fix(retrieval): fail open on registry resolution errors

DEV-LEDGER.md

@@ -6,17 +6,17 @@
 
 ## Orientation
 
-- **live_sha** (Dalidou `/health` build_sha): `2b86543` (verified 2026-04-23T15:20:53Z post-R14 deploy; status=ok)
-- **last_updated**: 2026-04-23 by Claude (R14 squash-merged + deployed; Orientation refreshed)
-- **main_tip**: `2b86543`
-- **test_count**: 548 (547 + 1 R14 regression test)
-- **harness**: `17/18 PASS` on live Dalidou (p04-constraints expects "Zerodur" — known content gap, not regression; consistent since 2026-04-19)
+- **live_sha** (Dalidou `/health` build_sha): `f44a211` (verified 2026-04-24T14:48:44Z post audit-improvements deploy; status=ok)
+- **last_updated**: 2026-04-24 by Codex (retrieval boundary deployed; project_id metadata branch started)
+- **main_tip**: `f44a211`
+- **test_count**: 567 on `codex/project-id-metadata-retrieval` (deployed main baseline: 553)
+- **harness**: `19/20 PASS` on live Dalidou, 0 blocking failures, 1 known content gap (`p04-constraints`)
 - **vectors**: 33,253
-- **active_memories**: 784 (up from 84 pre-density-batch — density gate CRUSHED vs V1-A's 100-target)
-- **candidate_memories**: 2 (triage queue drained)
-- **interactions**: 500+ (limit=2000 query returned 500 — density batch has been running; actual may be higher, confirm via /stats next update)
+- **active_memories**: 290 (`/admin/dashboard` 2026-04-24; note integrity panel reports a separate active_memory_count=951 and needs reconciliation)
+- **candidate_memories**: 0 (triage queue drained)
+- **interactions**: 951 (`/admin/dashboard` 2026-04-24)
 - **registered_projects**: atocore, p04-gigabit, p05-interferometer, p06-polisher, atomizer-v2, abb-space (aliased p08)
-- **project_state_entries**: 63 (atocore alone; full cross-project count not re-sampled this update)
+- **project_state_entries**: 128 across registered projects (`/admin/dashboard` 2026-04-24)
 - **entities**: 66 (up from 35 — V1-0 backfill + ongoing work; 0 open conflicts)
 - **off_host_backup**: `papa@192.168.86.39:/home/papa/atocore-backups/` via cron, verified
 - **nightly_pipeline**: backup → cleanup → rsync → OpenClaw import → vault refresh → extract → auto-triage → **auto-promote/expire (NEW)** → weekly synth/lint Sundays → **retrieval harness (NEW)** → **pipeline summary (NEW)**
@@ -170,6 +170,16 @@ One branch `codex/extractor-eval-loop` for Day 1-5, a second `codex/retrieval-ha
 
 ## Session Log
 
+- **2026-04-24 Codex (retrieval boundary deployed + project_id metadata tranche)** Merged `codex/audit-improvements-foundation` to `main` as `f44a211` and pushed to Dalidou Gitea. Took pre-deploy runtime backup `/srv/storage/atocore/backups/snapshots/20260424T144810Z` (DB + registry, no Chroma). Deployed via `papa@dalidou` canonical `deploy/dalidou/deploy.sh`; live `/health` reports build_sha `f44a2114970008a7eec4e7fc2860c8f072914e38`, build_time `2026-04-24T14:48:44Z`, status ok. Post-deploy retrieval harness: 20 fixtures, 19 pass, 0 blocking failures, 1 known issue (`p04-constraints`). The former blocker `p05-broad-status-no-atomizer` now passes. Manual p05 `context-build "current status"` spot check shows no p04/Atomizer source bleed in retrieved chunks. Started follow-up branch `codex/project-id-metadata-retrieval`: registered-project ingestion now writes explicit `project_id` into DB chunk metadata and Chroma vector metadata; retrieval prefers exact `project_id` when present and keeps path/tag matching as legacy fallback; added dry-run-by-default `scripts/backfill_chunk_project_ids.py` to backfill SQLite + Chroma metadata; added tests for project-id ingestion, registered refresh propagation, exact project-id retrieval, and collision fallback. Verified targeted suite (`test_ingestion.py`, `test_project_registry.py`, `test_retrieval.py`): 36 passed. Verified full suite: 556 passed in 72.44s. Branch not merged or deployed yet.
+
+- **2026-04-24 Codex (project_id audit response)** Applied independent-audit fixes on `codex/project-id-metadata-retrieval`. Closed the nightly `/ingest/sources` clobber risk by adding registry-level `derive_project_id_for_path()` and making unscoped `ingest_file()` derive ownership from registered ingest roots when possible; `refresh_registered_project()` still passes the canonical project id directly. Changed retrieval so empty `project_id` falls through to legacy path/tag ownership instead of short-circuiting as unowned. Hardened `scripts/backfill_chunk_project_ids.py`: `--apply` now requires `--chroma-snapshot-confirmed`, runs Chroma metadata updates before SQLite writes, batches updates, skips/report missing vectors, skips/report malformed metadata, reports already-tagged rows, and turns missing ingestion tables into a JSON `db_warning` instead of a traceback. Added tests for auto-derive ingestion, empty-project fallback, ingest-root overlap rejection, and backfill dry-run/apply/snapshot/missing-vector/malformed cases. Verified targeted suite (`test_backfill_chunk_project_ids.py`, `test_ingestion.py`, `test_project_registry.py`, `test_retrieval.py`): 45 passed. Verified full suite: 565 passed in 73.16s. Local dry-run on empty/default data returns 0 updates with `db_warning` rather than crashing. Branch still not merged/deployed.
+
+- **2026-04-24 Codex (project_id final hardening before merge)** Applied the final independent-review P2s on `codex/project-id-metadata-retrieval`: `ingest_file()` still fails open when project-id derivation fails, but now emits `project_id_derivation_failed` with file path and error; retrieval now catches registry failures both at project-scope resolution and the soft project-match boost path, logs warnings, and serves unscoped rather than raising. Added regression tests for both fail-open paths. Verified targeted suite (`test_ingestion.py`, `test_retrieval.py`, `test_backfill_chunk_project_ids.py`, `test_project_registry.py`): 47 passed. Verified full suite: 567 passed in 79.66s. Branch still not merged/deployed.
+
+- **2026-04-24 Codex (audit improvements foundation)** Started implementation of the audit recommendations on branch `codex/audit-improvements-foundation` from `origin/main@c53e61e`. First tranche: registry-aware project-scoped retrieval filtering (`ATOCORE_RANK_PROJECT_SCOPE_FILTER`, widened candidate pull before filtering), eval harness known-issue lane, two p05 project-bleed fixtures, `scripts/live_status.py`, README/current-state/master-plan status refresh. Verified `pytest -q`: 550 passed in 67.11s. Live retrieval harness against undeployed production: 20 fixtures, 18 pass, 1 known issue (`p04-constraints` Zerodur/1.2 content gap), 1 blocking guard (`p05-broad-status-no-atomizer`) still failing because production has not yet deployed the retrieval filter and currently pulls `P04-GigaBIT-M1-KB-design` into broad p05 status context. Live dashboard refresh: health ok, build `2b86543`, docs 1748, chunks/vectors 33253, interactions 948, active memories 289, candidates 0, project_state total 128. Noted count discrepancy: dashboard memories.active=289 while integrity active_memory_count=951; schedule reconciliation in a follow-up.
+
+- **2026-04-24 Codex (independent-audit hardening)** Applied the Opus independent audit's fast follow-ups before merge/deploy. Closed the two P1s by making project-scope ownership path/tag-based only, adding path-segment/tag-exact matching to avoid short-alias substring collisions, and keeping title/heading text out of provenance decisions. Added regression tests for title poisoning, substring collision, and unknown-project fallback. Added retrieval log fields `raw_results_count`, `post_filter_count`, `post_filter_dropped`, and `underfilled`. Added retrieval-eval run metadata (`generated_at`, `base_url`, `/health`) and `live_status.py` auth-token/status support. README now documents the ranking knobs and clarifies that the hard scope filter and soft project match boost are separate controls. Verified `pytest -q`: 553 passed in 66.07s. Live production remains expected-predeploy: 20 fixtures, 18 pass, 1 known content gap, 1 blocking p05 bleed guard. Latest live dashboard: build `2b86543`, docs 1748, chunks/vectors 33253, interactions 950, active memories 290, candidates 0, project_state total 128.
+
 - **2026-04-23 Codex + Claude (R14 closed)** Codex reviewed `claude/r14-promote-400` at `3888db9`, no findings: "The route change is narrowly scoped: `promote_entity()` still returns False for not-found/not-candidate cases, so the existing 404 behavior remains intact, while caller-fixable validation failures now surface as 400." Ran `pytest tests/test_v1_0_write_invariants.py -q` from an isolated worktree: 15 passed in 1.91s. Claude squash-merged to main as `0989fed`, followed by ledger close-out `2b86543`, then deployed via canonical script. Dalidou `/health` reports build_sha=`2b86543e6ad26011b39a44509cc8df3809725171`, build_time `2026-04-23T15:20:53Z`, status=ok. R14 closed. Orientation refreshed earlier this session also reflected the V1-A gate status: **density gate CLEARED** (784 active memories vs 100 target — density batch-extract ran between 2026-04-22 and 2026-04-23 and more than crushed the gate), **soak gate at day 5 of ~7** (F4 first run 2026-04-19; nightly clean 2026-04-19 through 2026-04-23; only chronic failure is the known p04-constraints "Zerodur" content gap). V1-A branches from a clean V1-0 baseline as soon as the soak is called done.
 
 - **2026-04-22 Codex + Antoine (V1-0 closed)** Codex approved `f16cd52` after re-running both original probes (legacy-candidate promote + supersede hook — both correct) and the three targeted regression suites (`test_v1_0_write_invariants.py`, `test_engineering_v1_phase5.py`, `test_inbox_crossproject.py` — all pass). Squash-merged to main as `2712c5d` ("feat(engineering): enforce V1-0 write invariants"). Deployed to Dalidou via the canonical deploy script; `/health` build_sha=`2712c5d2d03cb2a6af38b559664afd1c4cd0e050` status=ok. Validated backup snapshot at `/srv/storage/atocore/backups/snapshots/20260422T190624Z` taken BEFORE prod backfill. Prod backfill of `scripts/v1_0_backfill_provenance.py` against live DB: dry-run found 31 active/superseded entities with no provenance, list reviewed and looked sane; live run with default `hand_authored=1` flag path updated 31 rows; follow-up dry-run returned 0 rows remaining → no lingering F-8 violations in prod. Codex logged one residual P2 (R14): HTTP `POST /entities/{id}/promote` route doesn't translate the new service-layer `ValueError` into 400 — legacy bad candidate promoted through the API surfaces as 500. Not blocking. V1-0 closed. **Gates for V1-A**: soak window ends ~2026-04-26; 100-active-memory density target (currently 84 active + the ~31 newly flagged ones — need to check how those count in density math). V1-A holds until both gates clear.

README.md

@@ -6,7 +6,7 @@ Personal context engine that enriches LLM interactions with durable memory, stru
 
 ```bash
 pip install -e .
-uvicorn src.atocore.main:app --port 8100
+uvicorn atocore.main:app --port 8100
 ```
 
 ## Usage
@@ -37,6 +37,10 @@ python scripts/atocore_client.py audit-query "gigabit" 5
 | POST | /ingest | Ingest markdown file or folder |
 | POST | /query | Retrieve relevant chunks |
 | POST | /context/build | Build full context pack |
+| POST | /interactions | Capture prompt/response interactions |
+| GET/POST | /memory | List/create durable memories |
+| GET/POST | /entities | Engineering entity graph surface |
+| GET | /admin/dashboard | Operator dashboard |
 | GET | /health | Health check |
 | GET | /debug/context | Inspect last context pack |
 
@@ -66,8 +70,10 @@ unversioned forms.
 FastAPI (port 8100)
   |- Ingestion: markdown -> parse -> chunk -> embed -> store
   |- Retrieval: query -> embed -> vector search -> rank
-  |- Context Builder: retrieve -> boost -> budget -> format
-  |- SQLite (documents, chunks, memories, projects, interactions)
+  |- Context Builder: project state -> memories -> entities -> retrieval -> budget
+  |- Reflection: capture -> reinforce -> extract -> triage -> promote/expire
+  |- Engineering: typed entities, relationships, conflicts, wiki/mirror
+  |- SQLite (documents, chunks, memories, projects, interactions, entities)
   '- ChromaDB (vector embeddings)
 ```
 
@@ -82,6 +88,16 @@ Set via environment variables (prefix `ATOCORE_`):
 | ATOCORE_CHUNK_MAX_SIZE | 800 | Max chunk size (chars) |
 | ATOCORE_CONTEXT_BUDGET | 3000 | Context pack budget (chars) |
 | ATOCORE_EMBEDDING_MODEL | paraphrase-multilingual-MiniLM-L12-v2 | Embedding model |
+| ATOCORE_RANK_PROJECT_MATCH_BOOST | 2.0 | Soft boost for chunks whose metadata matches the project hint |
+| ATOCORE_RANK_PROJECT_SCOPE_FILTER | true | Filter project-hinted retrieval away from other registered project corpora |
+| ATOCORE_RANK_PROJECT_SCOPE_CANDIDATE_MULTIPLIER | 4 | Widen candidate pull before project-scope filtering |
+| ATOCORE_RANK_QUERY_TOKEN_STEP | 0.08 | Per-token boost when query terms appear in high-signal metadata |
+| ATOCORE_RANK_QUERY_TOKEN_CAP | 1.32 | Maximum query-token boost multiplier |
+| ATOCORE_RANK_PATH_HIGH_SIGNAL_BOOST | 1.18 | Boost current decision/status/requirements-like paths |
+| ATOCORE_RANK_PATH_LOW_SIGNAL_PENALTY | 0.72 | Down-rank archive/history-like paths |
+
+`ATOCORE_RANK_PROJECT_SCOPE_FILTER` gates the hard cross-project filter only.
+`ATOCORE_RANK_PROJECT_MATCH_BOOST` remains the separate soft-ranking knob.
 
 ## Testing
 
@@ -93,7 +109,11 @@ pytest
 ## Operations
 
 - `scripts/atocore_client.py` provides a live API client for project refresh, project-state inspection, and retrieval-quality audits.
+- `scripts/retrieval_eval.py` runs the live retrieval/context harness, separates blocking failures from known content gaps, and stamps JSON output with target/build metadata.
+- `scripts/live_status.py` renders a compact read-only status report from `/health`, `/stats`, `/projects`, and `/admin/dashboard`; set `ATOCORE_AUTH_TOKEN` or `--auth-token` when those endpoints are gated.
+- `scripts/backfill_chunk_project_ids.py` dry-runs or applies explicit `project_id` metadata backfills for SQLite chunks and Chroma vectors; `--apply` requires a confirmed Chroma snapshot.
 - `docs/operations.md` captures the current operational priority order: retrieval quality, Wave 2 trusted-operational ingestion, AtoDrive scoping, and restore validation.
+- `DEV-LEDGER.md` is the fast-moving source of operational truth during active development; copy claims into docs only after checking the live service.
 
 ## Architecture Notes
 

docs/current-state.md

@@ -1,6 +1,11 @@
-# AtoCore — Current State (2026-04-22)
+# AtoCore - Current State (2026-04-24)
 
-Live deploy: `2712c5d` · Dalidou health: ok · Harness: 17/18 · Tests: 547 passing.
+Update 2026-04-24: audit-improvements deployed as `f44a211`; live harness is
+19/20 with 0 blocking failures and 1 known content gap. Active follow-up branch
+`codex/project-id-metadata-retrieval` is at 567 passing tests.
+
+Live deploy: `2b86543` · Dalidou health: ok · Harness: 18/20 with 1 known
+content gap and 1 current blocking project-bleed guard · Tests: 553 passing.
 
 ## V1-0 landed 2026-04-22
 
@@ -13,9 +18,8 @@ supersede) with Q-3 fail-open. Prod backfill ran cleanly — 31 legacy
 active/superseded entities flagged `hand_authored=1`, follow-up dry-run
 returned 0 remaining rows. Test count 533 → 547 (+14).
 
-R14 (P2, non-blocking): `POST /entities/{id}/promote` route fix translates
-the new `ValueError` into 400. Branch `claude/r14-promote-400` pending
-Codex review + squash-merge.
+R14 is closed: `POST /entities/{id}/promote` now translates the new
+caller-fixable V1-0 `ValueError` into HTTP 400.
 
 **Next in the V1 track:** V1-A (minimal query slice + Q-6 killer-correctness
 integration). Gated on pipeline soak (~2026-04-26) + 100+ active memory
@@ -65,10 +69,10 @@ Last nightly run (2026-04-19 03:00 UTC): **31 promoted · 39 rejected · 0 needs
 | 7G | Re-extraction on prompt version bump | pending |
 | 7H | Chroma vector hygiene (delete vectors for superseded memories) | pending |
 
-## Known gaps (honest)
+## Known gaps (honest, refreshed 2026-04-24)
 
 1. **Capture surface is Claude-Code-and-OpenClaw only.** Conversations in Claude Desktop, Claude.ai web, phone, or any other LLM UI are NOT captured. Example: the rotovap/mushroom chat yesterday never reached AtoCore because no hook fired. See Q4 below.
-2. **OpenClaw is capture-only, not context-grounded.** The plugin POSTs `/interactions` on `llm_output` but does NOT call `/context/build` on `before_agent_start`. OpenClaw's underlying agent runs blind. See Q2 below.
-3. **Human interface (wiki) is thin and static.** 5 project cards + a "System" line. No dashboard for the autonomous activity. No per-memory detail page. See Q3/Q5.
-4. **Harness 17/18** — the `p04-constraints` fixture wants "Zerodur" but retrieval surfaces related-not-exact terms. Content gap, not a retrieval regression.
-5. **Two projects under-populated**: p05-interferometer (4 memories, 18 state) and atomizer-v2 (1 memory, 6 state). Batch re-extract with the new llm-0.6.0 prompt would help.
+2. **Project-scoped retrieval guard is deployed and passing.** The April 24 p05 broad-status bleed guard now passes on live Dalidou. The active follow-up branch adds explicit `project_id` chunk/vector metadata so the deployed path/tag heuristic can become a legacy fallback.
+3. **Human interface is useful but not yet the V1 Human Mirror.** Wiki/dashboard pages exist, but the spec routes, deterministic mirror files, disputed markers, and curated annotations remain V1-D work.
+4. **Harness known issue:** `p04-constraints` wants "Zerodur" and "1.2"; live retrieval surfaces related constraints but not those exact strings. Treat as content/state gap until fixed.
+5. **Formal docs lag the ledger during fast work.** Use `DEV-LEDGER.md` and `python scripts/live_status.py` for live truth, then copy verified claims into these docs.

docs/master-plan-status.md

@@ -70,9 +70,14 @@ read-only additive mode.
 - Phase 6 - AtoDrive
 - Phase 10 - Write-back
 - Phase 11 - Multi-model
-- Phase 12 - Evaluation
 - Phase 13 - Hardening
 
+### Partial / Operational Baseline
+
+- Phase 12 - Evaluation. The retrieval/context harness exists and runs
+  against live Dalidou, but coverage is still intentionally small and
+  should grow before this is complete in the intended sense.
+
 ### Engineering Layer Planning Sprint
 
 **Status: complete.** All 8 architecture docs are drafted. The
@@ -126,11 +131,13 @@ This sits implicitly between Phase 8 (OpenClaw) and Phase 11
 (multi-model). Memory-review and engineering-entity commands are
 deferred from the shared client until their workflows are exercised.
 
-## What Is Real Today (updated 2026-04-16)
+## What Is Real Today (updated 2026-04-24)
 
-- canonical AtoCore runtime on Dalidou (`775960c`, deploy.sh verified)
+- canonical AtoCore runtime on Dalidou (`2b86543`, deploy.sh verified)
 - 33,253 vectors across 6 registered projects
-- 234 captured interactions (192 claude-code, 38 openclaw, 4 test)
+- 951 captured interactions as of the 2026-04-24 live dashboard; refresh
+  exact live counts with
+  `python scripts/live_status.py`
 - 6 registered projects:
   - `p04-gigabit` (483 docs, 15 state entries)
   - `p05-interferometer` (109 docs, 18 state entries)
@@ -138,12 +145,14 @@ deferred from the shared client until their workflows are exercised.
   - `atomizer-v2` (568 docs, 5 state entries)
   - `abb-space` (6 state entries)
   - `atocore` (drive source, 47 state entries)
-- 110 Trusted Project State entries across all projects (decisions, requirements, facts, contacts, milestones)
-- 84 active memories (31 project, 23 knowledge, 10 episodic, 8 adaptation, 7 preference, 5 identity)
+- 128 Trusted Project State entries across all projects (decisions, requirements, facts, contacts, milestones)
+- 290 active memories and 0 candidate memories as of the 2026-04-24 live
+  dashboard
 - context pack assembly with 4 tiers: Trusted Project State > identity/preference > project memories > retrieved chunks
 - query-relevance memory ranking with overlap-density scoring
-- retrieval eval harness: 18 fixtures, 17/18 passing on live
-- 303 tests passing
+- retrieval eval harness: 20 fixtures; current live has 19 pass, 1 known
+  content gap, and 0 blocking failures after the audit-improvements deploy
+- 567 tests passing on the active `codex/project-id-metadata-retrieval` branch
 - nightly pipeline: backup → cleanup → rsync → OpenClaw import → vault refresh → extract → triage → **auto-promote/expire** → weekly synth/lint → **retrieval harness** → **pipeline summary to project state**
 - Phase 10 operational: reinforcement-based auto-promotion (ref_count ≥ 3, confidence ≥ 0.7) + stale candidate expiry (14 days unreinforced)
 - pipeline health visible in dashboard: interaction totals by client, pipeline last_run, harness results, triage stats
@@ -190,9 +199,9 @@ where surfaces are disjoint, pauses when they collide.
 | V1-E | Memory→entity graduation end-to-end + remaining Q-4 trust tests | pending V1-D (note: collides with memory extractor; pauses for multi-model triage work) |
 | V1-F | F-5 detector generalization + route alias + O-1/O-2/O-3 operational + D-1/D-3/D-4 docs | finish line |
 
-R14 (P2, non-blocking): `POST /entities/{id}/promote` route returns 500
-on the new V1-0 `ValueError` instead of 400. Fix on branch
-`claude/r14-promote-400`, pending Codex review.
+R14 is closed: `POST /entities/{id}/promote` now translates
+caller-fixable V1-0 provenance validation failures into HTTP 400 instead
+of leaking as HTTP 500.
 
 ## Next
 

scripts/backfill_chunk_project_ids.py

@@ -0,0 +1,178 @@
+"""Backfill explicit project_id into chunk and vector metadata.
+
+Dry-run by default. The script derives ownership from the registered project
+ingest roots and updates both SQLite source_chunks.metadata and Chroma vector
+metadata only when --apply is provided.
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sqlite3
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "src"))
+
+from atocore.models.database import get_connection  # noqa: E402
+from atocore.projects.registry import derive_project_id_for_path  # noqa: E402
+from atocore.retrieval.vector_store import get_vector_store  # noqa: E402
+
+DEFAULT_BATCH_SIZE = 500
+
+
+def _decode_metadata(raw: str | None) -> dict | None:
+    if not raw:
+        return {}
+    try:
+        parsed = json.loads(raw)
+    except json.JSONDecodeError:
+        return None
+    return parsed if isinstance(parsed, dict) else None
+
+
+def _chunk_rows() -> tuple[list[dict], str]:
+    try:
+        with get_connection() as conn:
+            rows = conn.execute(
+                """
+                SELECT
+                    sc.id AS chunk_id,
+                    sc.metadata AS chunk_metadata,
+                    sd.file_path AS file_path
+                FROM source_chunks sc
+                JOIN source_documents sd ON sd.id = sc.document_id
+                ORDER BY sd.file_path, sc.chunk_index
+                """
+            ).fetchall()
+    except sqlite3.OperationalError as exc:
+        if "source_chunks" in str(exc) or "source_documents" in str(exc):
+            return [], f"missing ingestion tables: {exc}"
+        raise
+    return [dict(row) for row in rows], ""
+
+
+def _batches(items: list, batch_size: int) -> list[list]:
+    return [items[i:i + batch_size] for i in range(0, len(items), batch_size)]
+
+
+def backfill(
+    apply: bool = False,
+    project_filter: str = "",
+    batch_size: int = DEFAULT_BATCH_SIZE,
+    require_chroma_snapshot: bool = False,
+) -> dict:
+    rows, db_warning = _chunk_rows()
+    updates: list[tuple[str, str, dict]] = []
+    by_project: dict[str, int] = {}
+    skipped_unowned = 0
+    already_tagged = 0
+    malformed_metadata = 0
+
+    for row in rows:
+        project_id = derive_project_id_for_path(row["file_path"])
+        if project_filter and project_id != project_filter:
+            continue
+        if not project_id:
+            skipped_unowned += 1
+            continue
+        metadata = _decode_metadata(row["chunk_metadata"])
+        if metadata is None:
+            malformed_metadata += 1
+            continue
+        if metadata.get("project_id") == project_id:
+            already_tagged += 1
+            continue
+        metadata["project_id"] = project_id
+        updates.append((row["chunk_id"], project_id, metadata))
+        by_project[project_id] = by_project.get(project_id, 0) + 1
+
+    missing_vectors: list[str] = []
+    applied_updates = 0
+    if apply and updates:
+        if not require_chroma_snapshot:
+            raise ValueError(
+                "--apply requires --chroma-snapshot-confirmed after taking a Chroma backup"
+            )
+        vector_store = get_vector_store()
+        for batch in _batches(updates, max(1, batch_size)):
+            chunk_ids = [chunk_id for chunk_id, _, _ in batch]
+            vector_payload = vector_store.get_metadatas(chunk_ids)
+            existing_vector_metadata = {
+                chunk_id: metadata
+                for chunk_id, metadata in zip(
+                    vector_payload.get("ids", []),
+                    vector_payload.get("metadatas", []),
+                    strict=False,
+                )
+                if isinstance(metadata, dict)
+            }
+
+            vector_ids = []
+            vector_metadatas = []
+            sql_updates = []
+            for chunk_id, project_id, chunk_metadata in batch:
+                vector_metadata = existing_vector_metadata.get(chunk_id)
+                if vector_metadata is None:
+                    missing_vectors.append(chunk_id)
+                    continue
+                vector_metadata = dict(vector_metadata)
+                vector_metadata["project_id"] = project_id
+                vector_ids.append(chunk_id)
+                vector_metadatas.append(vector_metadata)
+                sql_updates.append((json.dumps(chunk_metadata, ensure_ascii=True), chunk_id))
+
+            if not vector_ids:
+                continue
+
+            vector_store.update_metadatas(vector_ids, vector_metadatas)
+            with get_connection() as conn:
+                cursor = conn.executemany(
+                    "UPDATE source_chunks SET metadata = ? WHERE id = ?",
+                    sql_updates,
+                )
+                if cursor.rowcount != len(sql_updates):
+                    raise RuntimeError(
+                        f"SQLite rowcount mismatch: {cursor.rowcount} != {len(sql_updates)}"
+                    )
+            applied_updates += len(sql_updates)
+
+    return {
+        "apply": apply,
+        "total_chunks": len(rows),
+        "updates": len(updates),
+        "applied_updates": applied_updates,
+        "already_tagged": already_tagged,
+        "skipped_unowned": skipped_unowned,
+        "malformed_metadata": malformed_metadata,
+        "missing_vectors": len(missing_vectors),
+        "db_warning": db_warning,
+        "by_project": dict(sorted(by_project.items())),
+    }
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--apply", action="store_true", help="write SQLite and Chroma metadata updates")
+    parser.add_argument("--project", default="", help="optional canonical project_id filter")
+    parser.add_argument("--batch-size", type=int, default=DEFAULT_BATCH_SIZE)
+    parser.add_argument(
+        "--chroma-snapshot-confirmed",
+        action="store_true",
+        help="required with --apply; confirms a Chroma snapshot exists",
+    )
+    args = parser.parse_args()
+
+    payload = backfill(
+        apply=args.apply,
+        project_filter=args.project.strip(),
+        batch_size=args.batch_size,
+        require_chroma_snapshot=args.chroma_snapshot_confirmed,
+    )
+    print(json.dumps(payload, indent=2, ensure_ascii=True))
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

scripts/live_status.py

@@ -0,0 +1,131 @@
+"""Render a compact live-status report from a running AtoCore instance.
+
+This is intentionally read-only and stdlib-only so it can be used from a
+fresh checkout, a cron job, or a Codex/Claude session without installing the
+full app package. The output is meant to reduce docs drift: copy the report
+into status docs only after it was generated from the live service.
+"""
+
+from __future__ import annotations
+
+import argparse
+import errno
+import json
+import os
+import sys
+import urllib.error
+import urllib.request
+from typing import Any
+
+
+DEFAULT_BASE_URL = os.environ.get("ATOCORE_BASE_URL", "http://dalidou:8100").rstrip("/")
+DEFAULT_TIMEOUT = int(os.environ.get("ATOCORE_TIMEOUT_SECONDS", "30"))
+DEFAULT_AUTH_TOKEN = os.environ.get("ATOCORE_AUTH_TOKEN", "").strip()
+
+
+def request_json(base_url: str, path: str, timeout: int, auth_token: str = "") -> dict[str, Any]:
+    headers = {"Authorization": f"Bearer {auth_token}"} if auth_token else {}
+    req = urllib.request.Request(f"{base_url}{path}", method="GET", headers=headers)
+    with urllib.request.urlopen(req, timeout=timeout) as response:
+        body = response.read().decode("utf-8")
+        status = getattr(response, "status", None)
+    payload = json.loads(body) if body.strip() else {}
+    if not isinstance(payload, dict):
+        payload = {"value": payload}
+    if status is not None:
+        payload["_http_status"] = status
+    return payload
+
+
+def collect_status(base_url: str, timeout: int, auth_token: str = "") -> dict[str, Any]:
+    payload: dict[str, Any] = {"base_url": base_url}
+    for name, path in {
+        "health": "/health",
+        "stats": "/stats",
+        "projects": "/projects",
+        "dashboard": "/admin/dashboard",
+    }.items():
+        try:
+            payload[name] = request_json(base_url, path, timeout, auth_token)
+        except (urllib.error.URLError, TimeoutError, OSError, json.JSONDecodeError) as exc:
+            payload[name] = {"error": str(exc)}
+    return payload
+
+
+def render_markdown(status: dict[str, Any]) -> str:
+    health = status.get("health", {})
+    stats = status.get("stats", {})
+    projects = status.get("projects", {}).get("projects", [])
+    dashboard = status.get("dashboard", {})
+    memories = dashboard.get("memories", {}) if isinstance(dashboard.get("memories"), dict) else {}
+    project_state = dashboard.get("project_state", {}) if isinstance(dashboard.get("project_state"), dict) else {}
+    interactions = dashboard.get("interactions", {}) if isinstance(dashboard.get("interactions"), dict) else {}
+    pipeline = dashboard.get("pipeline", {}) if isinstance(dashboard.get("pipeline"), dict) else {}
+
+    lines = [
+        "# AtoCore Live Status",
+        "",
+        f"- base_url: `{status.get('base_url', '')}`",
+        "- endpoint_http_statuses: "
+        f"`health={health.get('_http_status', 'error')}, "
+        f"stats={stats.get('_http_status', 'error')}, "
+        f"projects={status.get('projects', {}).get('_http_status', 'error')}, "
+        f"dashboard={dashboard.get('_http_status', 'error')}`",
+        f"- service_status: `{health.get('status', 'unknown')}`",
+        f"- code_version: `{health.get('code_version', health.get('version', 'unknown'))}`",
+        f"- build_sha: `{health.get('build_sha', 'unknown')}`",
+        f"- build_branch: `{health.get('build_branch', 'unknown')}`",
+        f"- build_time: `{health.get('build_time', 'unknown')}`",
+        f"- env: `{health.get('env', 'unknown')}`",
+        f"- documents: `{stats.get('total_documents', 'unknown')}`",
+        f"- chunks: `{stats.get('total_chunks', 'unknown')}`",
+        f"- vectors: `{stats.get('total_vectors', health.get('vectors_count', 'unknown'))}`",
+        f"- registered_projects: `{len(projects)}`",
+        f"- active_memories: `{memories.get('active', 'unknown')}`",
+        f"- candidate_memories: `{memories.get('candidates', 'unknown')}`",
+        f"- interactions: `{interactions.get('total', 'unknown')}`",
+        f"- project_state_entries: `{project_state.get('total', 'unknown')}`",
+        f"- pipeline_last_run: `{pipeline.get('last_run', 'unknown')}`",
+    ]
+
+    if projects:
+        lines.extend(["", "## Projects"])
+        for project in projects:
+            aliases = ", ".join(project.get("aliases", []))
+            suffix = f" ({aliases})" if aliases else ""
+            lines.append(f"- `{project.get('id', '')}`{suffix}")
+
+    return "\n".join(lines) + "\n"
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="Render live AtoCore status")
+    parser.add_argument("--base-url", default=DEFAULT_BASE_URL)
+    parser.add_argument("--timeout", type=int, default=DEFAULT_TIMEOUT)
+    parser.add_argument(
+        "--auth-token",
+        default=DEFAULT_AUTH_TOKEN,
+        help="Bearer token; defaults to ATOCORE_AUTH_TOKEN when set",
+    )
+    parser.add_argument("--json", action="store_true", help="emit raw JSON")
+    args = parser.parse_args()
+
+    status = collect_status(args.base_url.rstrip("/"), args.timeout, args.auth_token)
+    if args.json:
+        output = json.dumps(status, indent=2, ensure_ascii=True) + "\n"
+    else:
+        output = render_markdown(status)
+
+    try:
+        sys.stdout.write(output)
+    except BrokenPipeError:
+        return 0
+    except OSError as exc:
+        if exc.errno in {errno.EINVAL, errno.EPIPE}:
+            return 0
+        raise
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

scripts/retrieval_eval.py

@@ -44,6 +44,7 @@ import urllib.error
 import urllib.parse
 import urllib.request
 from dataclasses import dataclass, field
+from datetime import datetime, timezone
 from pathlib import Path
 
 DEFAULT_BASE_URL = os.environ.get("ATOCORE_BASE_URL", "http://dalidou:8100")
@@ -52,6 +53,13 @@ DEFAULT_BUDGET = 3000
 DEFAULT_FIXTURES = Path(__file__).parent / "retrieval_eval_fixtures.json"
 
 
+def request_json(base_url: str, path: str, timeout: int) -> dict:
+    req = urllib.request.Request(f"{base_url}{path}", method="GET")
+    with urllib.request.urlopen(req, timeout=timeout) as resp:
+        body = resp.read().decode("utf-8")
+    return json.loads(body) if body.strip() else {}
+
+
 @dataclass
 class Fixture:
     name: str
@@ -60,6 +68,7 @@ class Fixture:
     budget: int = DEFAULT_BUDGET
     expect_present: list[str] = field(default_factory=list)
     expect_absent: list[str] = field(default_factory=list)
+    known_issue: bool = False
     notes: str = ""
 
 
@@ -70,8 +79,13 @@ class FixtureResult:
     missing_present: list[str]
     unexpected_absent: list[str]
     total_chars: int
+    known_issue: bool = False
     error: str = ""
 
+    @property
+    def blocking_failure(self) -> bool:
+        return not self.ok and not self.known_issue
+
 
 def load_fixtures(path: Path) -> list[Fixture]:
     data = json.loads(path.read_text(encoding="utf-8"))
@@ -89,6 +103,7 @@ def load_fixtures(path: Path) -> list[Fixture]:
                 budget=int(raw.get("budget", DEFAULT_BUDGET)),
                 expect_present=list(raw.get("expect_present", [])),
                 expect_absent=list(raw.get("expect_absent", [])),
+                known_issue=bool(raw.get("known_issue", False)),
                 notes=raw.get("notes", ""),
             )
         )
@@ -117,6 +132,7 @@ def run_fixture(fixture: Fixture, base_url: str, timeout: int) -> FixtureResult:
             missing_present=list(fixture.expect_present),
             unexpected_absent=[],
             total_chars=0,
+            known_issue=fixture.known_issue,
             error=f"http_error: {exc}",
         )
 
@@ -129,16 +145,26 @@ def run_fixture(fixture: Fixture, base_url: str, timeout: int) -> FixtureResult:
         missing_present=missing,
         unexpected_absent=unexpected,
         total_chars=len(formatted),
+        known_issue=fixture.known_issue,
     )
 
 
-def print_human_report(results: list[FixtureResult]) -> None:
+def print_human_report(results: list[FixtureResult], metadata: dict) -> None:
     total = len(results)
     passed = sum(1 for r in results if r.ok)
+    known = sum(1 for r in results if not r.ok and r.known_issue)
+    blocking = sum(1 for r in results if r.blocking_failure)
     print(f"Retrieval eval: {passed}/{total} fixtures passed")
+    print(
+        "Target: "
+        f"{metadata.get('base_url', 'unknown')} "
+        f"build={metadata.get('health', {}).get('build_sha', 'unknown')}"
+    )
+    if known or blocking:
+        print(f"Blocking failures: {blocking}  Known issues: {known}")
     print()
     for r in results:
-        marker = "PASS" if r.ok else "FAIL"
+        marker = "PASS" if r.ok else ("KNOWN" if r.known_issue else "FAIL")
         print(f"[{marker}] {r.fixture.name}  project={r.fixture.project}  chars={r.total_chars}")
         if r.error:
             print(f"       error: {r.error}")
@@ -150,15 +176,21 @@ def print_human_report(results: list[FixtureResult]) -> None:
             print(f"       notes: {r.fixture.notes}")
 
 
-def print_json_report(results: list[FixtureResult]) -> None:
+def print_json_report(results: list[FixtureResult], metadata: dict) -> None:
     payload = {
+        "generated_at": metadata.get("generated_at"),
+        "base_url": metadata.get("base_url"),
+        "health": metadata.get("health", {}),
         "total": len(results),
         "passed": sum(1 for r in results if r.ok),
+        "known_issues": sum(1 for r in results if not r.ok and r.known_issue),
+        "blocking_failures": sum(1 for r in results if r.blocking_failure),
         "fixtures": [
             {
                 "name": r.fixture.name,
                 "project": r.fixture.project,
                 "ok": r.ok,
+                "known_issue": r.known_issue,
                 "total_chars": r.total_chars,
                 "missing_present": r.missing_present,
                 "unexpected_absent": r.unexpected_absent,
@@ -179,15 +211,26 @@ def main() -> int:
     parser.add_argument("--json", action="store_true", help="emit machine-readable JSON")
     args = parser.parse_args()
 
+    base_url = args.base_url.rstrip("/")
+    try:
+        health = request_json(base_url, "/health", args.timeout)
+    except (urllib.error.URLError, TimeoutError, OSError, json.JSONDecodeError) as exc:
+        health = {"error": str(exc)}
+    metadata = {
+        "generated_at": datetime.now(timezone.utc).isoformat(),
+        "base_url": base_url,
+        "health": health,
+    }
+
     fixtures = load_fixtures(args.fixtures)
-    results = [run_fixture(f, args.base_url, args.timeout) for f in fixtures]
+    results = [run_fixture(f, base_url, args.timeout) for f in fixtures]
 
     if args.json:
-        print_json_report(results)
+        print_json_report(results, metadata)
     else:
-        print_human_report(results)
+        print_human_report(results, metadata)
 
-    return 0 if all(r.ok for r in results) else 1
+    return 0 if not any(r.blocking_failure for r in results) else 1
 
 
 if __name__ == "__main__":

scripts/retrieval_eval_fixtures.json

@@ -27,7 +27,8 @@
     "expect_absent": [
       "polisher suite"
     ],
-    "notes": "Key constraints are in Trusted Project State and in the mission-framing memory"
+    "known_issue": true,
+    "notes": "Known content gap as of 2026-04-24: live retrieval surfaces related constraints but not the exact Zerodur / 1.2 strings. Keep visible, but do not make nightly harness red until the source/state gap is fixed."
   },
   {
     "name": "p04-short-ambiguous",
@@ -80,6 +81,36 @@
     ],
     "notes": "CGH is a core p05 concept. Should surface via chunks and possibly the architecture memory. Must not bleed p06 polisher-suite terms."
   },
+  {
+    "name": "p05-broad-status-no-atomizer",
+    "project": "p05-interferometer",
+    "prompt": "current status",
+    "expect_present": [
+      "--- Trusted Project State ---",
+      "--- Project Memories ---",
+      "Zygo"
+    ],
+    "expect_absent": [
+      "atomizer-v2",
+      "ATOMIZER_PODCAST_BRIEFING",
+      "[Source: atomizer-v2/",
+      "P04-GigaBIT-M1-KB-design"
+    ],
+    "notes": "Regression guard for the April 24 audit finding: broad p05 status queries must not pull Atomizer/archive context into project-scoped packs."
+  },
+  {
+    "name": "p05-vendor-decision-no-archive-first",
+    "project": "p05-interferometer",
+    "prompt": "vendor selection decision",
+    "expect_present": [
+      "Selection-Decision"
+    ],
+    "expect_absent": [
+      "[Source: atomizer-v2/",
+      "ATOMIZER_PODCAST_BRIEFING"
+    ],
+    "notes": "Project-scoped decision query should stay inside p05 and prefer current decision/vendor material over unrelated project archives."
+  },
   {
     "name": "p06-suite-split",
     "project": "p06-polisher",

src/atocore/config.py

@@ -46,6 +46,8 @@ class Settings(BaseSettings):
     # All multipliers default to the values used since Wave 1; tighten or
     # loosen them via ATOCORE_* env vars without touching code.
     rank_project_match_boost: float = 2.0
+    rank_project_scope_filter: bool = True
+    rank_project_scope_candidate_multiplier: int = 4
     rank_query_token_step: float = 0.08
     rank_query_token_cap: float = 1.32
     rank_path_high_signal_boost: float = 1.18

src/atocore/ingestion/pipeline.py

@@ -32,10 +32,23 @@ def exclusive_ingestion():
         _INGESTION_LOCK.release()
 
 
-def ingest_file(file_path: Path) -> dict:
+def ingest_file(file_path: Path, project_id: str = "") -> dict:
     """Ingest a single markdown file. Returns stats."""
     start = time.time()
     file_path = file_path.resolve()
+    project_id = (project_id or "").strip()
+    if not project_id:
+        try:
+            from atocore.projects.registry import derive_project_id_for_path
+
+            project_id = derive_project_id_for_path(file_path)
+        except Exception as exc:
+            log.warning(
+                "project_id_derivation_failed",
+                file_path=str(file_path),
+                error=str(exc),
+            )
+            project_id = ""
 
     if not file_path.exists():
         raise FileNotFoundError(f"File not found: {file_path}")
@@ -65,6 +78,7 @@ def ingest_file(file_path: Path) -> dict:
         "source_file": str(file_path),
         "tags": parsed.tags,
         "title": parsed.title,
+        "project_id": project_id,
     }
     chunks = chunk_markdown(parsed.body, base_metadata=base_meta)
 
@@ -116,6 +130,7 @@ def ingest_file(file_path: Path) -> dict:
                         "source_file": str(file_path),
                         "tags": json.dumps(parsed.tags),
                         "title": parsed.title,
+                        "project_id": project_id,
                     })
 
                     conn.execute(
@@ -173,7 +188,17 @@ def ingest_folder(folder_path: Path, purge_deleted: bool = True) -> list[dict]:
         purge_deleted: If True, remove DB/vector entries for files
                        that no longer exist on disk.
     """
+    return ingest_project_folder(folder_path, purge_deleted=purge_deleted, project_id="")
+
+
+def ingest_project_folder(
+    folder_path: Path,
+    purge_deleted: bool = True,
+    project_id: str = "",
+) -> list[dict]:
+    """Ingest a folder and annotate chunks with an optional project id."""
     folder_path = folder_path.resolve()
+    project_id = (project_id or "").strip()
     if not folder_path.is_dir():
         raise NotADirectoryError(f"Not a directory: {folder_path}")
 
@@ -187,7 +212,7 @@ def ingest_folder(folder_path: Path, purge_deleted: bool = True) -> list[dict]:
     # Ingest new/changed files
     for md_file in md_files:
         try:
-            result = ingest_file(md_file)
+            result = ingest_file(md_file, project_id=project_id)
             results.append(result)
         except Exception as e:
             log.error("ingestion_error", file_path=str(md_file), error=str(e))

src/atocore/projects/registry.py

@@ -8,7 +8,6 @@ from dataclasses import asdict, dataclass
 from pathlib import Path
 
 import atocore.config as _config
-from atocore.ingestion.pipeline import ingest_folder
 
 
 # Reserved pseudo-projects. `inbox` holds pre-project / lead / quote
@@ -260,6 +259,7 @@ def load_project_registry() -> list[RegisteredProject]:
         )
 
     _validate_unique_project_names(projects)
+    _validate_ingest_root_overlaps(projects)
     return projects
 
 
@@ -307,6 +307,28 @@ def resolve_project_name(name: str | None) -> str:
     return name
 
 
+def derive_project_id_for_path(file_path: str | Path) -> str:
+    """Return the registered project that owns a source path, if any."""
+    if not file_path:
+        return ""
+    doc_path = Path(file_path).resolve(strict=False)
+    matches: list[tuple[int, int, str]] = []
+
+    for project in load_project_registry():
+        for source_ref in project.ingest_roots:
+            root_path = _resolve_ingest_root(source_ref)
+            try:
+                doc_path.relative_to(root_path)
+            except ValueError:
+                continue
+            matches.append((len(root_path.parts), len(str(root_path)), project.project_id))
+
+    if not matches:
+        return ""
+    matches.sort(reverse=True)
+    return matches[0][2]
+
+
 def refresh_registered_project(project_name: str, purge_deleted: bool = False) -> dict:
     """Ingest all configured source roots for a registered project.
 
@@ -322,6 +344,8 @@ def refresh_registered_project(project_name: str, purge_deleted: bool = False) -
     if project is None:
         raise ValueError(f"Unknown project: {project_name}")
 
+    from atocore.ingestion.pipeline import ingest_project_folder
+
     roots = []
     ingested_count = 0
     skipped_count = 0
@@ -346,7 +370,11 @@ def refresh_registered_project(project_name: str, purge_deleted: bool = False) -
             {
                 **root_result,
                 "status": "ingested",
-                "results": ingest_folder(resolved, purge_deleted=purge_deleted),
+                "results": ingest_project_folder(
+                    resolved,
+                    purge_deleted=purge_deleted,
+                    project_id=project.project_id,
+                ),
             }
         )
         ingested_count += 1
@@ -443,6 +471,33 @@ def _validate_unique_project_names(projects: list[RegisteredProject]) -> None:
             seen[key] = project.project_id
 
 
+def _validate_ingest_root_overlaps(projects: list[RegisteredProject]) -> None:
+    roots: list[tuple[str, Path]] = []
+    for project in projects:
+        for source_ref in project.ingest_roots:
+            roots.append((project.project_id, _resolve_ingest_root(source_ref)))
+
+    for i, (left_project, left_root) in enumerate(roots):
+        for right_project, right_root in roots[i + 1:]:
+            if left_project == right_project:
+                continue
+            try:
+                left_root.relative_to(right_root)
+                overlaps = True
+            except ValueError:
+                try:
+                    right_root.relative_to(left_root)
+                    overlaps = True
+                except ValueError:
+                    overlaps = False
+            if overlaps:
+                raise ValueError(
+                    "Project registry ingest root overlap: "
+                    f"'{left_root}' ({left_project}) and "
+                    f"'{right_root}' ({right_project})"
+                )
+
+
 def _find_name_collisions(
     project_id: str,
     aliases: list[str],

src/atocore/retrieval/retriever.py

@@ -1,5 +1,6 @@
 """Retrieval: query to ranked chunks."""
 
+import json
 import re
 import time
 from dataclasses import dataclass
@@ -7,7 +8,7 @@ from dataclasses import dataclass
 import atocore.config as _config
 from atocore.models.database import get_connection
 from atocore.observability.logger import get_logger
-from atocore.projects.registry import get_registered_project
+from atocore.projects.registry import RegisteredProject, get_registered_project, load_project_registry
 from atocore.retrieval.embeddings import embed_query
 from atocore.retrieval.vector_store import get_vector_store
 
@@ -83,6 +84,27 @@ def retrieve(
     """Retrieve the most relevant chunks for a query."""
     top_k = top_k or _config.settings.context_top_k
     start = time.time()
+    try:
+        scoped_project = get_registered_project(project_hint) if project_hint else None
+    except Exception as exc:
+        log.warning(
+            "project_scope_resolution_failed",
+            project_hint=project_hint,
+            error=str(exc),
+        )
+        scoped_project = None
+    scope_filter_enabled = bool(scoped_project and _config.settings.rank_project_scope_filter)
+    registered_projects = None
+    query_top_k = top_k
+    if scope_filter_enabled:
+        query_top_k = max(
+            top_k,
+            top_k * max(1, _config.settings.rank_project_scope_candidate_multiplier),
+        )
+        try:
+            registered_projects = load_project_registry()
+        except Exception:
+            registered_projects = None
 
     query_embedding = embed_query(query)
     store = get_vector_store()
@@ -101,11 +123,12 @@ def retrieve(
 
     results = store.query(
         query_embedding=query_embedding,
-        top_k=top_k,
+        top_k=query_top_k,
         where=where,
     )
 
     chunks = []
+    raw_result_count = len(results["ids"][0]) if results and results["ids"] and results["ids"][0] else 0
     if results and results["ids"] and results["ids"][0]:
         existing_ids = _existing_chunk_ids(results["ids"][0])
         for i, chunk_id in enumerate(results["ids"][0]):
@@ -117,6 +140,13 @@ def retrieve(
             meta = results["metadatas"][0][i] if results["metadatas"] else {}
             content = results["documents"][0][i] if results["documents"] else ""
 
+            if scope_filter_enabled and not _is_allowed_for_project_scope(
+                scoped_project,
+                meta,
+                registered_projects,
+            ):
+                continue
+
             score *= _query_match_boost(query, meta)
             score *= _path_signal_boost(meta)
             if project_hint:
@@ -137,42 +167,151 @@ def retrieve(
 
     duration_ms = int((time.time() - start) * 1000)
     chunks.sort(key=lambda chunk: chunk.score, reverse=True)
+    post_filter_count = len(chunks)
+    chunks = chunks[:top_k]
 
     log.info(
         "retrieval_done",
         query=query[:100],
         top_k=top_k,
+        query_top_k=query_top_k,
+        raw_results_count=raw_result_count,
+        post_filter_count=post_filter_count,
         results_count=len(chunks),
+        post_filter_dropped=max(0, raw_result_count - post_filter_count),
+        underfilled=bool(raw_result_count >= query_top_k and len(chunks) < top_k),
         duration_ms=duration_ms,
     )
 
     return chunks
 
 
+def _is_allowed_for_project_scope(
+    project: RegisteredProject,
+    metadata: dict,
+    registered_projects: list[RegisteredProject] | None = None,
+) -> bool:
+    """Return True when a chunk is target-project or not project-owned.
+
+    Project-hinted retrieval should not let one registered project's corpus
+    compete with another's. At the same time, unowned/global sources should
+    remain eligible because shared docs and cross-project references can be
+    genuinely useful. The registry gives us the boundary: if metadata matches
+    a registered project and it is not the requested project, filter it out.
+    """
+    if _metadata_matches_project(project, metadata):
+        return True
+
+    if registered_projects is None:
+        try:
+            registered_projects = load_project_registry()
+        except Exception:
+            return True
+
+    for other in registered_projects:
+        if other.project_id == project.project_id:
+            continue
+        if _metadata_matches_project(other, metadata):
+            return False
+    return True
+
+
+def _metadata_matches_project(project: RegisteredProject, metadata: dict) -> bool:
+    stored_project_id = str(metadata.get("project_id", "")).strip().lower()
+    if stored_project_id:
+        return stored_project_id == project.project_id.lower()
+
+    path = _metadata_source_path(metadata)
+    tags = _metadata_tags(metadata)
+    for term in _project_scope_terms(project):
+        if _path_matches_term(path, term) or term in tags:
+            return True
+    return False
+
+
+def _project_scope_terms(project: RegisteredProject) -> set[str]:
+    terms = {project.project_id.lower()}
+    terms.update(alias.lower() for alias in project.aliases)
+    for source_ref in project.ingest_roots:
+        normalized = source_ref.subpath.replace("\\", "/").strip("/").lower()
+        if normalized:
+            terms.add(normalized)
+            terms.add(normalized.split("/")[-1])
+    return {term for term in terms if term}
+
+
+def _metadata_searchable(metadata: dict) -> str:
+    return " ".join(
+        [
+            str(metadata.get("source_file", "")).replace("\\", "/").lower(),
+            str(metadata.get("title", "")).lower(),
+            str(metadata.get("heading_path", "")).lower(),
+            str(metadata.get("tags", "")).lower(),
+        ]
+    )
+
+
+def _metadata_source_path(metadata: dict) -> str:
+    return str(metadata.get("source_file", "")).replace("\\", "/").strip("/").lower()
+
+
+def _metadata_tags(metadata: dict) -> set[str]:
+    raw_tags = metadata.get("tags", [])
+    if isinstance(raw_tags, (list, tuple, set)):
+        return {str(tag).strip().lower() for tag in raw_tags if str(tag).strip()}
+    if isinstance(raw_tags, str):
+        try:
+            parsed = json.loads(raw_tags)
+        except json.JSONDecodeError:
+            parsed = [raw_tags]
+        if isinstance(parsed, (list, tuple, set)):
+            return {str(tag).strip().lower() for tag in parsed if str(tag).strip()}
+        if isinstance(parsed, str) and parsed.strip():
+            return {parsed.strip().lower()}
+    return set()
+
+
+def _path_matches_term(path: str, term: str) -> bool:
+    normalized = term.replace("\\", "/").strip("/").lower()
+    if not path or not normalized:
+        return False
+    if "/" in normalized:
+        return path == normalized or path.startswith(f"{normalized}/")
+    return normalized in set(path.split("/"))
+
+
+def _metadata_has_term(metadata: dict, term: str) -> bool:
+    normalized = term.replace("\\", "/").strip("/").lower()
+    if not normalized:
+        return False
+    if _path_matches_term(_metadata_source_path(metadata), normalized):
+        return True
+    if normalized in _metadata_tags(metadata):
+        return True
+    return re.search(
+        rf"(?<![a-z0-9]){re.escape(normalized)}(?![a-z0-9])",
+        _metadata_searchable(metadata),
+    ) is not None
+
+
 def _project_match_boost(project_hint: str, metadata: dict) -> float:
     """Return a project-aware relevance multiplier for raw retrieval."""
     hint_lower = project_hint.strip().lower()
     if not hint_lower:
         return 1.0
 
-    source_file = str(metadata.get("source_file", "")).lower()
-    title = str(metadata.get("title", "")).lower()
-    tags = str(metadata.get("tags", "")).lower()
-    searchable = " ".join([source_file, title, tags])
-
-    project = get_registered_project(project_hint)
-    candidate_names = {hint_lower}
-    if project is not None:
-        candidate_names.add(project.project_id.lower())
-        candidate_names.update(alias.lower() for alias in project.aliases)
-        candidate_names.update(
-            source_ref.subpath.replace("\\", "/").strip("/").split("/")[-1].lower()
-            for source_ref in project.ingest_roots
-            if source_ref.subpath.strip("/\\")
+    try:
+        project = get_registered_project(project_hint)
+    except Exception as exc:
+        log.warning(
+            "project_match_boost_resolution_failed",
+            project_hint=project_hint,
+            error=str(exc),
         )
-
+        project = None
+    candidate_names = _project_scope_terms(project) if project is not None else {hint_lower}
     for candidate in candidate_names:
-        if candidate and candidate in searchable:
+        if _metadata_has_term(metadata, candidate):
             return _config.settings.rank_project_match_boost
 
     return 1.0

src/atocore/retrieval/vector_store.py

@@ -64,6 +64,18 @@ class VectorStore:
             self._collection.delete(ids=ids)
             log.debug("vectors_deleted", count=len(ids))
 
+    def get_metadatas(self, ids: list[str]) -> dict:
+        """Fetch vector metadata by chunk IDs."""
+        if not ids:
+            return {"ids": [], "metadatas": []}
+        return self._collection.get(ids=ids, include=["metadatas"])
+
+    def update_metadatas(self, ids: list[str], metadatas: list[dict]) -> None:
+        """Update vector metadata without re-embedding documents."""
+        if ids:
+            self._collection.update(ids=ids, metadatas=metadatas)
+            log.debug("vector_metadatas_updated", count=len(ids))
+
     @property
     def count(self) -> int:
         return self._collection.count()

tests/test_backfill_chunk_project_ids.py

@@ -0,0 +1,154 @@
+"""Tests for explicit chunk project_id metadata backfill."""
+
+import json
+
+import atocore.config as config
+from atocore.models.database import get_connection, init_db
+from scripts import backfill_chunk_project_ids as backfill
+
+
+def _write_registry(tmp_path, monkeypatch):
+    vault_dir = tmp_path / "vault"
+    drive_dir = tmp_path / "drive"
+    config_dir = tmp_path / "config"
+    project_dir = vault_dir / "incoming" / "projects" / "p04-gigabit"
+    project_dir.mkdir(parents=True)
+    drive_dir.mkdir()
+    config_dir.mkdir()
+    registry_path = config_dir / "project-registry.json"
+    registry_path.write_text(
+        json.dumps(
+            {
+                "projects": [
+                    {
+                        "id": "p04-gigabit",
+                        "aliases": ["p04"],
+                        "ingest_roots": [
+                            {"source": "vault", "subpath": "incoming/projects/p04-gigabit"}
+                        ],
+                    }
+                ]
+            }
+        ),
+        encoding="utf-8",
+    )
+    monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
+    monkeypatch.setenv("ATOCORE_DRIVE_SOURCE_DIR", str(drive_dir))
+    monkeypatch.setenv("ATOCORE_PROJECT_REGISTRY_PATH", str(registry_path))
+    config.settings = config.Settings()
+    return project_dir
+
+
+def _insert_chunk(file_path, metadata=None, chunk_id="chunk-1"):
+    with get_connection() as conn:
+        conn.execute(
+            """
+            INSERT INTO source_documents (id, file_path, file_hash, title, doc_type, tags)
+            VALUES (?, ?, ?, ?, ?, ?)
+            """,
+            ("doc-1", str(file_path), "hash", "Title", "markdown", "[]"),
+        )
+        conn.execute(
+            """
+            INSERT INTO source_chunks
+                (id, document_id, chunk_index, content, heading_path, char_count, metadata)
+            VALUES (?, ?, ?, ?, ?, ?, ?)
+            """,
+            (
+                chunk_id,
+                "doc-1",
+                0,
+                "content",
+                "Overview",
+                7,
+                json.dumps(metadata if metadata is not None else {}),
+            ),
+        )
+
+
+class FakeVectorStore:
+    def __init__(self, metadatas):
+        self.metadatas = dict(metadatas)
+        self.updated = []
+
+    def get_metadatas(self, ids):
+        returned_ids = [chunk_id for chunk_id in ids if chunk_id in self.metadatas]
+        return {
+            "ids": returned_ids,
+            "metadatas": [self.metadatas[chunk_id] for chunk_id in returned_ids],
+        }
+
+    def update_metadatas(self, ids, metadatas):
+        self.updated.append((list(ids), list(metadatas)))
+        for chunk_id, metadata in zip(ids, metadatas, strict=True):
+            self.metadatas[chunk_id] = metadata
+
+
+def test_backfill_dry_run_is_non_mutating(tmp_data_dir, tmp_path, monkeypatch):
+    init_db()
+    project_dir = _write_registry(tmp_path, monkeypatch)
+    _insert_chunk(project_dir / "status.md")
+
+    result = backfill.backfill(apply=False)
+
+    assert result["updates"] == 1
+    with get_connection() as conn:
+        row = conn.execute("SELECT metadata FROM source_chunks WHERE id = ?", ("chunk-1",)).fetchone()
+    assert json.loads(row["metadata"]) == {}
+
+
+def test_backfill_apply_updates_chroma_then_sql(tmp_data_dir, tmp_path, monkeypatch):
+    init_db()
+    project_dir = _write_registry(tmp_path, monkeypatch)
+    _insert_chunk(project_dir / "status.md", metadata={"source_file": "status.md"})
+    fake_store = FakeVectorStore({"chunk-1": {"source_file": "status.md"}})
+    monkeypatch.setattr(backfill, "get_vector_store", lambda: fake_store)
+
+    result = backfill.backfill(apply=True, require_chroma_snapshot=True)
+
+    assert result["applied_updates"] == 1
+    assert fake_store.metadatas["chunk-1"]["project_id"] == "p04-gigabit"
+    with get_connection() as conn:
+        row = conn.execute("SELECT metadata FROM source_chunks WHERE id = ?", ("chunk-1",)).fetchone()
+    assert json.loads(row["metadata"])["project_id"] == "p04-gigabit"
+
+
+def test_backfill_apply_requires_snapshot_confirmation(tmp_data_dir, tmp_path, monkeypatch):
+    init_db()
+    project_dir = _write_registry(tmp_path, monkeypatch)
+    _insert_chunk(project_dir / "status.md")
+
+    try:
+        backfill.backfill(apply=True)
+    except ValueError as exc:
+        assert "Chroma backup" in str(exc)
+    else:
+        raise AssertionError("Expected snapshot confirmation requirement")
+
+
+def test_backfill_missing_vector_skips_sql_update(tmp_data_dir, tmp_path, monkeypatch):
+    init_db()
+    project_dir = _write_registry(tmp_path, monkeypatch)
+    _insert_chunk(project_dir / "status.md")
+    fake_store = FakeVectorStore({})
+    monkeypatch.setattr(backfill, "get_vector_store", lambda: fake_store)
+
+    result = backfill.backfill(apply=True, require_chroma_snapshot=True)
+
+    assert result["updates"] == 1
+    assert result["applied_updates"] == 0
+    assert result["missing_vectors"] == 1
+    with get_connection() as conn:
+        row = conn.execute("SELECT metadata FROM source_chunks WHERE id = ?", ("chunk-1",)).fetchone()
+    assert json.loads(row["metadata"]) == {}
+
+
+def test_backfill_skips_malformed_metadata(tmp_data_dir, tmp_path, monkeypatch):
+    init_db()
+    project_dir = _write_registry(tmp_path, monkeypatch)
+    _insert_chunk(project_dir / "status.md", metadata=[])
+
+    result = backfill.backfill(apply=False)
+
+    assert result["updates"] == 0
+    assert result["malformed_metadata"] == 1

tests/test_config.py

@@ -46,6 +46,8 @@ def test_settings_keep_legacy_db_path_when_present(tmp_path, monkeypatch):
 
 def test_ranking_weights_are_tunable_via_env(monkeypatch):
     monkeypatch.setenv("ATOCORE_RANK_PROJECT_MATCH_BOOST", "3.5")
+    monkeypatch.setenv("ATOCORE_RANK_PROJECT_SCOPE_FILTER", "false")
+    monkeypatch.setenv("ATOCORE_RANK_PROJECT_SCOPE_CANDIDATE_MULTIPLIER", "6")
     monkeypatch.setenv("ATOCORE_RANK_QUERY_TOKEN_STEP", "0.12")
     monkeypatch.setenv("ATOCORE_RANK_QUERY_TOKEN_CAP", "1.5")
     monkeypatch.setenv("ATOCORE_RANK_PATH_HIGH_SIGNAL_BOOST", "1.25")
@@ -54,6 +56,8 @@ def test_ranking_weights_are_tunable_via_env(monkeypatch):
     settings = config.Settings()
 
     assert settings.rank_project_match_boost == 3.5
+    assert settings.rank_project_scope_filter is False
+    assert settings.rank_project_scope_candidate_multiplier == 6
     assert settings.rank_query_token_step == 0.12
     assert settings.rank_query_token_cap == 1.5
     assert settings.rank_path_high_signal_boost == 1.25

tests/test_ingestion.py

@@ -1,8 +1,10 @@
 """Tests for the ingestion pipeline."""
 
+import json
+
 from atocore.ingestion.parser import parse_markdown
 from atocore.models.database import get_connection, init_db
-from atocore.ingestion.pipeline import ingest_file, ingest_folder
+from atocore.ingestion.pipeline import ingest_file, ingest_folder, ingest_project_folder
 
 
 def test_parse_markdown(sample_markdown):
@@ -69,6 +71,153 @@ def test_ingest_updates_changed(tmp_data_dir, sample_markdown):
     assert result["status"] == "ingested"
 
 
+def test_ingest_file_records_project_id_metadata(tmp_data_dir, sample_markdown, monkeypatch):
+    """Project-aware ingestion should tag DB and vector metadata exactly."""
+    init_db()
+
+    class FakeVectorStore:
+        def __init__(self):
+            self.metadatas = []
+
+        def add(self, ids, documents, metadatas):
+            self.metadatas.extend(metadatas)
+
+        def delete(self, ids):
+            return None
+
+    fake_store = FakeVectorStore()
+    monkeypatch.setattr("atocore.ingestion.pipeline.get_vector_store", lambda: fake_store)
+
+    result = ingest_file(sample_markdown, project_id="p04-gigabit")
+
+    assert result["status"] == "ingested"
+    assert fake_store.metadatas
+    assert all(meta["project_id"] == "p04-gigabit" for meta in fake_store.metadatas)
+
+    with get_connection() as conn:
+        rows = conn.execute("SELECT metadata FROM source_chunks").fetchall()
+    assert rows
+    assert all(
+        json.loads(row["metadata"])["project_id"] == "p04-gigabit"
+        for row in rows
+    )
+
+
+def test_ingest_file_derives_project_id_from_registry_root(tmp_data_dir, tmp_path, monkeypatch):
+    """Unscoped ingest should preserve ownership for files under registered roots."""
+    import atocore.config as config
+
+    vault_dir = tmp_path / "vault"
+    drive_dir = tmp_path / "drive"
+    config_dir = tmp_path / "config"
+    project_dir = vault_dir / "incoming" / "projects" / "p04-gigabit"
+    project_dir.mkdir(parents=True)
+    drive_dir.mkdir()
+    config_dir.mkdir()
+    note = project_dir / "status.md"
+    note.write_text(
+        "# Status\n\nCurrent project status with enough detail to create "
+        "a retrievable chunk for the ingestion pipeline test.",
+        encoding="utf-8",
+    )
+    registry_path = config_dir / "project-registry.json"
+    registry_path.write_text(
+        json.dumps(
+            {
+                "projects": [
+                    {
+                        "id": "p04-gigabit",
+                        "aliases": ["p04"],
+                        "ingest_roots": [
+                            {"source": "vault", "subpath": "incoming/projects/p04-gigabit"}
+                        ],
+                    }
+                ]
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    class FakeVectorStore:
+        def __init__(self):
+            self.metadatas = []
+
+        def add(self, ids, documents, metadatas):
+            self.metadatas.extend(metadatas)
+
+        def delete(self, ids):
+            return None
+
+    fake_store = FakeVectorStore()
+    monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
+    monkeypatch.setenv("ATOCORE_DRIVE_SOURCE_DIR", str(drive_dir))
+    monkeypatch.setenv("ATOCORE_PROJECT_REGISTRY_PATH", str(registry_path))
+    config.settings = config.Settings()
+    monkeypatch.setattr("atocore.ingestion.pipeline.get_vector_store", lambda: fake_store)
+
+    init_db()
+    result = ingest_file(note)
+
+    assert result["status"] == "ingested"
+    assert fake_store.metadatas
+    assert all(meta["project_id"] == "p04-gigabit" for meta in fake_store.metadatas)
+
+
+def test_ingest_file_logs_and_fails_open_when_project_derivation_fails(
+    tmp_data_dir,
+    sample_markdown,
+    monkeypatch,
+):
+    """A broken registry should be visible but should not block ingestion."""
+    init_db()
+    warnings = []
+
+    class FakeVectorStore:
+        def __init__(self):
+            self.metadatas = []
+
+        def add(self, ids, documents, metadatas):
+            self.metadatas.extend(metadatas)
+
+        def delete(self, ids):
+            return None
+
+    fake_store = FakeVectorStore()
+    monkeypatch.setattr("atocore.ingestion.pipeline.get_vector_store", lambda: fake_store)
+    monkeypatch.setattr(
+        "atocore.projects.registry.derive_project_id_for_path",
+        lambda path: (_ for _ in ()).throw(ValueError("registry broken")),
+    )
+    monkeypatch.setattr(
+        "atocore.ingestion.pipeline.log.warning",
+        lambda event, **kwargs: warnings.append((event, kwargs)),
+    )
+
+    result = ingest_file(sample_markdown)
+
+    assert result["status"] == "ingested"
+    assert fake_store.metadatas
+    assert all(meta["project_id"] == "" for meta in fake_store.metadatas)
+    assert warnings[0][0] == "project_id_derivation_failed"
+    assert "registry broken" in warnings[0][1]["error"]
+
+
+def test_ingest_project_folder_passes_project_id_to_files(tmp_data_dir, sample_folder, monkeypatch):
+    seen = []
+
+    def fake_ingest_file(path, project_id=""):
+        seen.append((path.name, project_id))
+        return {"file": str(path), "status": "ingested"}
+
+    monkeypatch.setattr("atocore.ingestion.pipeline.ingest_file", fake_ingest_file)
+    monkeypatch.setattr("atocore.ingestion.pipeline._purge_deleted_files", lambda *args, **kwargs: 0)
+
+    ingest_project_folder(sample_folder, project_id="p05-interferometer")
+
+    assert seen
+    assert {project_id for _, project_id in seen} == {"p05-interferometer"}
+
+
 def test_parse_markdown_uses_supplied_text(sample_markdown):
     """Parsing should be able to reuse pre-read content from ingestion."""
     latin_text = """---\ntags: parser\n---\n# Parser Title\n\nBody text."""

tests/test_project_registry.py

@@ -5,6 +5,7 @@ import json
 import atocore.config as config
 from atocore.projects.registry import (
     build_project_registration_proposal,
+    derive_project_id_for_path,
     get_registered_project,
     get_project_registry_template,
     list_registered_projects,
@@ -103,6 +104,98 @@ def test_project_registry_resolves_alias(tmp_path, monkeypatch):
     assert project.project_id == "p05-interferometer"
 
 
+def test_derive_project_id_for_path_uses_registered_roots(tmp_path, monkeypatch):
+    vault_dir = tmp_path / "vault"
+    drive_dir = tmp_path / "drive"
+    config_dir = tmp_path / "config"
+    project_dir = vault_dir / "incoming" / "projects" / "p04-gigabit"
+    project_dir.mkdir(parents=True)
+    drive_dir.mkdir()
+    config_dir.mkdir()
+    note = project_dir / "status.md"
+    note.write_text("# Status\n\nCurrent work.", encoding="utf-8")
+
+    registry_path = config_dir / "project-registry.json"
+    registry_path.write_text(
+        json.dumps(
+            {
+                "projects": [
+                    {
+                        "id": "p04-gigabit",
+                        "aliases": ["p04"],
+                        "ingest_roots": [
+                            {"source": "vault", "subpath": "incoming/projects/p04-gigabit"}
+                        ],
+                    }
+                ]
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
+    monkeypatch.setenv("ATOCORE_DRIVE_SOURCE_DIR", str(drive_dir))
+    monkeypatch.setenv("ATOCORE_PROJECT_REGISTRY_PATH", str(registry_path))
+
+    original_settings = config.settings
+    try:
+        config.settings = config.Settings()
+        assert derive_project_id_for_path(note) == "p04-gigabit"
+        assert derive_project_id_for_path(tmp_path / "elsewhere.md") == ""
+    finally:
+        config.settings = original_settings
+
+
+def test_project_registry_rejects_cross_project_ingest_root_overlap(tmp_path, monkeypatch):
+    vault_dir = tmp_path / "vault"
+    drive_dir = tmp_path / "drive"
+    config_dir = tmp_path / "config"
+    vault_dir.mkdir()
+    drive_dir.mkdir()
+    config_dir.mkdir()
+
+    registry_path = config_dir / "project-registry.json"
+    registry_path.write_text(
+        json.dumps(
+            {
+                "projects": [
+                    {
+                        "id": "parent",
+                        "aliases": [],
+                        "ingest_roots": [
+                            {"source": "vault", "subpath": "incoming/projects/parent"}
+                        ],
+                    },
+                    {
+                        "id": "child",
+                        "aliases": [],
+                        "ingest_roots": [
+                            {"source": "vault", "subpath": "incoming/projects/parent/child"}
+                        ],
+                    },
+                ]
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
+    monkeypatch.setenv("ATOCORE_DRIVE_SOURCE_DIR", str(drive_dir))
+    monkeypatch.setenv("ATOCORE_PROJECT_REGISTRY_PATH", str(registry_path))
+
+    original_settings = config.settings
+    try:
+        config.settings = config.Settings()
+        try:
+            list_registered_projects()
+        except ValueError as exc:
+            assert "ingest root overlap" in str(exc)
+        else:
+            raise AssertionError("Expected overlapping ingest roots to raise")
+    finally:
+        config.settings = original_settings
+
+
 def test_refresh_registered_project_ingests_registered_roots(tmp_path, monkeypatch):
     vault_dir = tmp_path / "vault"
     drive_dir = tmp_path / "drive"
@@ -133,8 +226,8 @@ def test_refresh_registered_project_ingests_registered_roots(tmp_path, monkeypat
 
     calls = []
 
-    def fake_ingest_folder(path, purge_deleted=True):
-        calls.append((str(path), purge_deleted))
+    def fake_ingest_folder(path, purge_deleted=True, project_id=""):
+        calls.append((str(path), purge_deleted, project_id))
         return [{"file": str(path / "README.md"), "status": "ingested"}]
 
     monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
@@ -144,7 +237,7 @@ def test_refresh_registered_project_ingests_registered_roots(tmp_path, monkeypat
     original_settings = config.settings
     try:
         config.settings = config.Settings()
-        monkeypatch.setattr("atocore.projects.registry.ingest_folder", fake_ingest_folder)
+        monkeypatch.setattr("atocore.ingestion.pipeline.ingest_project_folder", fake_ingest_folder)
         result = refresh_registered_project("polisher")
     finally:
         config.settings = original_settings
@@ -153,6 +246,7 @@ def test_refresh_registered_project_ingests_registered_roots(tmp_path, monkeypat
     assert len(calls) == 1
     assert calls[0][0].endswith("p06-polisher")
     assert calls[0][1] is False
+    assert calls[0][2] == "p06-polisher"
     assert result["roots"][0]["status"] == "ingested"
     assert result["status"] == "ingested"
     assert result["roots_ingested"] == 1
@@ -188,7 +282,7 @@ def test_refresh_registered_project_reports_nothing_to_ingest_when_all_missing(
         encoding="utf-8",
     )
 
-    def fail_ingest_folder(path, purge_deleted=True):
+    def fail_ingest_folder(path, purge_deleted=True, project_id=""):
         raise AssertionError(f"ingest_folder should not be called for missing root: {path}")
 
     monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
@@ -198,7 +292,7 @@ def test_refresh_registered_project_reports_nothing_to_ingest_when_all_missing(
     original_settings = config.settings
     try:
         config.settings = config.Settings()
-        monkeypatch.setattr("atocore.projects.registry.ingest_folder", fail_ingest_folder)
+        monkeypatch.setattr("atocore.ingestion.pipeline.ingest_project_folder", fail_ingest_folder)
         result = refresh_registered_project("ghost")
     finally:
         config.settings = original_settings
@@ -238,7 +332,7 @@ def test_refresh_registered_project_reports_partial_status(tmp_path, monkeypatch
         encoding="utf-8",
     )
 
-    def fake_ingest_folder(path, purge_deleted=True):
+    def fake_ingest_folder(path, purge_deleted=True, project_id=""):
         return [{"file": str(path / "README.md"), "status": "ingested"}]
 
     monkeypatch.setenv("ATOCORE_VAULT_SOURCE_DIR", str(vault_dir))
@@ -248,7 +342,7 @@ def test_refresh_registered_project_reports_partial_status(tmp_path, monkeypatch
     original_settings = config.settings
     try:
         config.settings = config.Settings()
-        monkeypatch.setattr("atocore.projects.registry.ingest_folder", fake_ingest_folder)
+        monkeypatch.setattr("atocore.ingestion.pipeline.ingest_project_folder", fake_ingest_folder)
         result = refresh_registered_project("mixed")
     finally:
         config.settings = original_settings

tests/test_retrieval.py

@@ -70,8 +70,28 @@ def test_retrieve_skips_stale_vector_entries(tmp_data_dir, sample_markdown, monk
 
 
 def test_retrieve_project_hint_boosts_matching_chunks(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+    other_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p05-interferometer",
+            "aliases": ("p05", "interferometer"),
+            "ingest_roots": (),
+        },
+    )()
+
     class FakeStore:
         def query(self, query_embedding, top_k=10, where=None):
+            assert top_k == 8
             return {
                 "ids": [["chunk-a", "chunk-b"]],
                 "documents": [["project doc", "other doc"]],
@@ -102,22 +122,501 @@ def test_retrieve_project_hint_boosts_matching_chunks(monkeypatch):
     )
     monkeypatch.setattr(
         "atocore.retrieval.retriever.get_registered_project",
-        lambda project_name: type(
-            "Project",
-            (),
-            {
-                "project_id": "p04-gigabit",
-                "aliases": ("p04", "gigabit"),
-                "ingest_roots": (),
-            },
-        )(),
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, other_project],
     )
 
     results = retrieve("mirror architecture", top_k=2, project_hint="p04")
 
-    assert len(results) == 2
+    assert len(results) == 1
     assert results[0].chunk_id == "chunk-a"
-    assert results[0].score > results[1].score
+
+
+def test_retrieve_project_scope_allows_unowned_global_chunks(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            return {
+                "ids": [["chunk-a", "chunk-global"]],
+                "documents": [["project doc", "global doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/pkm/_index.md",
+                        "tags": '["p04-gigabit"]',
+                        "title": "P04",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "shared/engineering-rules.md",
+                        "tags": "[]",
+                        "title": "Shared engineering rules",
+                        "document_id": "doc-global",
+                    },
+                ]],
+                "distances": [[0.2, 0.21]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project],
+    )
+
+    results = retrieve("mirror architecture", top_k=2, project_hint="p04")
+
+    assert [r.chunk_id for r in results] == ["chunk-a", "chunk-global"]
+
+
+def test_retrieve_project_scope_filter_can_be_disabled(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+    other_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p05-interferometer",
+            "aliases": ("p05", "interferometer"),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            assert top_k == 2
+            return {
+                "ids": [["chunk-a", "chunk-b"]],
+                "documents": [["project doc", "other project doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/pkm/_index.md",
+                        "tags": '["p04-gigabit"]',
+                        "title": "P04",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p05-interferometer/pkm/_index.md",
+                        "tags": '["p05-interferometer"]',
+                        "title": "P05",
+                        "document_id": "doc-b",
+                    },
+                ]],
+                "distances": [[0.2, 0.2]],
+            }
+
+    monkeypatch.setattr("atocore.config.settings.rank_project_scope_filter", False)
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, other_project],
+    )
+
+    results = retrieve("mirror architecture", top_k=2, project_hint="p04")
+
+    assert {r.chunk_id for r in results} == {"chunk-a", "chunk-b"}
+
+
+def test_retrieve_project_scope_ignores_title_for_ownership(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+    other_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p06-polisher",
+            "aliases": ("p06", "polisher", "p11"),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            return {
+                "ids": [["chunk-target", "chunk-poisoned-title"]],
+                "documents": [["p04 doc", "p06 doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/pkm/_index.md",
+                        "tags": '["p04-gigabit"]',
+                        "title": "P04",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p06-polisher/pkm/architecture.md",
+                        "tags": '["p06-polisher"]',
+                        "title": "GigaBIT M1 mirror lessons",
+                        "document_id": "doc-b",
+                    },
+                ]],
+                "distances": [[0.2, 0.19]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, other_project],
+    )
+
+    results = retrieve("mirror architecture", top_k=2, project_hint="p04")
+
+    assert [r.chunk_id for r in results] == ["chunk-target"]
+
+
+def test_retrieve_project_scope_uses_path_segments_not_substrings(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p05-interferometer",
+            "aliases": ("p05", "interferometer"),
+            "ingest_roots": (),
+        },
+    )()
+    abb_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "abb-space",
+            "aliases": ("abb",),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            return {
+                "ids": [["chunk-target", "chunk-global"]],
+                "documents": [["p05 doc", "global doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p05-interferometer/pkm/_index.md",
+                        "tags": '["p05-interferometer"]',
+                        "title": "P05",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Abbreviation notes",
+                        "source_file": "shared/cabbage-abbreviations.md",
+                        "tags": "[]",
+                        "title": "ABB-style abbreviations",
+                        "document_id": "doc-global",
+                    },
+                ]],
+                "distances": [[0.2, 0.21]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, abb_project],
+    )
+
+    results = retrieve("abbreviations", top_k=2, project_hint="p05")
+
+    assert [r.chunk_id for r in results] == ["chunk-target", "chunk-global"]
+
+
+def test_retrieve_project_scope_prefers_exact_project_id(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+    other_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p06-polisher",
+            "aliases": ("p06", "polisher"),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            return {
+                "ids": [["chunk-target", "chunk-other", "chunk-global"]],
+                "documents": [["target doc", "other doc", "global doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "legacy/unhelpful-path.md",
+                        "tags": "[]",
+                        "title": "Target",
+                        "project_id": "p04-gigabit",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/title-poisoned.md",
+                        "tags": '["p04-gigabit"]',
+                        "title": "Looks target-owned but is explicit p06",
+                        "project_id": "p06-polisher",
+                        "document_id": "doc-b",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "shared/global.md",
+                        "tags": "[]",
+                        "title": "Shared",
+                        "project_id": "",
+                        "document_id": "doc-global",
+                    },
+                ]],
+                "distances": [[0.2, 0.19, 0.21]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, other_project],
+    )
+
+    results = retrieve("mirror architecture", top_k=3, project_hint="p04")
+
+    assert [r.chunk_id for r in results] == ["chunk-target", "chunk-global"]
+
+
+def test_retrieve_empty_project_id_falls_back_to_path_ownership(monkeypatch):
+    target_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p04-gigabit",
+            "aliases": ("p04", "gigabit"),
+            "ingest_roots": (),
+        },
+    )()
+    other_project = type(
+        "Project",
+        (),
+        {
+            "project_id": "p05-interferometer",
+            "aliases": ("p05", "interferometer"),
+            "ingest_roots": (),
+        },
+    )()
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            return {
+                "ids": [["chunk-target", "chunk-other"]],
+                "documents": [["target doc", "other doc"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/status.md",
+                        "tags": "[]",
+                        "title": "Target",
+                        "project_id": "",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p05-interferometer/status.md",
+                        "tags": "[]",
+                        "title": "Other",
+                        "project_id": "",
+                        "document_id": "doc-b",
+                    },
+                ]],
+                "distances": [[0.2, 0.19]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: target_project,
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.load_project_registry",
+        lambda: [target_project, other_project],
+    )
+
+    results = retrieve("mirror architecture", top_k=2, project_hint="p04")
+
+    assert [r.chunk_id for r in results] == ["chunk-target"]
+
+
+def test_retrieve_unknown_project_hint_does_not_widen_or_filter(monkeypatch):
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            assert top_k == 2
+            return {
+                "ids": [["chunk-a", "chunk-b"]],
+                "documents": [["doc a", "doc b"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "project-a/file.md",
+                        "tags": "[]",
+                        "title": "A",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "project-b/file.md",
+                        "tags": "[]",
+                        "title": "B",
+                        "document_id": "doc-b",
+                    },
+                ]],
+                "distances": [[0.2, 0.21]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: None,
+    )
+
+    results = retrieve("overview", top_k=2, project_hint="unknown-project")
+
+    assert [r.chunk_id for r in results] == ["chunk-a", "chunk-b"]
+
+
+def test_retrieve_fails_open_when_project_scope_resolution_fails(monkeypatch):
+    warnings = []
+
+    class FakeStore:
+        def query(self, query_embedding, top_k=10, where=None):
+            assert top_k == 2
+            return {
+                "ids": [["chunk-a", "chunk-b"]],
+                "documents": [["doc a", "doc b"]],
+                "metadatas": [[
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p04-gigabit/file.md",
+                        "tags": "[]",
+                        "title": "A",
+                        "document_id": "doc-a",
+                    },
+                    {
+                        "heading_path": "Overview",
+                        "source_file": "p05-interferometer/file.md",
+                        "tags": "[]",
+                        "title": "B",
+                        "document_id": "doc-b",
+                    },
+                ]],
+                "distances": [[0.2, 0.21]],
+            }
+
+    monkeypatch.setattr("atocore.retrieval.retriever.get_vector_store", lambda: FakeStore())
+    monkeypatch.setattr("atocore.retrieval.retriever.embed_query", lambda query: [0.0, 0.1])
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever._existing_chunk_ids",
+        lambda chunk_ids: set(chunk_ids),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.get_registered_project",
+        lambda project_name: (_ for _ in ()).throw(ValueError("registry overlap")),
+    )
+    monkeypatch.setattr(
+        "atocore.retrieval.retriever.log.warning",
+        lambda event, **kwargs: warnings.append((event, kwargs)),
+    )
+
+    results = retrieve("overview", top_k=2, project_hint="p04")
+
+    assert [r.chunk_id for r in results] == ["chunk-a", "chunk-b"]
+    assert {warning[0] for warning in warnings} == {
+        "project_scope_resolution_failed",
+        "project_match_boost_resolution_failed",
+    }
+    assert all("registry overlap" in warning[1]["error"] for warning in warnings)
 
 
 def test_retrieve_downranks_archive_noise_and_prefers_high_signal_paths(monkeypatch):