge.backfill_all_people()
-            logger.info(
-                "WorldModelContactBridge initialized — backfill created=%d linked=%d skipped=%d",
-                backfill_stats["created"], backfill_stats["linked"], backfill_stats["skipped"],
-            )
-            # Prune shadow contacts whose Person node no longer exists
-            pruned = await bridge.prune_orphaned_shadows()
-            if pruned:
-                logger.info("Pruned %d orphaned shadow contacts", pruned)
-        except Exception as exc:
-            logger.warning("WorldModelContactBridge init failed: %s", exc)
-    else:
-        logger.info("WorldModelContactBridge skipped — contacts_store or graph unavailable")
-
     # --- 8d. Relationship profiler (standing + psyche + approach briefs) ---
     if contacts_store is not None:
         try:

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/setup.py

@@ -1946,7 +1946,7 @@ def run_init(root_dir: str | None = None, args=None) -> int:
         root_dir: Root directory for config files
         args: Parsed argparse Namespace for non-interactive mode
     """
-    if (getattr(args, 'owner_handle', None) or getattr(args, 'preferences_only', False) or getattr(args, 'preview', False)
+    if (getattr(args, 'owner_handle', None) or getattr(args, 'preferences_only', False) or getattr(args, 'skills_only', False) or getattr(args, 'preview', False)
             or getattr(args, 'whatsapp_read_receipts', None) is not None):
         if (getattr(args, 'no_harness', False) or getattr(args, 'mcp_harnesses', None)
                 or getattr(args, 'host_framework', None) not in (None, 'hermes')):

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/setup_hermes.py

@@ -569,14 +569,25 @@ def run(root_dir=None, args=None):
     try:
         receipt_choice = getattr(args, 'whatsapp_read_receipts', None)
         preferences_only = bool(getattr(args, 'preferences_only', False))
+        skills_only = bool(getattr(args, 'skills_only', False))
         preview = bool(getattr(args, 'preview', False))
-        if preferences_only:
+        if preferences_only or skills_only:
             home = setup._resolve_hermes_home(getattr(args, 'hermes_home', None))
             selected_python = None
         else:
             home, selected_python = _select_home(args, ask)
         if preview and not preferences_only:
             raise ValueError('--preview requires --preferences-only')
+        if skills_only:
+            if root_dir or receipt_choice or any(getattr(args, name, None) for name in (
+                    'preferences_only', 'preview', 'start', 'refresh_adapter', 'replace_memory_provider',
+                    'local_work', 'native_goals', 'native_reviews', 'model_url', 'model', 'agent_name',
+                    'agent_values', 'timezone', 'quiet_hours', 'contact_name', 'owner_handle', 'encrypt',
+                    'passphrase', 'claim_genesis', 'mcp_harnesses', 'no_harness')):
+                raise ValueError('--skills-only cannot be combined with instance or preference changes')
+            from .setup_skills import prepare, install
+            install(prepare(home, _adapter_resources(getattr(args, 'adapter_wheel', None)), refresh=True))
+            return 0
         if preferences_only:
             if receipt_choice is None:
                 raise ValueError('--preferences-only requires --whatsapp-read-receipts on or off')
@@ -673,6 +684,8 @@ def run(root_dir=None, args=None):
         resources = _adapter_resources(getattr(args, 'adapter_wheel', None))
         _preflight_outbox(home, resources)
         binding = _adapter_binding(python, resources)
+        from .setup_skills import prepare as prepare_skills, install as install_skills
+        skill_updates = prepare_skills(home, resources)
         owner_name = ask('Your name', getattr(args, 'contact_name', None) or os.environ.get('USER', 'Owner'), True)
         owner_handles, owner_platforms = _owner_handles(args, ask, noninteractive)
         agent_name = ask('Agent name', getattr(args, 'agent_name', None) or 'Assistant', True)
@@ -858,6 +871,7 @@ def run(root_dir=None, args=None):
                 guiding = ('Guiding values: ' + ', '.join(agent_preferences['values']) + '.\n'
                            if agent_preferences['values'] else '')
                 create(home/'SOUL.md', f'# {agent_name}\n\nYou are {agent_name}, the personal assistant of {owner_name}.\n{guiding}Use retained evidence with its provenance; ask about uncertainty.\nYour opinions are revisable interpretations; distinguish them from facts and permissions.\nOwner consent is required for consequential external actions; an existing task-scoped consent covers only its stated scope.\n')
+            install_skills(skill_updates)
         except Exception:
             # Undo only this installation's exact bytes. Concurrent edits stay
             # intact, with original files still retained in the private state.

apsimo-1.4.6/apsimo/setup_skills.py

@@ -0,0 +1,90 @@
+"""Install owned bundled skills into one native Hermes catalog."""
+from __future__ import annotations
+
+import hashlib
+import json
+from pathlib import Path
+import re
+
+
+SKILL_NAME = 'apsimo-deep-research'
+BUNDLE_PREFIX = 'apsimo_hermes/bundled_skills/'
+SKILL_RESOURCE = f'{BUNDLE_PREFIX}{SKILL_NAME}/SKILL.md'
+
+
+def _read_owned_path(path):
+    for parent in (path, *path.parents):
+        if parent.is_symlink():
+            raise ValueError('Bundled skill destination is symlinked; existing files were preserved')
+    return path.read_bytes() if path.exists() else None
+
+
+def prepare(home, resources, *, refresh=False):
+    """Validate all packaged skill preimages before any setup writes/probe."""
+    updates = []
+    for path, content in sorted(resources.items()):
+        if not path.startswith(BUNDLE_PREFIX) or not path.endswith('/SKILL.md'):
+            continue
+        name = path[len(BUNDLE_PREFIX):-len('/SKILL.md')]
+        if not re.fullmatch(r'apsimo-[a-z0-9-]{1,56}', name):
+            raise ValueError('Bundled skill must have a canonical apsimo- name')
+        updates.extend(_prepare_skill(home, name, content, refresh=refresh))
+    if not updates:
+        raise ValueError('Selected adapter has no bundled skills')
+    return updates
+
+
+def _prepare_skill(home, name, content, *, refresh):
+    if not content:
+        raise ValueError('Selected adapter has an empty bundled skill')
+    directory = Path(home)/'skills'/name
+    skill, marker = directory/'SKILL.md', directory/'.apsimo-owned.json'
+    previous, recorded = _read_owned_path(skill), _read_owned_path(marker)
+    digest = hashlib.sha256(content).hexdigest()
+    if recorded is None:
+        if directory.exists():
+            raise ValueError('Unowned bundled skill destination was preserved; choose another profile or move your copy')
+    else:
+        try:
+            record = json.loads(recorded)
+            owned = (record['owner'] == 'apsimo-hermes' and record['version'] == 1
+                     and previous is not None
+                     and record['sha256'] == hashlib.sha256(previous).hexdigest())
+        except (ValueError, KeyError, TypeError):
+            owned = False
+        if not owned:
+            raise ValueError('Locally modified bundled skill was preserved; keep your copy or reconcile it before refreshing')
+        if previous != content and not refresh:
+            raise ValueError('Bundled skill update requires explicit apsimo init --skills-only')
+    after = (json.dumps({'owner': 'apsimo-hermes', 'version': 1, 'sha256': digest},
+                        sort_keys=True, indent=2)+'\n').encode()
+    return [(skill, previous, content), (marker, recorded, after)]
+
+
+def install(updates):
+    """Replace only previously verified owned bytes; retain local edits on conflict."""
+    from .setup import _atomic_hermes_config_write
+    for path, before, _ in updates:
+        if _read_owned_path(path) != before:
+            raise ValueError('Bundled skill changed during installation; current files were preserved')
+    completed = []
+    try:
+        for path, before, after in updates:
+            if before != after:
+                path.parent.mkdir(parents=True, exist_ok=True, mode=0o700)
+                _atomic_hermes_config_write(path, before, after)
+                completed.append((path, before, after))
+    except Exception:
+        for path, before, after in reversed(completed):
+            if _read_owned_path(path) == after:
+                if before is None:
+                    path.unlink()
+                else:
+                    _atomic_hermes_config_write(path, after, before)
+        # A failed first installation leaves no false ownership claim.
+        for directory in {path.parent for path, _, _ in updates}:
+            if directory.is_dir() and not any(directory.iterdir()):
+                directory.rmdir()
+        raise
+    names = sorted({path.parent.name for path, _, _ in updates})
+    print('Bundled skills available: '+', '.join(names)+'. With this Apsimo adapter version active, ongoing conversations refresh skill discovery on their next request.')

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/turns/idempotency.py

@@ -150,6 +150,11 @@ class TurnIdempotencyLedger:
                         )
                     )
                 """)
+                conn.execute("""
+                    CREATE INDEX IF NOT EXISTS source_observation_origin ON turn_sources
+                    (contact_id, json_extract(messages_json, '$[0]._observation_sources[0].source_id'), turn_id)
+                    WHERE json_extract(messages_json, '$[0]._native_tool_observation') = 'native-tool-observation-v1'
+                """)
                 conn.execute("""
                     CREATE VIRTUAL TABLE IF NOT EXISTS turn_source_search USING fts5(
                         turn_id UNINDEXED, role UNINDEXED, content,

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/turns/source_annotations.py

@@ -173,9 +173,11 @@ def expand(ledger, candidates, *, contact_id, session_id, covered=()):
                 own_annotation = conn.execute('SELECT * FROM source_annotations WHERE annotation_source_id=?',
                                               (identifier,)).fetchone()
                 for message in row['messages']:
-                    if (message.get('role') == 'assistant'
-                            and source_message_hash(row['session_id'], message) in selected_hashes):
-                        for ref in message.get('_supplied_sources', []):
+                    dependencies = (message.get('_supplied_sources', []) if message.get('role') == 'assistant'
+                        else message.get('_observation_sources', []) if message.get('role') == 'tool'
+                        and message.get('_native_tool_observation') == 'native-tool-observation-v1' else [])
+                    if source_message_hash(row['session_id'], message) in selected_hashes:
+                        for ref in dependencies:
                             parent = source(ref['source_id'])
                             if parent and canonical_turn_digest(parent['messages']) == ref['source_version']:
                                 # Dedicated annotations have exact target message

{apsimo-1.4.4 → apsimo-1.4.6}/apsimo/turns/source_attribution.py

@@ -71,7 +71,9 @@ def correct(ledger, *, operation_id, performed_by, old_contact_id, contact_id,
                 if row['turn_id'] in selected or row['turn_id'] in descendants:
                     continue
                 if any(ref.get('source_id') in pending for message in json.loads(row['messages_json'])
-                       for ref in message.get('_supplied_sources', [])):
+                       for ref in (message.get('_supplied_sources', []) if message.get('role') == 'assistant'
+                           else message.get('_observation_sources', []) if message.get('role') == 'tool'
+                           and message.get('_native_tool_observation') == 'native-tool-observation-v1' else [])):
                     found.add(row['turn_id'])
             descendants.update(found)
             pending = found