docs(claude): record plan 002 phase 3 in the project status

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

CLAUDE.md

@@ -34,9 +34,100 @@ e2e suite in the default pytest run (`tests/e2e/test_ingestion_slice.py`:
 duplicate upload, retry after failure, tenant isolation, capacity, timeout,
 parse and Qdrant failure), and the one Compose-based test — `scripts/smoke.sh`
 driving `tests/e2e/test_compose_smoke.py` against a real uvicorn process, which
-skips itself unless `SMOKE_BASE_URL` is set. Not built yet: `/v1/points` CRUD
+skips itself unless `SMOKE_BASE_URL` is set. That maps to plan 001 Phases 1-6
-and keyword search (plan 002), and `src/agent/`. That maps to plan 001 Phases
+done.
-1-6 done.
+
+Plan 002 (`/v1/points` CRUD and keyword search) is **Phases 1-3 done**. Phase 1
+landed the `PointRepository` port (`src/application/ports/point_repository.py`)
+with its `Point` read model (`src/application/points/point.py`), the Qdrant adapter
+(`src/infrastructure/qdrant/point_repository.py`), request/response schemas
+(`src/api/schemas/points.py`), and lifespan wiring. This port is **separate from
+`PointStorage`**, which stays exactly the two bulk operations ingestion
+performs — reads, single-point edits, and keyword search have a different caller
+and a different tenant-filter obligation, so do not accrete them onto the
+ingestion port. `tenant_id` is a required keyword argument on every
+`PointRepository` method by design; keep it that way, because it is what turns a
+forgotten tenant filter into a type error. The `chunks` collection also gained
+full-text `content`, `is_active`, and `chunk_index` payload indexes, so a
+deployed environment needs `qdrant_bootstrap` re-run (indexes are additive — no
+rebuild, no re-embedding).
+
+Two adapter mechanics there are load-bearing and easy to "simplify" into bugs:
+reads go through `scroll` with a `HasIdCondition` rather than `retrieve` (which
+takes no filter, and would move the tenant check to *after* Qdrant answered),
+and ordered listing paginates by `order_id` value rather than offset (Qdrant
+returns no page offset under `order_by`, and an offset cursor skips or repeats
+rows under a concurrent insert).
+
+Phase 2 added the **read routes**: `GET /v1/points/{point_id}`,
+`GET /v1/points?file_id=...`, `GET /v1/points/count`, `GET /v1/points/search`,
+and `GET /v1/files/{file_id}/points`, over `src/application/points/queries.py`
+(`src/api/routers/points.py`). All are gated on `points:read`, which — with
+`points:write` — is now in `DEFAULT_SCOPES`; `GET /v1/files/{file_id}/points`
+uses `points:read` rather than `files:write`, so the scope follows the data
+rather than the URL prefix. `PointNotFoundError` maps to `404` in
+`src/api/errors.py`, never `403`. Three route-level rules are load-bearing:
+`/count` and `/search` are declared **before** `/{point_id}` (FastAPI matches in
+declaration order, so reordering them makes `/v1/points/count` a `422`),
+`file_id` is **required** on the listing (the cursor is an `order_id` value and
+`order_id` is unique only within one file), and `search_points` folds the query
+with `normalize_persian_text` before matching, because ingestion letter-folds
+content and an unfolded Arabic-keyboard query would return an empty result set
+silently rather than erroring (ADR-0002).
+
+Phase 3 added **soft delete**: `DELETE /v1/points/{point_id}` and
+`DELETE /v1/files/{file_id}`, over `src/application/points/deletion.py` (with
+the pure relinking primitive in `src/application/points/relinking.py`) and
+`src/application/files/deletion.py`. Both are gated on `points:write` — the
+file route included, since the data it destroys is points. Nothing is ever
+removed from Qdrant.
+
+Four rules there are load-bearing, and three of them look like complications
+until the concurrency is taken seriously:
+
+- `patches_for_removal` computes **what is still missing between the state just
+  read and the desired end state**, not "the patches a delete implies". That is
+  what makes a normal delete, a second delete of an already-inactive point (a
+  no-op success, never `404`), and recovery from a half-applied batch one code
+  path. Rewriting it as a straight-line "deactivate, patch prev, patch next"
+  breaks all three.
+- Qdrant has no multi-point transaction and reports success for a filtered
+  `set_payload` that matched nothing, so a batch whose second operation loses a
+  version race applies its first anyway. `soft_delete_point` therefore re-plans
+  and re-applies up to three times, verifying by read-back, and only then raises
+  `PointVersionConflictError` (`409`). A single-shot delete would be able to
+  leave a stale pointer, which ADR-0002 calls a defect.
+- A soft-deleted point **keeps its own** `previous_chunk_id`/`next_chunk_id`;
+  only the surviving neighbours are rewritten. Those pointers are unreachable
+  rather than stale, they are the only record of where the point sat, and the
+  retry re-plans from them. The whole-file sweep follows from the same rule:
+  every point leaves at once, so no survivor can dangle and no pointer is
+  touched at all.
+- `DELETE /v1/files/{file_id}` marks the `source_files` row `soft_deleted`
+  **after** the point sweep, in its own short transaction (no session is held
+  across the Qdrant work). Order matters: a half-finished sweep leaves the row
+  `active` and a retried `DELETE` finishes it, and retiring the row is what
+  makes a later re-upload of the same bytes re-ingest instead of matching
+  `find_active_by_content_hash` and returning a file whose points are gone.
+
+Audit rows are still Phase 4/6 work; Phase 3 emits log events only
+(`points.soft_deleted`, `files.soft_deleted`, `points.relink.neighbour_missing`,
+and the two `*.conflict` warnings). The completion and conflict events carry
+ADR-0011's `duration_ms` plus `rounds`, and the pair is what makes them
+diagnostic: relinking itself is O(1) (that is what the adjacency pointers buy),
+so a single-point delete costs a fixed ~5 Qdrant round trips and a `rounds`
+above 1 means contention, not a slow store. The whole-file sweep is the one
+whose cost scales — two round trips per 100-point page.
+
+Also worth knowing before touching the points tests: `tests/support/point_contract.py`
+holds **one** scenario suite run against both `FakePointRepository` (unit) and
+`QdrantPointRepository` (integration), so new repository behaviour belongs there
+rather than in one of the two runners — that is what keeps the fake from drifting
+more permissive than the real store.
+
+Not built yet: plan 002 Phases 4-6 — create/replace/patch, reorder and batch,
+the `api_request_logs`/`point_audit_events` tables, and the runbook section on
+inspecting and repairing a file's pointer chain — and `src/agent/`.
 
 Architecture decisions live in `docs/adr/` (18 ADRs plus the 0000 template;
 0001–0004 are `Accepted` — 0004 amended by 0018; 0014 is `Superseded by 0017`;

docs/adr/0002-chunk-crud-and-search-api.md

@@ -75,6 +75,51 @@ retrieval used by the AI agent in ADR-0003; the two "search" concepts serve
 different callers (a human/admin managing chunks vs. an agent retrieving
 context) and should not be conflated in the API or in future discussion.
 
+Two properties follow from the index being a *filter*: results carry no
+relevance score, and their order is unspecified. The API therefore returns
+neither a score field nor a ranked list, and callers must not read the array
+order as relevance. A caller that wants ranking wants ADR-0003's path.
+
+#### The query is normalized the way ingested content was
+
+`normalize_persian_text` (ADR-0018) folds Arabic letterforms to their Persian
+equivalents — U+064A to U+06CC, U+0643 to U+06A9 — on every text block before
+chunking, so stored `content` is uniformly Persian-formed. A query string is
+not chunk content and never passes through that path, so a term typed on an
+Arabic keyboard reaches the index as a different codepoint sequence than the
+document it should match.
+
+The service therefore applies the same folding to the query before matching.
+Without it the endpoint fails in the worst available way: an exact-looking
+query returns an empty result set, with no error, no warning, and nothing in
+the logs to distinguish "no such term" from "the term is spelled with the
+other yeh". Note this is a *query-side* transformation only — it changes what
+is compared, never what is stored.
+
+This does not extend to stemming or synonyms. Qdrant's full-text index offers
+neither, and adding a Farsi analyzer here would duplicate the benchmarked BM25
+sparse pipeline (ADR-0005) in a code path that is not benchmarked against
+anything.
+
+#### Listing is scoped to one file, and paginates by `order_id`
+
+`GET /points?file_id=...` requires `file_id` rather than treating it as one
+optional filter among several, and its pagination cursor is an `order_id`
+value rather than an offset. Both follow from `order_id` being per-file:
+
+- A cursor is only meaningful against a totally ordered key. `order_id` orders
+  points within one file and says nothing across files, so an unscoped listing
+  has no stable sort to paginate along.
+- An offset cursor is wrong even within one file. Insert, reorder, and delete
+  all shift positions, so a page-two request issued after a concurrent insert
+  ahead of the cursor would repeat a row already returned — silently. Ranging
+  on `order_id > cursor` is unaffected: the reader has passed that value, and a
+  point inserted behind it was already served.
+
+The second point depends on `order_id` being unique within a file, which the
+gap-exhaustion rule below preserves by rejecting a reorder whose computed gap
+would collapse onto a neighbour value.
+
 ### Delete is soft by default
 
 `DELETE /points/{point_id}` and `DELETE /points?file_id=...` set
@@ -105,6 +150,41 @@ Qdrant's `update_filter`, giving an optimistic-concurrency-style guard
 against races between a concurrent ingestion re-run (ADR-0001) and a manual
 edit through this API.
 
+### Re-ingestion versus manual edits
+
+A file can be re-uploaded after someone has hand-edited one of its points
+through this API. **The newly ingested file wins.** Ingestion is authoritative
+for the content of the file it ingested; a manual edit is a correction that
+survives only until the source document is replaced.
+
+Concretely:
+
+- A point that still exists in the new version (same `file_id` +
+  `chunk_index`, hence the same deterministic point ID) is **overwritten in
+  place**. Ingestion performs a read-check-write so `version` is incremented
+  from whatever the manual edit left it at, rather than reset to `1`.
+- A point from the previous ingestion that is **absent** from the new version
+  is flagged `is_active: false` with `deleted_at` set. It is never removed
+  from Qdrant — the soft-delete rule above applies to re-ingestion exactly as
+  it applies to `DELETE`.
+- A manually created point (`POST /points`) is assigned a `chunk_index` past
+  the ingested range, so the same sweep deactivates it on the next upload of
+  its file. This is the intended consequence of "the new file wins", not an
+  accident of the sweep's bounds.
+
+Because the point ID is derived from the immutable `chunk_index`, an
+overwritten point cannot hold both the manual edit and the new file's content.
+The clobbered content is therefore recorded in `point_audit_events`
+(ADR-0009) as a `reingest_overwrite` operation carrying `before_version`, so
+the edit is recoverable from the audit trail even though it is no longer a
+live point.
+
+Rejected alternative: preserving manual edits by having ingestion skip points
+with `version > 1`. It breaks the guarantee that a successful upload leaves
+Qdrant matching the uploaded document, and it needs a second, separate rule
+for edited points that no longer exist in the new version — two divergent
+notions of authority over one file.
+
 ### Re-embedding on content edit
 
 `PUT /points/{point_id}` can change `content`, which leaves the stored

docs/plans/002-point-crud-and-keyword-search.md

@@ -15,8 +15,9 @@ are; this document defines order, scope, and verification criteria.
 
 ## Prerequisite
 
-Plan 001 must be complete through **Phase 5** before Phase 3 of this plan
+Plan 001 is complete through Phase 6, so this prerequisite is satisfied. It
-starts. Specifically this plan depends on: the `chunks` collection and its
+required plan 001 through **Phase 5** before Phase 3 of this plan starts.
+Specifically this plan depends on: the `chunks` collection and its
 payload indexes actually existing, API-key authentication and `AuthContext`
 tenant derivation, the application-lifetime Qdrant client from the FastAPI
 lifespan, and the request-lifetime `AsyncSession` wiring. Phases 1–2 below
@@ -71,7 +72,9 @@ project owner accepts them, and update the ADR rather than diverging silently.
   (bulk soft delete of a file's points), from ADR-0008.
 - Soft delete as the default for every delete path, with neighbor relinking.
 - Optimistic concurrency on every mutating path via the `version` payload field.
-- Audit rows in Postgres for mutating operations.
+- Audit rows in Postgres for mutating operations: both ADR-0009 tables,
+  `api_request_logs` (one row per API call, written from the request middleware)
+  and `point_audit_events` with the real `api_request_log_id` foreign key.
 - Automated tests for tenant isolation, pointer integrity, concurrency
   conflicts, and pagination.
 
@@ -113,40 +116,22 @@ project owner accepts them, and update the ADR rather than diverging silently.
 9. Routers contain no Qdrant SDK calls and no filter construction. The Qdrant
    client is injected from the lifespan (ADR-0012).
 
-## Decisions needed before the affected phase
+## Decisions resolved before implementation
 
-### Re-embedding on content edit (blocks Phase 4)
+An earlier revision of this plan listed three open decisions here. All are now
+settled, and one further question this plan deferred to a Phase 6 test has been
+settled too. They are recorded in the ADRs — these lines are a pointer, not a
+second source of truth.
 
-`PUT /v1/points/{point_id}` can change `content`. The stored vectors then no
+| Question | Resolution | Recorded in |
-longer match the text. Three options, in order of preference:
+|---|---|---|
+| Re-embedding on content edit | Re-embed inline, reusing ingestion's ports and bounds and its `502`/`504` codes. The re-embed happens *before* the version-guarded write, so a stale edit still `409`s rather than re-embedding for nothing. | ADR-0002, "Re-embedding on content edit" |
+| Fractional-key exhaustion | No renormalize endpoint in this slice. Log `points.order_id.gap_low` under a safety threshold; reject with `409` and a distinct error code if the gap would collapse onto a neighbor value. Recovery is a runbook operation. | ADR-0002, "`order_id` gap exhaustion" |
+| Batch semantics | All-or-nothing, capped at 100 operations. Every operation's `version` precondition is validated before any is applied; one failure rejects the whole request and nothing reaches Qdrant. | ADR-0002, "`POST /points/batch` semantics" |
+| Re-ingestion versus manual edits | The newly uploaded file wins. Surviving points are overwritten in place with an incremented `version`; points absent from the new version are flagged inactive, never removed; manually created points sit past the ingested `chunk_index` range and are swept by the same rule. Clobbered content is recorded in `point_audit_events` as `reingest_overwrite`. | ADR-0002, "Re-ingestion versus manual edits" |
 
-1. **Re-embed inline** on content change, reusing plan 001's embedding ports and
+Phase 6's cross-slice end-to-end test therefore *verifies* the re-ingestion rule
-   bounds. Consistent, but puts embedder latency and `502`/`504` failure modes
+rather than forcing the decision.
-   on an admin edit path.
-2. **Require caller-supplied vectors** when content changes, and reject the edit
-   otherwise. Simple and honest, but pushes model knowledge to the client.
-3. **Mark the point stale** (a payload flag) and re-embed later. Needs
-   background work, which ADR-0017 currently rules out.
-
-Default to (1) for parity with ingestion, with the same batch/semaphore bounds
-and the same status codes. Record whichever is chosen in ADR-0002 before
-implementing Phase 4 — this is a real behavioral contract, not an
-implementation detail.
-
-### Fractional-key exhaustion
-
-ADR-0001 notes float keys eventually need renormalization. Decide now whether
-this slice ships a renormalize path (an internal operation rewriting a file's
-`order_id` values to `1000, 2000, 3000, ...`) or explicitly defers it with a
-logged warning when the gap between neighbors falls under a threshold. Deferring
-is acceptable; silently producing unrepresentable gaps is not.
-
-### Batch semantics
-
-`POST /v1/points/batch` must define, in the API schema and the tests: whether
-operations are all-or-nothing, what happens when operation 3 of 5 fails a
-version check, and the maximum operation count per request. Decide before
-Phase 5; do not let the answer be "whatever Qdrant happened to do."
 
 ## Build order
 
@@ -251,8 +236,8 @@ of mutations.
    ordering behavior, isolated per test by unique collection or tenant keys.
 2. An end-to-end test crossing plan 001 and this slice: ingest a CSV, list its
    points, reorder one, soft-delete another, re-upload the same file, and assert
-   the manual edits interact with re-ingestion exactly as ADR-0001/0002 specify.
+   the manual edits interact with re-ingestion exactly as ADR-0002's
-   If that interaction is not yet decided, this test is what forces the decision.
+   "Re-ingestion versus manual edits" specifies.
 3. Structured logging at the mutation boundary with stable event names
    (`points.updated`, `points.reordered`, `points.soft_deleted`) carrying
    `request_id`, `tenant_id`, `file_id`, and the resulting version.

docs/runbook.md

@@ -80,10 +80,22 @@ Re-running with the same `--slug` reuses the tenant and any domains it already
 has, and issues an **additional** key. Both keys stay valid; this adds a key, it
 does not rotate one.
 
-Scopes are the security boundary between uploading and managing the allowlist.
+Scopes are the security boundary between uploading, reading chunks, and
-Give an upload client `files:write` only. `domains:write` lets its holder create
+managing the allowlist. Give an upload client `files:write` only. `domains:write`
-new domains, which is exactly what the allowlist exists to prevent an upload key
+lets its holder create new domains, which is exactly what the allowlist exists to
-from doing.
+prevent an upload key from doing, and `points:read` lets its holder read the text
+of every chunk of every file — so an upload-only key gets neither.
+
+| Scope | Grants |
+|---|---|
+| `files:write` | Upload a document and read its ingestion status. |
+| `points:read` | Read, list, count, and keyword-search this tenant's points, including `GET /v1/files/{file_id}/points`. |
+| `points:write` | Create, edit, reorder, and soft-delete points (plan 002 Phases 3-5; no route uses it yet). |
+| `domains:read` / `domains:write` | Inspect and manage the domain allowlist. |
+| `admin` | Satisfies every scope check. |
+
+The command's `--scopes` default issues all of the above except `admin`, which
+suits a first operator key; narrow it explicitly for per-client keys.
 
 ### Domains after the first one
 

src/api/errors.py

@@ -17,7 +17,11 @@ from src.application.auth.errors import (
     TenantInactiveError,
 )
 from src.application.domains.errors import DomainAlreadyExistsError, UnknownDomainError
-from src.application.files.errors import FileTooLargeError, InvalidUploadError
+from src.application.files.errors import (
+    FileTooLargeError,
+    InvalidUploadError,
+    SourceFileNotFoundError,
+)
 from src.application.ingestion.errors import (
     ChunkLimitExceededError,
     DocumentParseError,
@@ -27,6 +31,8 @@ from src.application.ingestion.errors import (
     PointIndexingError,
     UnsupportedSourceTypeError,
 )
+from src.application.points.errors import PointVersionConflictError
+from src.application.points.point import PointNotFoundError
 
 logger = structlog.get_logger(__name__)
 
@@ -41,6 +47,13 @@ _MAPPING: tuple[tuple[type[Exception], int, str], ...] = (
     (TenantInactiveError, status.HTTP_401_UNAUTHORIZED, "tenant_not_found"),
     (MissingScopeError, status.HTTP_403_FORBIDDEN, "missing_scope"),
     (InvalidUploadError, status.HTTP_400_BAD_REQUEST, "validation_error"),
+    # 404, never 403: a cross-tenant point id must be indistinguishable from a
+    # nonexistent one, or the API becomes an existence oracle (ADR-0016).
+    (PointNotFoundError, status.HTTP_404_NOT_FOUND, "not_found"),
+    (SourceFileNotFoundError, status.HTTP_404_NOT_FOUND, "not_found"),
+    # Not "the version guard fired once" — that is retried. This is the service
+    # giving up after repeated re-plans, i.e. a genuinely contended point.
+    (PointVersionConflictError, status.HTTP_409_CONFLICT, "conflict"),
     (UnknownDomainError, status.HTTP_400_BAD_REQUEST, "unknown_domain"),
     (DomainAlreadyExistsError, status.HTTP_409_CONFLICT, "conflict"),
     (DocumentParseError, status.HTTP_400_BAD_REQUEST, "validation_error"),

src/api/router.py

@@ -2,7 +2,9 @@ from fastapi import APIRouter
 
 from src.api.routers.domains import router as domains_router
 from src.api.routers.files import router as files_router
+from src.api.routers.points import router as points_router
 
 router = APIRouter()
 router.include_router(domains_router)
 router.include_router(files_router)
+router.include_router(points_router)

src/api/routers/files.py

@@ -1,4 +1,4 @@
-"""`POST /v1/files`, `GET /v1/files/{file_id}` (ADR-0008).
+"""`POST /v1/files`, `GET /v1/files/{file_id}`, `DELETE /v1/files/{file_id}` (ADR-0008).
 
 Routes adapt HTTP to `application/files` calls; they do not parse, hash,
 touch MinIO/Qdrant, or otherwise carry ingestion business logic (ADR-0015).
@@ -13,18 +13,23 @@ from fastapi import APIRouter, Depends, Form, HTTPException, Response, UploadFil
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from src.api.dependencies.auth import require_scope
-from src.api.schemas.files import FileStatusResponse, FileUploadResponse
+from src.api.schemas.files import FileDeleteResponse, FileStatusResponse, FileUploadResponse
+from src.api.schemas.points import DEFAULT_PAGE_SIZE, LimitQuery, PointListResponse
 from src.application.auth.context import AuthContext
+from src.application.files.deletion import delete_source_file
 from src.application.files.status import get_file_status
 from src.application.files.upload import upload_source_file
+from src.application.points.queries import list_file_points
 from src.application.ports.embedding import DenseEmbedder, SparseEmbedder
 from src.application.ports.object_storage import ObjectStorage
+from src.application.ports.point_repository import PointRepository
 from src.application.ports.point_storage import PointStorage
 from src.bootstrap.dependencies import (
     get_dense_embedders,
     get_ingestion_concurrency_limiter,
     get_ingestion_limiter,
     get_object_storage,
+    get_point_repository,
     get_point_storage,
     get_sessionmaker,
     get_settings,
@@ -35,9 +40,12 @@ from src.config import Settings
 router = APIRouter(prefix="/files", tags=["files"])
 
 _RequireFilesWrite = Annotated[AuthContext, Depends(require_scope("files:write"))]
+_RequirePointsRead = Annotated[AuthContext, Depends(require_scope("points:read"))]
+_RequirePointsWrite = Annotated[AuthContext, Depends(require_scope("points:write"))]
 _SessionmakerDep = Annotated[async_sessionmaker[AsyncSession], Depends(get_sessionmaker)]
 _ObjectStorageDep = Annotated[ObjectStorage, Depends(get_object_storage)]
 _PointStorageDep = Annotated[PointStorage, Depends(get_point_storage)]
+_PointRepositoryDep = Annotated[PointRepository, Depends(get_point_repository)]
 _SettingsDep = Annotated[Settings, Depends(get_settings)]
 _IngestionLimiterDep = Annotated[CapacityLimiter, Depends(get_ingestion_limiter)]
 _ConcurrencyLimiterDep = Annotated[Semaphore, Depends(get_ingestion_concurrency_limiter)]
@@ -92,3 +100,58 @@ async def get_file(
     if result is None:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
     return FileStatusResponse.from_result(result)
+
+
+@router.delete("/{file_id}")
+async def delete_file(
+    file_id: uuid.UUID,
+    auth: _RequirePointsWrite,
+    sessionmaker: _SessionmakerDep,
+    repository: _PointRepositoryDep,
+) -> FileDeleteResponse:
+    """Soft-delete a file: every active point, then the `source_files` row.
+
+    Gated on `points:write` rather than `files:write` for the same reason as the
+    listing above — the data this destroys is points. Nothing is removed from
+    Qdrant (ADR-0002); the points are flagged inactive and the row is marked
+    `soft_deleted`, which is also what makes a later re-upload of the same bytes
+    ingest afresh instead of matching the duplicate path.
+
+    Deleting an already-deleted file is a success reporting `0` points.
+    """
+    points_soft_deleted = await delete_source_file(
+        sessionmaker,
+        repository,
+        tenant_id=auth.tenant_id,
+        source_file_id=file_id,
+        actor=f"api_key:{auth.api_key_id}",
+    )
+    return FileDeleteResponse(
+        file_id=file_id, status="soft_deleted", points_soft_deleted=points_soft_deleted
+    )
+
+
+@router.get("/{file_id}/points")
+async def list_points_for_file(
+    file_id: uuid.UUID,
+    auth: _RequirePointsRead,
+    repository: _PointRepositoryDep,
+    limit: LimitQuery = DEFAULT_PAGE_SIZE,
+    cursor: str | None = None,
+    include_inactive: bool = False,
+) -> PointListResponse:
+    """The same listing as `GET /v1/points?file_id=...`, addressed by file.
+
+    Gated on `points:read`, not `files:write`: the resource being read is the
+    file's chunks, so the scope follows the data rather than the URL prefix. An
+    upload-only key must not become a way to read every chunk of every file.
+    """
+    page = await list_file_points(
+        repository,
+        tenant_id=auth.tenant_id,
+        file_id=file_id,
+        limit=limit,
+        cursor=cursor,
+        include_inactive=include_inactive,
+    )
+    return PointListResponse.from_page(page)

src/api/routers/points.py

@@ -0,0 +1,162 @@
+"""`/v1/points` read and soft-delete paths (ADR-0002, ADR-0008).
+
+Routes adapt HTTP to `application/points` calls. They build no Qdrant filters
+and hold no CRUD semantics (ADR-0015), and they never read a tenant from the
+request — `auth.tenant_id` is the only source, which is what makes ADR-0002's
+isolation rule structural rather than a habit.
+
+**Route order is load-bearing.** `/count` and `/search` are declared before
+`/{point_id}`. FastAPI matches in declaration order, so with `/{point_id}` first
+a request for `/v1/points/count` would try to parse `"count"` as a UUID and
+fail with `422` instead of counting anything. The failure is loud but confusing,
+and it comes back the moment someone reorders these for tidiness.
+
+Gated on `points:read`, separately from `files:write`: a key that can upload
+documents should not thereby be able to read every chunk of every file, and
+plan 002's mutating paths will want `points:write` distinct again.
+"""
+
+import uuid
+from typing import Annotated
+
+from fastapi import APIRouter, Depends, Query
+
+from src.api.dependencies.auth import require_scope
+from src.api.schemas.points import (
+    DEFAULT_PAGE_SIZE,
+    LimitQuery,
+    PointCountResponse,
+    PointListResponse,
+    PointResponse,
+    PointSearchResponse,
+)
+from src.application.auth.context import AuthContext
+from src.application.points.deletion import soft_delete_point
+from src.application.points.queries import (
+    count_points,
+    get_point,
+    list_file_points,
+    search_points,
+)
+from src.application.ports.point_repository import PointRepository
+from src.bootstrap.dependencies import get_point_repository
+
+router = APIRouter(prefix="/points", tags=["points"])
+
+_RequirePointsRead = Annotated[AuthContext, Depends(require_scope("points:read"))]
+_RequirePointsWrite = Annotated[AuthContext, Depends(require_scope("points:write"))]
+_PointRepositoryDep = Annotated[PointRepository, Depends(get_point_repository)]
+
+
+@router.get("/count")
+async def count_tenant_points(
+    auth: _RequirePointsRead,
+    repository: _PointRepositoryDep,
+    domain: str | None = None,
+    file_id: uuid.UUID | None = None,
+    include_inactive: bool = False,
+) -> PointCountResponse:
+    count = await count_points(
+        repository,
+        tenant_id=auth.tenant_id,
+        domain=domain,
+        file_id=file_id,
+        include_inactive=include_inactive,
+    )
+    return PointCountResponse(count=count)
+
+
+@router.get("/search")
+async def search_tenant_points(
+    auth: _RequirePointsRead,
+    repository: _PointRepositoryDep,
+    q: Annotated[str, Query(min_length=1)],
+    limit: LimitQuery = DEFAULT_PAGE_SIZE,
+    cursor: str | None = None,
+    domain: str | None = None,
+    file_id: uuid.UUID | None = None,
+    include_inactive: bool = False,
+) -> PointSearchResponse:
+    """Keyword search over point content — **not** semantic retrieval.
+
+    Matches Qdrant's full-text payload index on `content`, combined with the
+    structured filters below. Results are unranked: the index filters rather
+    than scores, so there is no relevance order and no score to return. Callers
+    wanting ranked answers want the agent retrieval path (plan 003), not this.
+    """
+    page = await search_points(
+        repository,
+        tenant_id=auth.tenant_id,
+        query=q,
+        limit=limit,
+        cursor=cursor,
+        domain=domain,
+        file_id=file_id,
+        include_inactive=include_inactive,
+    )
+    return PointSearchResponse.from_search(page, query=q)
+
+
+@router.get("")
+async def list_tenant_points(
+    auth: _RequirePointsRead,
+    repository: _PointRepositoryDep,
+    file_id: uuid.UUID,
+    limit: LimitQuery = DEFAULT_PAGE_SIZE,
+    cursor: str | None = None,
+    include_inactive: bool = False,
+) -> PointListResponse:
+    """A file's points in `order_id` order.
+
+    `file_id` is required rather than optional: the pagination cursor is an
+    `order_id` value, and `order_id` is only unique within one file. Listing
+    across files would silently drop or repeat rows at every page boundary.
+    """
+    page = await list_file_points(
+        repository,
+        tenant_id=auth.tenant_id,
+        file_id=file_id,
+        limit=limit,
+        cursor=cursor,
+        include_inactive=include_inactive,
+    )
+    return PointListResponse.from_page(page)
+
+
+@router.get("/{point_id}")
+async def get_tenant_point(
+    point_id: uuid.UUID,
+    auth: _RequirePointsRead,
+    repository: _PointRepositoryDep,
+    with_vectors: bool = False,
+) -> PointResponse:
+    point = await get_point(
+        repository, tenant_id=auth.tenant_id, point_id=point_id, with_vectors=with_vectors
+    )
+    return PointResponse.from_point(point)
+
+
+@router.delete("/{point_id}")
+async def delete_tenant_point(
+    point_id: uuid.UUID,
+    auth: _RequirePointsWrite,
+    repository: _PointRepositoryDep,
+) -> PointResponse:
+    """Soft-delete one point and relink its neighbours around the gap.
+
+    The point is never removed from Qdrant (ADR-0002): it is flagged
+    `is_active=false` with `deleted_at` set, and its old neighbours are pointed
+    at each other in the same batch, so context-window expansion never walks
+    into it.
+
+    Deleting an already-inactive point is a no-op success rather than a `404` —
+    the response is the point as it stands, so the resulting `version` and
+    `deleted_at` are visible either way.
+    """
+    point = await soft_delete_point(
+        repository,
+        tenant_id=auth.tenant_id,
+        point_id=point_id,
+        actor=f"api_key:{auth.api_key_id}",
+    )
+    return PointResponse.from_point(point)

src/api/schemas/files.py

@@ -28,6 +28,20 @@ class FileUploadResponse(BaseModel):
         )
 
 
+class FileDeleteResponse(BaseModel):
+    """What `DELETE /v1/files/{file_id}` did.
+
+    `points_soft_deleted` is reported rather than left implicit because the
+    delete is a soft one: nothing is removed from Qdrant, and the count is the
+    only way a caller can tell "deactivated 40 points" from "the file was
+    already deleted" — both of which are successes.
+    """
+
+    file_id: uuid.UUID
+    status: str
+    points_soft_deleted: int
+
+
 class FileStatusResponse(BaseModel):
     file_id: uuid.UUID
     source_filename: str

src/api/schemas/points.py

@@ -0,0 +1,165 @@
+"""Public request/response models for `/v1/points` (ADR-0002, ADR-0008).
+
+The shape callers see, kept separate from `application/points`' domain models
+(ADR-0015). Two rules are encoded here rather than left to route code:
+
+- **Vectors are opt-in.** `PointResponse` omits them unless the caller asked,
+  so a listing does not ship megabytes of floats nobody reads (ADR-0008).
+- **Server-owned fields are not accepted on input.** The request models simply
+  do not declare `tenant_id`, `version`, or `chunk_index`, and forbid extra
+  keys, so a client that sends one gets `422` from Pydantic instead of having
+  it silently ignored — ADR-0002's isolation rule enforced at the boundary.
+"""
+
+import uuid
+from datetime import datetime
+from typing import Annotated
+
+from fastapi import Query
+from pydantic import BaseModel, ConfigDict, Field
+
+from src.application.points.point import Point
+from src.application.ports.point_repository import PointPage
+
+# A page ceiling the caller cannot raise. Scroll pages are materialized in
+# memory both here and in Qdrant, so an unbounded `limit` is a cheap way for one
+# request to hurt every other tenant sharing the process. Declared once because
+# two routers paginate points -- `/v1/points` and `/v1/files/{file_id}/points` --
+# and a ceiling that differs between them is a ceiling in only one of them.
+DEFAULT_PAGE_SIZE = 50
+MAX_PAGE_SIZE = 200
+
+LimitQuery = Annotated[int, Query(ge=1, le=MAX_PAGE_SIZE)]
+
+
+class PointResponse(BaseModel):
+    point_id: uuid.UUID
+    domain: str
+    file_id: uuid.UUID
+    chunk_id: uuid.UUID
+
+    content: str
+    content_type: str
+    source_filename: str
+    source_type: str
+
+    order_id: float
+    chunk_index: int
+    previous_chunk_id: uuid.UUID | None
+    next_chunk_id: uuid.UUID | None
+
+    is_active: bool
+    deleted_at: datetime | None
+    created_at: datetime
+    updated_at: datetime
+    created_by: str
+    updated_by: str
+
+    version: int
+    content_hash: str
+    embedding_model_version: str
+
+    vectors: dict[str, object] | None = None
+
+    @classmethod
+    def from_point(cls, point: Point) -> "PointResponse":
+        # `tenant_id` is present on `Point` and deliberately absent here: the
+        # caller already knows which tenant it authenticated as, and echoing it
+        # back invites clients to start sending it.
+        return cls.model_validate(point.model_dump(exclude={"tenant_id"}))
+
+
+class PointListResponse(BaseModel):
+    """A page of points plus the cursor for the next one.
+
+    Cursor-based rather than `limit`/`offset`: an offset cursor silently skips
+    or repeats rows when a concurrent insert shifts positions, which is exactly
+    the pagination defect plan 002 requires a test for.
+    """
+
+    points: list[PointResponse]
+    next_cursor: str | None = None
+
+    @classmethod
+    def from_page(cls, page: PointPage) -> "PointListResponse":
+        return cls(
+            points=[PointResponse.from_point(point) for point in page.points],
+            next_cursor=page.next_cursor,
+        )
+
+
+class PointCountResponse(BaseModel):
+    count: int
+
+
+class PointSearchResponse(PointListResponse):
+    """Results of a **keyword** match, not of semantic retrieval.
+
+    Named and documented so it cannot be mistaken for ADR-0003's hybrid
+    retrieval: these points matched a full-text filter on `content`, they are
+    not ranked by relevance, and there is no score to report. Anything that
+    wants ranked results wants the agent retrieval path in plan 003.
+    """
+
+    query: str
+
+    @classmethod
+    def from_search(cls, page: PointPage, *, query: str) -> "PointSearchResponse":
+        return cls(
+            query=query,
+            points=[PointResponse.from_point(point) for point in page.points],
+            next_cursor=page.next_cursor,
+        )
+
+
+class PointCreateRequest(BaseModel):
+    """Create one point. The server assigns identity, ordering, and provenance.
+
+    `after_point_id` positions the new point rather than a raw `order_id`: the
+    caller says where in the sequence it goes and the server computes the
+    fractional key and relinks neighbours, which a client-supplied `order_id`
+    could not do correctly (ADR-0002). `None` means "at the start of the file".
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    file_id: uuid.UUID
+    content: str = Field(min_length=1)
+    content_type: str = "paragraph"
+    after_point_id: uuid.UUID | None = None
+
+
+class PointReplaceRequest(BaseModel):
+    """Replace a point's content under a version guard.
+
+    `version` here is the *expected* version, not a value being written — the
+    optimistic-concurrency precondition. A mismatch is `409`.
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    content: str = Field(min_length=1)
+    content_type: str | None = None
+    version: int
+
+
+class PointPayloadPatchRequest(BaseModel):
+    """Payload-only update of caller-writable fields, under a version guard."""
+
+    model_config = ConfigDict(extra="forbid")
+
+    payload: dict[str, object]
+    version: int
+
+
+class PointReorderRequest(BaseModel):
+    """Move a point to sit immediately after `after_point_id`.
+
+    `None` moves it to the front of the file. Expressed as a neighbour rather
+    than an `order_id` for the same reason as `PointCreateRequest`.
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    after_point_id: uuid.UUID | None = None
+    version: int

src/application/files/deletion.py

@@ -0,0 +1,81 @@
+"""`DELETE /v1/files/{file_id}` — retire a file and deactivate its points.
+
+Two stores have to agree here, and the phase boundaries are the same ones
+ingestion uses (ADR-0017): a short Postgres transaction to authorize, then the
+Qdrant work with **no session held**, then a short transaction to record the
+outcome. Holding a session across the sweep would pin a pool connection for the
+length of a multi-page delete.
+
+The order — points first, Postgres second — is deliberate. If the sweep dies
+half way, the row stays `active` and a retried `DELETE` finishes the job, since
+the sweep only ever looks at points that are still active. The reverse order
+would leave a row marked deleted while its points are still live and still
+retrievable by the agent, which is the failure that actually matters.
+"""
+
+import uuid
+from datetime import UTC, datetime
+from time import perf_counter
+
+import structlog
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from src.application.files.errors import SourceFileNotFoundError
+from src.application.points.deletion import soft_delete_file_points
+from src.application.ports.point_repository import PointRepository
+from src.infrastructure.postgres.repositories import source_files as source_files_repo
+
+logger = structlog.get_logger(__name__)
+
+
+async def delete_source_file(
+    sessionmaker: async_sessionmaker[AsyncSession],
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    source_file_id: uuid.UUID,
+    actor: str,
+) -> int:
+    """Soft-delete a file: every active point, then the `source_files` row.
+
+    Returns how many points the sweep deactivated. Raises
+    `SourceFileNotFoundError` (`404`) when the file is not this tenant's — the
+    check happens before anything is written, so a probe for another tenant's
+    file id cannot deactivate a single point.
+
+    Idempotent: a second call finds no active points and a row already marked
+    `soft_deleted`, and returns `0`.
+    """
+    started = perf_counter()
+    async with sessionmaker() as session:
+        source_file = await source_files_repo.get_by_id(
+            session, tenant_id=tenant_id, source_file_id=source_file_id
+        )
+        if source_file is None:
+            raise SourceFileNotFoundError(f"file {source_file_id} not found")
+
+    points_soft_deleted = await soft_delete_file_points(
+        repository, tenant_id=tenant_id, file_id=source_file_id, actor=actor
+    )
+
+    async with sessionmaker() as session:
+        source_file = await source_files_repo.get_by_id(
+            session, tenant_id=tenant_id, source_file_id=source_file_id
+        )
+        if source_file is None:
+            raise SourceFileNotFoundError(f"file {source_file_id} not found")
+        source_files_repo.mark_soft_deleted(source_file, deleted_at=datetime.now(UTC))
+        await session.commit()
+
+    logger.info(
+        "files.soft_deleted",
+        tenant_id=str(tenant_id),
+        file_id=str(source_file_id),
+        points_soft_deleted=points_soft_deleted,
+        actor=actor,
+        # End to end, including both Postgres transactions. Comparing it with
+        # the sweep's own `duration_ms` on `points.file_soft_deleted` is what
+        # separates a slow Qdrant from a slow database.
+        duration_ms=round((perf_counter() - started) * 1000, 2),
+    )
+    return points_soft_deleted

src/application/files/errors.py

@@ -15,3 +15,11 @@ class InvalidUploadError(FilesError):
 
 class FileTooLargeError(FilesError):
     """The upload exceeds `INGESTION_MAX_UPLOAD_SIZE_MB`. Maps to `413`."""
+
+
+class SourceFileNotFoundError(FilesError):
+    """No such source file *within the requesting tenant*. Maps to `404`.
+
+    Same non-disclosure rule as points (ADR-0016): a cross-tenant file id and a
+    nonexistent one are indistinguishable to the caller, so this is never `403`.
+    """

src/application/points/__init__.py

@@ -5,9 +5,11 @@ dispatches payload construction, batching, bounded-concurrency upserts, and the
 post-success soft-delete sweep. `build_chunk_payload` and the batching helpers
 stay internal, exported mainly for their own unit tests.
 
-Direct `/v1/points` CRUD (single-point edits, reordering, keyword search) is
+The `/v1/points` surface lives here too, in its own modules with their own
-plan 002's surface, not this package's — plan 001 scopes it to "the reusable
+entry points: `queries.py` for the read paths and `deletion.py` for soft delete
-service layer required by ingestion".
+with neighbour relinking. They share this package because they share ADR-0001's
+payload schema, not because they share a caller — `index_chunks` writes a whole
+file at once, while those serve one admin edit at a time.
 """
 
 from src.application.points.indexing import IndexingResult, index_chunks

src/application/points/deletion.py

@@ -0,0 +1,253 @@
+"""Soft delete for `/v1/points` and for a whole file's points (ADR-0002).
+
+The caller-facing entry points are `soft_delete_point` and
+`soft_delete_file_points`. Routers call these; `patches_for_removal` and the
+planning helpers stay internal, because getting a delete right is exactly the
+composition a caller should not have to reassemble: read the point, load its
+neighbours, compute the patches still missing, send them in **one** batch,
+verify they landed, and retry against fresh versions if they did not.
+
+Why the retry exists. Qdrant has no multi-point transaction, so a batch whose
+second operation loses a version race applies its first operation anyway — and
+a filtered `set_payload` that matched nothing still reports success. That
+combination means "did my write land?" is only answerable by reading back, and
+a single-shot delete would be able to leave the deactivation applied and a
+neighbour's pointer stale. Since `patches_for_removal` plans from current state
+towards a fixed end state, simply re-planning emits precisely the patches that
+did not land, so the loop converges instead of re-doing work. Only exhausting
+the attempts raises `PointVersionConflictError` (`409`).
+
+Deleting an already-inactive point falls out of the same machinery rather than
+needing a special case: its neighbours were relinked by the first delete, so the
+plan is empty and the call is a no-op success — not a `404`, and not a second
+relink.
+"""
+
+import uuid
+from collections.abc import Mapping, Sequence
+from datetime import UTC, datetime
+from time import perf_counter
+
+import structlog
+
+from src.application.points.errors import PointVersionConflictError
+from src.application.points.point import Point, PointNotFoundError
+from src.application.points.relinking import (
+    neighbour_ids,
+    patch_for_deactivation,
+    patches_for_removal,
+)
+from src.application.ports.point_repository import PayloadPatch, PointRepository
+
+logger = structlog.get_logger(__name__)
+
+# Three plan-apply rounds, then a final verifying plan. Each round only re-emits
+# what a concurrent writer displaced, so a caller that legitimately needs more
+# than this is contending on the same points continuously and deserves the
+# `409` rather than an unbounded loop inside a request.
+_MAX_ATTEMPTS = 3
+
+# One sweep page. Matches ADR-0002's 100-operation batch cap, so a page of
+# points is always expressible as a single `points/batch` request.
+_SWEEP_BATCH_SIZE = 100
+
+# A hard ceiling on sweep rounds, so a file being concurrently re-ingested while
+# it is deleted cannot spin here for the life of the request.
+_MAX_SWEEP_ROUNDS = 1_000
+
+
+def _elapsed_ms(started: float) -> float:
+    """Wall-clock milliseconds since `started` (ADR-0011's `duration_ms`).
+
+    Worth carrying on these events even though the relinking itself is O(1):
+    what a delete actually spends is Qdrant round trips, and the whole-file
+    sweep spends a number of them proportional to the file's length. Timing the
+    operation is the only way to tell a slow store from a contended one, which
+    `rounds` on the same event then disambiguates.
+    """
+    return round((perf_counter() - started) * 1000, 2)
+
+
+async def soft_delete_point(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    point_id: uuid.UUID,
+    actor: str,
+) -> Point:
+    """Deactivate one point and relink its neighbours around the gap.
+
+    Returns the point as it now stands. Raises `PointNotFoundError` (`404`) if
+    it is not this tenant's — the same non-disclosure rule the read paths
+    follow — or `PointVersionConflictError` (`409`) if concurrent writers keep
+    displacing the plan.
+    """
+    started = perf_counter()
+    rounds = 0
+    point, patches = await _plan_removal(
+        repository, tenant_id=tenant_id, point_id=point_id, actor=actor
+    )
+
+    for _ in range(_MAX_ATTEMPTS):
+        if not patches:
+            break
+        await repository.apply_patches(tenant_id=tenant_id, patches=patches)
+        rounds += 1
+        # The next plan doubles as verification: anything that did not land is
+        # still missing from the end state and comes back as a patch.
+        point, patches = await _plan_removal(
+            repository, tenant_id=tenant_id, point_id=point_id, actor=actor
+        )
+
+    if patches:
+        logger.warning(
+            "points.soft_delete.conflict",
+            tenant_id=str(tenant_id),
+            point_id=str(point_id),
+            file_id=str(point.file_id),
+            unsettled_points=[str(patch.point_id) for patch in patches],
+            rounds=rounds,
+            duration_ms=_elapsed_ms(started),
+        )
+        raise PointVersionConflictError(
+            f"point {point_id} could not be soft-deleted under concurrent modification"
+        )
+
+    if rounds:
+        logger.info(
+            "points.soft_deleted",
+            tenant_id=str(tenant_id),
+            point_id=str(point_id),
+            file_id=str(point.file_id),
+            version=point.version,
+            actor=actor,
+            # `rounds` is 1 unless a concurrent writer forced a re-plan, so a
+            # rising value here is contention, not slow relinking.
+            rounds=rounds,
+            duration_ms=_elapsed_ms(started),
+        )
+    return point
+
+
+async def soft_delete_file_points(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    file_id: uuid.UUID,
+    actor: str,
+) -> int:
+    """Deactivate every active point of one file, in batches.
+
+    No relinking: the whole file leaves the sequence at once, so no surviving
+    active point can be left pointing at a deactivated one, and the chain is
+    preserved intact for whoever reads the deleted file later.
+
+    Returns how many points were active when the sweep reached them. Each round
+    re-lists from the start rather than paging with a cursor — deactivated
+    points drop straight out of the default listing, so the listing itself is
+    the progress check, and a round that attempts the exact same ids as the one
+    before it made no progress and raises `PointVersionConflictError`.
+    """
+    started = perf_counter()
+    swept: set[uuid.UUID] = set()
+    previous_attempt: frozenset[uuid.UUID] = frozenset()
+    rounds = 0
+
+    for _ in range(_MAX_SWEEP_ROUNDS):
+        page = await repository.list_by_file(
+            tenant_id=tenant_id, file_id=file_id, limit=_SWEEP_BATCH_SIZE
+        )
+        if not page.points:
+            if swept:
+                logger.info(
+                    "points.file_soft_deleted",
+                    tenant_id=str(tenant_id),
+                    file_id=str(file_id),
+                    points_soft_deleted=len(swept),
+                    actor=actor,
+                    # Two Qdrant round trips per round, so this is the delete
+                    # path whose cost tracks the size of the file.
+                    rounds=rounds,
+                    duration_ms=_elapsed_ms(started),
+                )
+            return len(swept)
+
+        attempt = frozenset(point.point_id for point in page.points)
+        if attempt == previous_attempt:
+            logger.warning(
+                "points.file_soft_delete.conflict",
+                tenant_id=str(tenant_id),
+                file_id=str(file_id),
+                unsettled_points=[str(point_id) for point_id in sorted(attempt, key=str)],
+                rounds=rounds,
+                duration_ms=_elapsed_ms(started),
+            )
+            raise PointVersionConflictError(
+                f"file {file_id} could not be soft-deleted under concurrent modification"
+            )
+        previous_attempt = attempt
+
+        now = datetime.now(UTC)
+        await repository.apply_patches(
+            tenant_id=tenant_id,
+            patches=[patch_for_deactivation(point, actor=actor, now=now) for point in page.points],
+        )
+        swept |= attempt
+        rounds += 1
+
+    logger.warning(
+        "points.file_soft_delete.conflict",
+        tenant_id=str(tenant_id),
+        file_id=str(file_id),
+        reason="sweep_rounds_exhausted",
+        rounds=rounds,
+        duration_ms=_elapsed_ms(started),
+    )
+    raise PointVersionConflictError(f"file {file_id} still had active points after the sweep")
+
+
+async def _plan_removal(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    point_id: uuid.UUID,
+    actor: str,
+) -> tuple[Point, tuple[PayloadPatch, ...]]:
+    point = await repository.get(tenant_id=tenant_id, point_id=point_id)
+    if point is None:
+        raise PointNotFoundError(f"point {point_id} not found")
+
+    neighbours = await _load_neighbours(repository, tenant_id=tenant_id, point=point)
+    _warn_on_missing_neighbours(point, neighbours, tenant_id=tenant_id)
+    patches = patches_for_removal(point, neighbours, actor=actor, now=datetime.now(UTC))
+    return point, patches
+
+
+async def _load_neighbours(
+    repository: PointRepository, *, tenant_id: uuid.UUID, point: Point
+) -> dict[uuid.UUID, Point]:
+    wanted: Sequence[uuid.UUID] = neighbour_ids(point)
+    if not wanted:
+        return {}
+    found = await repository.get_many(tenant_id=tenant_id, point_ids=wanted)
+    return {neighbour.point_id: neighbour for neighbour in found}
+
+
+def _warn_on_missing_neighbours(
+    point: Point, neighbours: Mapping[uuid.UUID, Point], *, tenant_id: uuid.UUID
+) -> None:
+    """A pointer naming a point that is not there means the chain is already broken.
+
+    Worth a log line rather than an exception: the delete can still complete the
+    part of the relink that does exist, and refusing would leave the caller with
+    a point it cannot remove through any endpoint.
+    """
+    missing = [pointer for pointer in neighbour_ids(point) if pointer not in neighbours]
+    if missing:
+        logger.warning(
+            "points.relink.neighbour_missing",
+            tenant_id=str(tenant_id),
+            point_id=str(point.point_id),
+            file_id=str(point.file_id),
+            missing_neighbours=[str(pointer) for pointer in missing],
+        )

src/application/points/errors.py

@@ -0,0 +1,19 @@
+"""Mutation failures for the `/v1/points` write paths (ADR-0002).
+
+No HTTP knowledge here — `src/api/errors.py` owns the status mapping. Absence
+lives on `PointNotFoundError` in `point.py`, next to the model whose read paths
+raise it; this module is for the failures only a *write* can produce.
+"""
+
+
+class PointVersionConflictError(Exception):
+    """A version-guarded write could not be landed against a moving target.
+
+    Raised when the service has re-read, recomputed, and re-applied its patches
+    the allowed number of times and the desired state still has not settled —
+    something else is writing the same points concurrently. Maps to `409`.
+
+    This is not "the guard fired once": a single stale guard is expected and is
+    retried, because Qdrant reports success for a filtered `set_payload` that
+    matched nothing. It means the retries were exhausted.
+    """

src/application/points/point.py

@@ -0,0 +1,126 @@
+"""The caller-facing point model for `/v1/points` (ADR-0001, ADR-0002).
+
+`ChunkPoint` in `models.py` is the *write* shape ingestion upserts: an id, its
+named vectors, and an opaque payload dict. This module is the *read/edit* shape
+the `/v1/points` surface works in, where the payload's individual fields matter
+and the distinction between what a caller may write and what the server owns is
+a security boundary rather than a convention.
+
+That split is the reason this is a model and not a dict. ADR-0002's isolation
+rule ("never accepted as client-supplied input") and its optimistic-concurrency
+guard both fail open if a caller can smuggle `tenant_id` or `version` through a
+payload update, so the writable field set is enumerated in one place here and
+every write path validates against it.
+"""
+
+import uuid
+from collections.abc import Mapping
+from datetime import datetime
+from typing import Self
+
+from pydantic import BaseModel, ConfigDict, Field
+
+# Fields the server derives and a caller may never set, patch, or override.
+# `tenant_id` is authority, `version` is the concurrency guard, `chunk_index`
+# derives the point id, and the rest are provenance the server timestamps.
+SERVER_OWNED_FIELDS: frozenset[str] = frozenset(
+    {
+        "tenant_id",
+        "version",
+        "chunk_index",
+        "chunk_id",
+        "is_active",
+        "deleted_at",
+        "created_at",
+        "created_by",
+        "updated_at",
+        "updated_by",
+        "content_hash",
+        "embedding_model_version",
+    }
+)
+
+# Fields a caller may supply on create, replace, or payload patch. `order_id`
+# is writable on create but moves only through `PATCH /v1/points/{id}/order`
+# afterwards, because a bare `order_id` write would not relink neighbours.
+CALLER_WRITABLE_FIELDS: frozenset[str] = frozenset(
+    {
+        "content",
+        "content_type",
+        "domain",
+        "source_filename",
+        "source_type",
+        "order_id",
+        "previous_chunk_id",
+        "next_chunk_id",
+    }
+)
+
+
+class Point(BaseModel):
+    """One Qdrant point, read back with its ADR-0001 payload fields typed.
+
+    Vectors are deliberately absent: ADR-0008 returns them only when explicitly
+    requested, and every read path that does not ask for them should not pay to
+    deserialize them.
+    """
+
+    model_config = ConfigDict(frozen=True)
+
+    point_id: uuid.UUID
+
+    tenant_id: uuid.UUID
+    domain: str
+    file_id: uuid.UUID
+    chunk_id: uuid.UUID
+
+    content: str
+    content_type: str
+    source_filename: str
+    source_type: str
+
+    order_id: float
+    chunk_index: int
+    previous_chunk_id: uuid.UUID | None = None
+    next_chunk_id: uuid.UUID | None = None
+
+    is_active: bool = True
+    deleted_at: datetime | None = None
+
+    created_at: datetime
+    updated_at: datetime
+    created_by: str
+    updated_by: str
+
+    version: int
+    content_hash: str
+    embedding_model_version: str
+
+    # Only populated when the caller explicitly asked for vectors.
+    vectors: dict[str, object] | None = Field(default=None)
+
+    @classmethod
+    def from_payload(
+        cls,
+        point_id: uuid.UUID,
+        payload: Mapping[str, object],
+        *,
+        vectors: Mapping[str, object] | None = None,
+    ) -> Self:
+        """Build a `Point` from a raw Qdrant payload dict.
+
+        Lives here rather than in the Qdrant adapter so the payload field names
+        are declared once, next to the model that mirrors them. The adapter
+        stays responsible for talking to the SDK, not for knowing ADR-0001's
+        schema twice.
+        """
+        return cls.model_validate({**payload, "point_id": point_id, "vectors": vectors})
+
+
+class PointNotFoundError(LookupError):
+    """No such point *within the requesting tenant*.
+
+    Routes map this to `404`, never `403` — a caller must not be able to probe
+    for the existence of another tenant's point ids (ADR-0016). The error
+    deliberately carries no hint about which of the two cases occurred.
+    """

src/application/points/queries.py

@@ -0,0 +1,115 @@
+"""Read paths for `/v1/points` (ADR-0002, ADR-0008).
+
+The caller-facing entry points for point reads. Routers call these; they never
+touch the `PointRepository` directly, and never build a filter.
+
+This module is thin on purpose but not empty, and the two things it does own are
+exactly the ones a route would otherwise get wrong:
+
+- **`tenant_id` always comes from the caller's `AuthContext`.** Every function
+  takes it as a required keyword and hands it to the repository. Nothing here
+  reads a tenant from a query string or body.
+- **A keyword query is Persian-normalized before it reaches the index.**
+  Ingestion letter-folds chunk content (`normalize_persian_text`, ADR-0018), so
+  stored text contains Persian yeh/keheh. A query typed on an Arabic keyboard
+  carries U+064A/U+0643 and would match nothing at all — a silent empty result,
+  not an error. Folding the query the same way is what makes the two comparable.
+
+Reads emit no log events. The request middleware already records every call, and
+ADR-0011 reserves `INFO` for lifecycle events rather than per-read volume;
+mutations get their own events when those paths land.
+"""
+
+import uuid
+
+from src.application.ingestion.normalization import normalize_persian_text
+from src.application.points.point import Point, PointNotFoundError
+from src.application.ports.point_repository import PointPage, PointRepository
+
+
+async def get_point(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    point_id: uuid.UUID,
+    with_vectors: bool = False,
+) -> Point:
+    """One point, or `PointNotFoundError` if it is not this tenant's.
+
+    Raises rather than returning `None` so a route cannot forget the check and
+    serve `200 null`. "Absent" and "another tenant's" are the same outcome by
+    design (ADR-0016: cross-tenant access is `404`, never `403`).
+    """
+    point = await repository.get(tenant_id=tenant_id, point_id=point_id, with_vectors=with_vectors)
+    if point is None:
+        raise PointNotFoundError(f"point {point_id} not found")
+    return point
+
+
+async def list_file_points(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    file_id: uuid.UUID,
+    limit: int,
+    cursor: str | None = None,
+    include_inactive: bool = False,
+) -> PointPage:
+    """One file's points in display (`order_id`) order.
+
+    An unknown or foreign `file_id` yields an empty page rather than an error:
+    the two are indistinguishable to the caller, which is the same
+    non-disclosure property `get_point` gets from raising.
+    """
+    return await repository.list_by_file(
+        tenant_id=tenant_id,
+        file_id=file_id,
+        limit=limit,
+        cursor=cursor,
+        include_inactive=include_inactive,
+    )
+
+
+async def count_points(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    domain: str | None = None,
+    file_id: uuid.UUID | None = None,
+    include_inactive: bool = False,
+) -> int:
+    return await repository.count(
+        tenant_id=tenant_id,
+        domain=domain,
+        file_id=file_id,
+        include_inactive=include_inactive,
+    )
+
+
+async def search_points(
+    repository: PointRepository,
+    *,
+    tenant_id: uuid.UUID,
+    query: str,
+    limit: int,
+    cursor: str | None = None,
+    domain: str | None = None,
+    file_id: uuid.UUID | None = None,
+    include_inactive: bool = False,
+) -> PointPage:
+    """Keyword match on `content`, within this tenant.
+
+    **Not semantic retrieval.** Qdrant's full-text index filters rather than
+    scores, so results carry no relevance ranking and their order is
+    unspecified. Ranked retrieval is ADR-0003's hybrid path in plan 003; this
+    function must not grow a semantic mode (ADR-0002).
+    """
+    return await repository.keyword_search(
+        tenant_id=tenant_id,
+        query=normalize_persian_text(query),
+        limit=limit,
+        cursor=cursor,
+        domain=domain,
+        file_id=file_id,
+        include_inactive=include_inactive,
+    )

src/application/points/relinking.py

@@ -0,0 +1,135 @@
+"""Adjacency-pointer maintenance for a point leaving a file's sequence.
+
+ADR-0001 keeps `previous_chunk_id`/`next_chunk_id` on every point so ADR-0003's
+context-window expansion can walk a file in O(1) steps. ADR-0002 makes keeping
+them correct an obligation of every operation that changes a point's position:
+a partial relink is a defect, not a degraded-but-acceptable outcome.
+
+The function below is the primitive that obligation reduces to. It is pure, and
+it is written as **"what is still missing between the state I just read and the
+state I want"** rather than "the patches a delete implies". That framing is what
+makes the caller's retry loop correct: re-planning after a partial apply emits
+exactly the patches that did not land, and re-planning after a completed delete
+emits nothing at all. The three cases the plan calls out — a normal delete, a
+second delete of an already-inactive point, and recovery from a half-applied
+batch — are then one code path instead of three.
+
+Note what is deliberately *not* patched: the departing point's own
+`previous_chunk_id`/`next_chunk_id`. Nothing active points at it once its
+neighbours are relinked, so those pointers are unreachable rather than stale,
+and leaving them records where the point sat — which is what a later restore or
+an audit reader would need. `src/application/points/deletion.py` relies on that
+when it re-plans: the departing point's pointers are the only surviving record
+of which two neighbours have to be joined.
+"""
+
+import uuid
+from collections.abc import Mapping
+from datetime import datetime
+
+from src.application.points.point import Point
+from src.application.ports.point_repository import PayloadPatch
+
+
+def _optional_id(value: uuid.UUID | None) -> str | None:
+    return str(value) if value is not None else None
+
+
+def _provenance(point: Point, *, actor: str, now: datetime) -> dict[str, object]:
+    """The fields every mutation writes: who, when, and the next version.
+
+    Bumping `version` on a relinked *neighbour* is intentional. The neighbour's
+    payload really did change, so a concurrent editor holding the old version
+    must get a `409` rather than overwrite the pointer we just fixed.
+    """
+    return {
+        "updated_at": now.isoformat(),
+        "updated_by": actor,
+        "version": point.version + 1,
+    }
+
+
+def neighbour_ids(point: Point) -> tuple[uuid.UUID, ...]:
+    """The ids `patches_for_removal` needs loaded, skipping the nulls."""
+    return tuple(
+        pointer for pointer in (point.previous_chunk_id, point.next_chunk_id) if pointer is not None
+    )
+
+
+def patches_for_removal(
+    point: Point,
+    neighbours: Mapping[uuid.UUID, Point],
+    *,
+    actor: str,
+    now: datetime,
+) -> tuple[PayloadPatch, ...]:
+    """The patches still needed to remove `point` from its file's sequence.
+
+    Returns an empty tuple when the removal is already complete, which the
+    caller reads as both "converged" and "this was a no-op".
+
+    A neighbour absent from `neighbours` is skipped rather than patched blind:
+    its id came from the departing point's payload, so a missing one means the
+    chain was already broken, and inventing a patch for a point that is not
+    there would not fix it. The caller logs that case.
+    """
+    patches: list[PayloadPatch] = []
+
+    if point.is_active:
+        patches.append(
+            PayloadPatch(
+                point_id=point.point_id,
+                payload={
+                    "is_active": False,
+                    "deleted_at": now.isoformat(),
+                    **_provenance(point, actor=actor, now=now),
+                },
+                expected_version=point.version,
+            )
+        )
+
+    previous = neighbours.get(point.previous_chunk_id) if point.previous_chunk_id else None
+    if previous is not None and previous.next_chunk_id != point.next_chunk_id:
+        patches.append(
+            PayloadPatch(
+                point_id=previous.point_id,
+                payload={
+                    "next_chunk_id": _optional_id(point.next_chunk_id),
+                    **_provenance(previous, actor=actor, now=now),
+                },
+                expected_version=previous.version,
+            )
+        )
+
+    following = neighbours.get(point.next_chunk_id) if point.next_chunk_id else None
+    if following is not None and following.previous_chunk_id != point.previous_chunk_id:
+        patches.append(
+            PayloadPatch(
+                point_id=following.point_id,
+                payload={
+                    "previous_chunk_id": _optional_id(point.previous_chunk_id),
+                    **_provenance(following, actor=actor, now=now),
+                },
+                expected_version=following.version,
+            )
+        )
+
+    return tuple(patches)
+
+
+def patch_for_deactivation(point: Point, *, actor: str, now: datetime) -> PayloadPatch:
+    """Deactivate one point without touching any pointer.
+
+    Used by the whole-file sweep, where every point in the file leaves at once:
+    no active point survives to dangle, so there is no neighbour to relink and
+    the chain stays intact for a later reader of the deactivated file.
+    """
+    return PayloadPatch(
+        point_id=point.point_id,
+        payload={
+            "is_active": False,
+            "deleted_at": now.isoformat(),
+            **_provenance(point, actor=actor, now=now),
+        },
+        expected_version=point.version,
+    )

src/application/ports/point_repository.py

@@ -0,0 +1,131 @@
+"""The point read/edit port for `/v1/points` (ADR-0002, ADR-0015).
+
+Separate from `PointStorage`, which stays exactly the two bulk operations
+ingestion performs. Reads, single-point edits, reordering, and keyword search
+have a different caller, a different failure vocabulary, and a different
+tenant-filter obligation, so they get their own port rather than accreting onto
+the ingestion one.
+
+`tenant_id` is a required keyword argument on **every** method. That is not
+style: ADR-0002's isolation rule has to hold on every code path that touches the
+collection, and an optional tenant filter is one forgotten argument away from a
+cross-tenant read. Making it required moves that from a review question to a
+type error.
+
+`src/infrastructure/qdrant/point_repository.py` is the production adapter;
+`tests.fakes.FakePointRepository` is the test double.
+"""
+
+import uuid
+from collections.abc import Sequence
+from typing import Protocol
+
+from pydantic import BaseModel
+
+from src.application.points.point import Point
+
+
+class PointPage(BaseModel):
+    """One page of points plus the cursor that continues it.
+
+    `next_cursor` is opaque to callers and encoded by the adapter: ordered
+    scrolls and keyword searches paginate by different Qdrant mechanisms, and
+    neither is a plain integer offset. `None` means the listing is exhausted.
+    """
+
+    points: tuple[Point, ...]
+    next_cursor: str | None = None
+
+
+class PayloadPatch(BaseModel):
+    """Set these payload fields on one point, optionally guarded by `version`.
+
+    When `expected_version` is set, the adapter attaches it to the operation's
+    filter, so a concurrent write that has already moved the version on means
+    this patch matches nothing rather than clobbering it. The guard is what
+    makes a lost update impossible; detecting that it fired is the service's
+    job (see `apply_patches`).
+    """
+
+    point_id: uuid.UUID
+    payload: dict[str, object]
+    expected_version: int | None = None
+
+
+class PointRepository(Protocol):
+    async def get(
+        self, *, tenant_id: uuid.UUID, point_id: uuid.UUID, with_vectors: bool = False
+    ) -> Point | None:
+        """One point, or `None` if it does not exist *under this tenant*.
+
+        The two cases are deliberately indistinguishable — the route maps both
+        to `404` so a caller cannot probe for another tenant's point ids.
+        """
+        ...
+
+    async def get_many(
+        self, *, tenant_id: uuid.UUID, point_ids: Sequence[uuid.UUID]
+    ) -> tuple[Point, ...]:
+        """The subset of `point_ids` that exists under this tenant.
+
+        Order is not guaranteed and missing ids are silently absent: callers are
+        neighbour-relinking and batch precondition checks, both of which match
+        on id rather than position.
+        """
+        ...
+
+    async def list_by_file(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        file_id: uuid.UUID,
+        limit: int,
+        cursor: str | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        """One file's points in `order_id` order (ADR-0008's `scroll`).
+
+        Scoped to a single file because the cursor is an `order_id` value, and
+        `order_id` is only unique within a file.
+        """
+        ...
+
+    async def count(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> int: ...
+
+    async def keyword_search(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        query: str,
+        limit: int,
+        cursor: str | None = None,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        """Full-text payload match on `content`, plus structured filters.
+
+        Keyword matching, **not** semantic retrieval (ADR-0002). Qdrant's
+        full-text index is a filter, not a scorer, so results carry no relevance
+        ranking and their order is unspecified.
+        """
+        ...
+
+    async def apply_patches(self, *, tenant_id: uuid.UUID, patches: Sequence[PayloadPatch]) -> None:
+        """Apply every patch in one Qdrant `points/batch` request.
+
+        Qdrant has no multi-point transaction, so this is not atomic and does
+        not pretend to be. ADR-0002's all-or-nothing rule is implemented one
+        layer up as validate-every-precondition-then-apply; the per-patch
+        `expected_version` guard here is what makes the residual window safe,
+        turning a lost update into a no-op the service can detect rather than a
+        silent clobber.
+        """
+        ...

src/application/tenants/provisioning.py

@@ -28,7 +28,13 @@ from src.infrastructure.postgres.repositories import tenants as tenants_repo
 
 logger = structlog.get_logger(__name__)
 
-DEFAULT_SCOPES = ("files:write", "domains:read", "domains:write")
+DEFAULT_SCOPES = (
+    "files:write",
+    "domains:read",
+    "domains:write",
+    "points:read",
+    "points:write",
+)
 
 
 @dataclass(frozen=True)

src/bootstrap/dependencies.py

@@ -9,6 +9,7 @@ from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker
 
 from src.application.ports.embedding import DenseEmbedder, SparseEmbedder
 from src.application.ports.object_storage import ObjectStorage
+from src.application.ports.point_repository import PointRepository
 from src.application.ports.point_storage import PointStorage
 from src.config import Settings
 
@@ -22,6 +23,7 @@ class AppResources:
     qdrant_client: AsyncQdrantClient
     object_storage: ObjectStorage
     point_storage: PointStorage
+    point_repository: PointRepository
     ingestion_limiter: CapacityLimiter
     dense_embedders: Sequence[DenseEmbedder]
     sparse_embedder: SparseEmbedder
@@ -52,6 +54,10 @@ def get_point_storage(request: Request) -> PointStorage:
     return _resources(request).point_storage
 
 
+def get_point_repository(request: Request) -> PointRepository:
+    return _resources(request).point_repository
+
+
 def get_ingestion_limiter(request: Request) -> CapacityLimiter:
     return _resources(request).ingestion_limiter
 

src/bootstrap/lifespan.py

@@ -20,6 +20,7 @@ from src.infrastructure.minio.storage import MinioObjectStorage
 from src.infrastructure.observability.logging import configure_logging
 from src.infrastructure.postgres.database import create_engine, create_sessionmaker
 from src.infrastructure.qdrant.client import create_client as create_qdrant_client
+from src.infrastructure.qdrant.point_repository import QdrantPointRepository
 from src.infrastructure.qdrant.points import QdrantPointStorage
 
 logger = structlog.get_logger(__name__)
@@ -85,6 +86,9 @@ def create_lifespan(
         point_storage = QdrantPointStorage(
             qdrant_client, collection=resolved_settings.qdrant.collection
         )
+        point_repository = QdrantPointRepository(
+            qdrant_client, collection=resolved_settings.qdrant.collection
+        )
         logger.info("lifespan.qdrant.client.created")
 
         nomic_settings = resolved_settings.embedding.nomic
@@ -145,6 +149,7 @@ def create_lifespan(
             qdrant_client=qdrant_client,
             object_storage=object_storage,
             point_storage=point_storage,
+            point_repository=point_repository,
             ingestion_limiter=ingestion_limiter,
             dense_embedders=dense_embedders,
             sparse_embedder=sparse_embedder,

src/infrastructure/postgres/repositories/source_files.py

@@ -7,6 +7,7 @@ signature error rather than a cross-tenant leak.
 """
 
 import uuid
+from datetime import datetime
 
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
@@ -67,3 +68,19 @@ def create(
     )
     session.add(source_file)
     return source_file
+
+
+def mark_soft_deleted(source_file: SourceFile, *, deleted_at: datetime) -> None:
+    """Retire a file: `status='soft_deleted'` plus `deleted_at` (ADR-0009).
+
+    Takes the already-loaded row rather than an id, because the caller fetched
+    it under its tenant filter and re-fetching here would be a second place
+    that could forget that filter.
+
+    Retiring the row matters beyond bookkeeping: `find_active_by_content_hash`
+    matches only `active` files, so a re-upload of the same bytes after a delete
+    creates a fresh file and re-ingests it, instead of taking the duplicate path
+    and returning a file whose points have all been deactivated.
+    """
+    source_file.status = "soft_deleted"
+    source_file.deleted_at = deleted_at

src/infrastructure/qdrant/collection.py

@@ -80,14 +80,25 @@ def _sparse_vectors_config() -> dict[str, models.SparseVectorParams]:
     return {SPARSE_VECTOR: models.SparseVectorParams(modifier=models.Modifier.IDF)}
 
 
+# `content`'s full-text index backs ADR-0002's keyword search. The
+# `multilingual` tokenizer is the one that segments Persian correctly; `word`
+# splits on non-alphanumerics, which mis-handles ZWNJ-joined compounds. No
+# stemmer or stopword list is configured: `content` is already letter-folded by
+# `normalize_persian_text` at ingest (ADR-0018), and the *ranked* Farsi lexical
+# path is the benchmarked BM25 sparse vector, not this index. This one exists
+# for exact keyword/filter matching, which ADR-0002 keeps deliberately distinct
+# from retrieval.
+_CONTENT_INDEX = models.TextIndexParams(
+    type=models.TextIndexType.TEXT,
+    tokenizer=models.TokenizerType.MULTILINGUAL,
+    lowercase=True,
+)
+
 # (field name, schema). `order_id` is float because Qdrant's `Range` conditions
 # and `order_by` only support numeric/datetime payloads -- a keyword key could
 # only be sorted client-side after fetching every chunk (ADR-0001).
-#
+_PayloadIndexSchema = models.PayloadSchemaType | models.KeywordIndexParams | models.TextIndexParams
-# The full-text index on `content` is deliberately absent: it belongs to plan
+_PAYLOAD_INDEXES: tuple[tuple[str, _PayloadIndexSchema], ...] = (
-# 002's keyword search, and payload indexes -- unlike vector config -- can be
-# added to a live collection later.
-_PAYLOAD_INDEXES: tuple[tuple[str, models.PayloadSchemaType | models.KeywordIndexParams], ...] = (
     # `is_tenant` co-locates a tenant's vectors on disk for sequential reads,
     # which is the whole point of payload-partitioned multitenancy.
     (
@@ -99,6 +110,13 @@ _PAYLOAD_INDEXES: tuple[tuple[str, models.PayloadSchemaType | models.KeywordInde
     ("order_id", models.PayloadSchemaType.FLOAT),
     ("previous_chunk_id", models.PayloadSchemaType.KEYWORD),
     ("next_chunk_id", models.PayloadSchemaType.KEYWORD),
+    ("content", _CONTENT_INDEX),
+    # Every read path filters on `is_active` (ADR-0002 implies `is_active: true`
+    # unless the caller opts in), and the re-ingestion sweep and `/v1/points`
+    # both range over `chunk_index`. Both were unindexed while ingestion was the
+    # only reader; plan 002 makes them hot.
+    ("is_active", models.PayloadSchemaType.BOOL),
+    ("chunk_index", models.PayloadSchemaType.INTEGER),
 )
 
 

src/infrastructure/qdrant/point_repository.py

@@ -0,0 +1,247 @@
+"""Qdrant adapter for the `PointRepository` port (ADR-0002, ADR-0015).
+
+Every Qdrant filter for the `/v1/points` surface is built here. Routers and
+application services never import `qdrant_client` — they pass a `tenant_id` and
+get `Point` models back.
+
+Two mechanics are worth reading before changing anything:
+
+**Reads go through `scroll`, not `retrieve`.** `retrieve` fetches by id and
+takes no filter, which would force the tenant check to happen *after* Qdrant
+answered — exactly the "check it in Python afterwards" shape ADR-0002's
+isolation rule exists to prevent. `scroll` with a `HasIdCondition` plus the
+tenant condition pushes the check server-side, so a foreign id returns an empty
+page rather than a row this code has to remember to reject.
+
+**Ordered listing paginates by `order_id` value, not by offset.** Qdrant does
+not return a `next_page_offset` when `order_by` is set, and an offset-based
+cursor would skip or repeat rows when a concurrent insert shifts positions
+underneath the reader. Ranging on `order_id > cursor` is stable instead: a point
+inserted ahead of the cursor was already returned, and one inserted after it
+shows up on a later page. This relies on `order_id` being unique within a file,
+which ADR-0002 guarantees by rejecting a reorder whose gap would collapse onto a
+neighbour value.
+"""
+
+import uuid
+from collections.abc import Sequence
+
+from qdrant_client import AsyncQdrantClient, models
+
+from src.application.points.point import Point
+from src.application.ports.point_repository import PayloadPatch, PointPage
+
+# Qdrant's scroll returns `(records, next_page_offset)`; a record's id is a
+# `str | int` union in the SDK, and every id this service writes is a UUID.
+type _ScrollRecord = models.Record
+
+
+def _uuid_of(record: _ScrollRecord) -> uuid.UUID:
+    return uuid.UUID(str(record.id))
+
+
+def _to_point(record: _ScrollRecord, *, with_vectors: bool) -> Point:
+    vectors = record.vector if with_vectors and isinstance(record.vector, dict) else None
+    return Point.from_payload(_uuid_of(record), record.payload or {}, vectors=vectors)
+
+
+def _conditions(
+    *,
+    tenant_id: uuid.UUID,
+    domain: str | None = None,
+    file_id: uuid.UUID | None = None,
+    include_inactive: bool = False,
+) -> list[models.Condition]:
+    """The base filter every point query carries.
+
+    `tenant_id` is unconditional and first. `is_active` is added unless the
+    caller explicitly opted into inactive points, which is ADR-0002's
+    "`is_active: true` implied" rule expressed once rather than per method.
+    """
+    conditions: list[models.Condition] = [
+        models.FieldCondition(key="tenant_id", match=models.MatchValue(value=str(tenant_id)))
+    ]
+    if domain is not None:
+        conditions.append(
+            models.FieldCondition(key="domain", match=models.MatchValue(value=domain))
+        )
+    if file_id is not None:
+        conditions.append(
+            models.FieldCondition(key="file_id", match=models.MatchValue(value=str(file_id)))
+        )
+    if not include_inactive:
+        conditions.append(
+            models.FieldCondition(key="is_active", match=models.MatchValue(value=True))
+        )
+    return conditions
+
+
+class QdrantPointRepository:
+    """A `PointRepository` (see `src/application/ports/point_repository.py`)."""
+
+    def __init__(self, client: AsyncQdrantClient, *, collection: str) -> None:
+        self._client = client
+        self._collection = collection
+
+    async def get(
+        self, *, tenant_id: uuid.UUID, point_id: uuid.UUID, with_vectors: bool = False
+    ) -> Point | None:
+        records, _ = await self._client.scroll(
+            collection_name=self._collection,
+            scroll_filter=models.Filter(
+                must=[
+                    *_conditions(tenant_id=tenant_id, include_inactive=True),
+                    models.HasIdCondition(has_id=[str(point_id)]),
+                ]
+            ),
+            limit=1,
+            with_payload=True,
+            with_vectors=with_vectors,
+        )
+        if not records:
+            return None
+        return _to_point(records[0], with_vectors=with_vectors)
+
+    async def get_many(
+        self, *, tenant_id: uuid.UUID, point_ids: Sequence[uuid.UUID]
+    ) -> tuple[Point, ...]:
+        if not point_ids:
+            return ()
+        records, _ = await self._client.scroll(
+            collection_name=self._collection,
+            scroll_filter=models.Filter(
+                must=[
+                    *_conditions(tenant_id=tenant_id, include_inactive=True),
+                    models.HasIdCondition(has_id=[str(point_id) for point_id in point_ids]),
+                ]
+            ),
+            limit=len(point_ids),
+            with_payload=True,
+            with_vectors=False,
+        )
+        return tuple(_to_point(record, with_vectors=False) for record in records)
+
+    async def list_by_file(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        file_id: uuid.UUID,
+        limit: int,
+        cursor: str | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        conditions = _conditions(
+            tenant_id=tenant_id, file_id=file_id, include_inactive=include_inactive
+        )
+        if cursor is not None:
+            conditions.append(
+                models.FieldCondition(key="order_id", range=models.Range(gt=float(cursor)))
+            )
+
+        records, _ = await self._client.scroll(
+            collection_name=self._collection,
+            scroll_filter=models.Filter(must=conditions),
+            order_by=models.OrderBy(key="order_id", direction=models.Direction.ASC),
+            limit=limit,
+            with_payload=True,
+            with_vectors=False,
+        )
+        points = tuple(_to_point(record, with_vectors=False) for record in records)
+        # A short page means the listing is exhausted. A full page might be, but
+        # claiming so would need an extra round trip; handing back a cursor that
+        # yields an empty final page is the cheaper honest answer.
+        next_cursor = repr(points[-1].order_id) if len(points) == limit else None
+        return PointPage(points=points, next_cursor=next_cursor)
+
+    async def count(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> int:
+        result = await self._client.count(
+            collection_name=self._collection,
+            count_filter=models.Filter(
+                must=_conditions(
+                    tenant_id=tenant_id,
+                    domain=domain,
+                    file_id=file_id,
+                    include_inactive=include_inactive,
+                )
+            ),
+            exact=True,
+        )
+        return result.count
+
+    async def keyword_search(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        query: str,
+        limit: int,
+        cursor: str | None = None,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        conditions = _conditions(
+            tenant_id=tenant_id,
+            domain=domain,
+            file_id=file_id,
+            include_inactive=include_inactive,
+        )
+        conditions.append(models.FieldCondition(key="content", match=models.MatchText(text=query)))
+
+        # No `order_by` here, so Qdrant does return a page offset: the full-text
+        # index filters rather than scores, and imposing `order_id` ordering
+        # across files would be meaningless (`order_id` is per-file).
+        records, next_offset = await self._client.scroll(
+            collection_name=self._collection,
+            scroll_filter=models.Filter(must=conditions),
+            limit=limit,
+            offset=cursor,
+            with_payload=True,
+            with_vectors=False,
+        )
+        return PointPage(
+            points=tuple(_to_point(record, with_vectors=False) for record in records),
+            next_cursor=str(next_offset) if next_offset is not None else None,
+        )
+
+    async def apply_patches(self, *, tenant_id: uuid.UUID, patches: Sequence[PayloadPatch]) -> None:
+        if not patches:
+            return
+        await self._client.batch_update_points(
+            collection_name=self._collection,
+            update_operations=[
+                models.SetPayloadOperation(
+                    set_payload=models.SetPayload(
+                        payload=patch.payload,
+                        filter=models.Filter(must=self._patch_conditions(tenant_id, patch)),
+                    )
+                )
+                for patch in patches
+            ],
+        )
+
+    @staticmethod
+    def _patch_conditions(tenant_id: uuid.UUID, patch: PayloadPatch) -> list[models.Condition]:
+        """Address one point by id, under this tenant, at an expected version.
+
+        `include_inactive=True`: soft-deleting and relinking both have to reach
+        points the default read filter hides, and a patch is addressed by an
+        explicit id rather than discovered by a listing.
+        """
+        conditions: list[models.Condition] = [
+            *_conditions(tenant_id=tenant_id, include_inactive=True),
+            models.HasIdCondition(has_id=[str(patch.point_id)]),
+        ]
+        if patch.expected_version is not None:
+            conditions.append(
+                models.FieldCondition(
+                    key="version", match=models.MatchValue(value=patch.expected_version)
+                )
+            )
+        return conditions

tests/fakes.py

@@ -8,6 +8,8 @@ from datetime import datetime
 
 from src.application.ingestion.models import SparseVector
 from src.application.points.models import ChunkPoint
+from src.application.points.point import Point
+from src.application.ports.point_repository import PayloadPatch, PointPage
 
 
 @dataclass
@@ -139,3 +141,161 @@ class FakePointStorage:
             point.payload["is_active"] = False
             point.payload["deleted_at"] = deleted_at.isoformat()
         return len(stale)
+
+
+@dataclass
+class FakePointRepository:
+    """An in-memory `PointRepository`.
+
+    Stores `Point` models keyed by point id. The filter, ordering, and version
+    semantics below are reimplemented in Python rather than stubbed, because
+    every service this fake stands behind is being tested *for* those semantics:
+    a stub that returned points in insertion order would pass a reorder test
+    that real Qdrant fails.
+
+    Three behaviours are modelled deliberately:
+
+    - `is_active` is filtered out unless `include_inactive`, matching ADR-0002's
+      implied read filter.
+    - `list_by_file` sorts by `order_id` and paginates by value, the same cursor
+      mechanism the Qdrant adapter uses, so a test can catch a cursor that skips
+      or repeats.
+    - `apply_patches` honours `expected_version` by silently matching nothing on
+      a mismatch — the no-op-not-error behaviour Qdrant's filtered `set_payload`
+      actually has, which is what makes the service's post-check necessary.
+    """
+
+    points: dict[str, Point] = field(default_factory=dict)
+    patch_batches: list[list[PayloadPatch]] = field(default_factory=list)
+    fail_next: bool = False
+
+    def add(self, point: Point) -> None:
+        """Seed a point. Test-only helper, not part of the port."""
+        self.points[str(point.point_id)] = point
+
+    def _visible(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> list[Point]:
+        return [
+            point
+            for point in self.points.values()
+            if point.tenant_id == tenant_id
+            and (domain is None or point.domain == domain)
+            and (file_id is None or point.file_id == file_id)
+            and (include_inactive or point.is_active)
+        ]
+
+    async def get(
+        self, *, tenant_id: uuid.UUID, point_id: uuid.UUID, with_vectors: bool = False
+    ) -> Point | None:
+        point = self.points.get(str(point_id))
+        if point is None or point.tenant_id != tenant_id:
+            return None
+        return point if with_vectors else point.model_copy(update={"vectors": None})
+
+    async def get_many(
+        self, *, tenant_id: uuid.UUID, point_ids: Sequence[uuid.UUID]
+    ) -> tuple[Point, ...]:
+        wanted = {str(point_id) for point_id in point_ids}
+        return tuple(
+            point
+            for key, point in self.points.items()
+            if key in wanted and point.tenant_id == tenant_id
+        )
+
+    async def list_by_file(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        file_id: uuid.UUID,
+        limit: int,
+        cursor: str | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        ordered = sorted(
+            self._visible(tenant_id=tenant_id, file_id=file_id, include_inactive=include_inactive),
+            key=lambda point: point.order_id,
+        )
+        if cursor is not None:
+            ordered = [point for point in ordered if point.order_id > float(cursor)]
+
+        page = tuple(ordered[:limit])
+        next_cursor = repr(page[-1].order_id) if len(page) == limit else None
+        return PointPage(points=page, next_cursor=next_cursor)
+
+    async def count(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> int:
+        return len(
+            self._visible(
+                tenant_id=tenant_id,
+                domain=domain,
+                file_id=file_id,
+                include_inactive=include_inactive,
+            )
+        )
+
+    async def keyword_search(
+        self,
+        *,
+        tenant_id: uuid.UUID,
+        query: str,
+        limit: int,
+        cursor: str | None = None,
+        domain: str | None = None,
+        file_id: uuid.UUID | None = None,
+        include_inactive: bool = False,
+    ) -> PointPage:
+        # Whole-token containment, lowercased: an approximation of Qdrant's
+        # full-text index good enough to tell "matched" from "did not", which is
+        # all the service layer branches on. Ranking is not modelled because the
+        # real index does not rank either (ADR-0002).
+        terms = query.lower().split()
+        matches = [
+            point
+            for point in self._visible(
+                tenant_id=tenant_id,
+                domain=domain,
+                file_id=file_id,
+                include_inactive=include_inactive,
+            )
+            if all(term in point.content.lower().split() for term in terms)
+        ]
+        start = int(cursor) if cursor is not None else 0
+        page = tuple(matches[start : start + limit])
+        next_start = start + limit
+        return PointPage(
+            points=page, next_cursor=str(next_start) if next_start < len(matches) else None
+        )
+
+    async def apply_patches(self, *, tenant_id: uuid.UUID, patches: Sequence[PayloadPatch]) -> None:
+        self.patch_batches.append(list(patches))
+        if self.fail_next:
+            self.fail_next = False
+            raise RuntimeError("simulated point repository failure")
+
+        for patch in patches:
+            point = self.points.get(str(patch.point_id))
+            if point is None or point.tenant_id != tenant_id:
+                continue
+            if patch.expected_version is not None and point.version != patch.expected_version:
+                continue
+            # Re-validated rather than `model_copy`d, because a patch payload
+            # carries wire values (an ISO `deleted_at`, a stringified
+            # `previous_chunk_id`) exactly as it would reach Qdrant. Copying
+            # without validation would leave the fake holding a `str` where a
+            # read from real Qdrant returns a `datetime`, and a service bug that
+            # depends on the difference would pass here and fail in production.
+            updated = point.model_dump()
+            updated.update(patch.payload)
+            self.points[str(patch.point_id)] = Point.model_validate(updated)

tests/integration/qdrant/test_collection.py

@@ -65,10 +65,42 @@ async def test_ensure_chunks_collection_creates_the_payload_indexes(
         "order_id",
         "previous_chunk_id",
         "next_chunk_id",
+        "content",
+        "is_active",
+        "chunk_index",
     }
     # order_id must be numeric: Qdrant's Range/order_by reject keyword payloads.
     assert schema["order_id"].data_type == models.PayloadSchemaType.FLOAT
     assert schema["tenant_id"].data_type == models.PayloadSchemaType.KEYWORD
+    # `content` must be TEXT, not KEYWORD: ADR-0002's keyword search is a
+    # full-text match on it, and a keyword index would only match the entire
+    # chunk verbatim -- which never happens and would fail silently.
+    assert schema["content"].data_type == models.PayloadSchemaType.TEXT
+    assert schema["is_active"].data_type == models.PayloadSchemaType.BOOL
+    assert schema["chunk_index"].data_type == models.PayloadSchemaType.INTEGER
+
+
+async def test_ensure_chunks_collection_adds_a_missing_index_to_a_live_collection(
+    qdrant_client: AsyncQdrantClient, qdrant_settings: QdrantSettings
+) -> None:
+    """Payload indexes are additive, unlike vector config.
+
+    This is the operational claim the runbook makes when a new index ships:
+    re-running the bootstrap against an existing collection adds it in place, so
+    plan 002's `content`/`is_active`/`chunk_index` indexes do not require
+    recreating a collection that already holds a tenant's points.
+    """
+    await ensure_chunks_collection(qdrant_client, collection=qdrant_settings.collection)
+    await qdrant_client.delete_payload_index(
+        collection_name=qdrant_settings.collection, field_name="content"
+    )
+    info = await qdrant_client.get_collection(qdrant_settings.collection)
+    assert "content" not in info.payload_schema
+
+    assert not await ensure_chunks_collection(qdrant_client, collection=qdrant_settings.collection)
+
+    info = await qdrant_client.get_collection(qdrant_settings.collection)
+    assert info.payload_schema["content"].data_type == models.PayloadSchemaType.TEXT
 
 
 async def test_ensure_chunks_collection_is_idempotent(

tests/integration/qdrant/test_point_repository.py

@@ -0,0 +1,86 @@
+"""`QdrantPointRepository` against the shared `PointRepository` contract.
+
+The identical scenarios run against the in-memory fake in
+`tests/unit/application/points/test_point_repository_contract.py`. This file is
+the half that decides whether the fake is telling the truth: filter
+construction, `order_by: order_id` scroll, cursor pagination, full-text
+matching, and the filtered `set_payload` version guard are all Qdrant
+behaviours a fake can only approximate, and plan 002 Phase 1's exit criterion is
+that the approximation holds.
+
+Seeding differs from the fake's (real points need vectors), so it lives here;
+everything asserted lives in `tests/support/point_contract.py`.
+"""
+
+import uuid
+from collections.abc import Awaitable, Callable
+
+import pytest
+from qdrant_client import AsyncQdrantClient, models
+
+from src.config import QdrantSettings
+from src.infrastructure.qdrant.collection import ensure_chunks_collection
+from src.infrastructure.qdrant.point_repository import QdrantPointRepository
+from src.infrastructure.qdrant.points import QdrantPointStorage
+from tests.support import point_contract
+from tests.support.point_contract import chunk_point_for, seed_specs
+
+pytestmark = [
+    pytest.mark.integration,
+    pytest.mark.qdrant,
+    pytest.mark.asyncio(loop_scope="session"),
+]
+
+type Scenario = Callable[..., Awaitable[None]]
+
+TENANT_A = uuid.UUID("11111111-1111-4111-8111-111111111111")
+TENANT_B = uuid.UUID("22222222-2222-4222-8222-222222222222")
+FILE_A = uuid.UUID("33333333-3333-4333-8333-333333333333")
+FILE_B = uuid.UUID("44444444-4444-4444-8444-444444444444")
+FILE_C = uuid.UUID("55555555-5555-4555-8555-555555555555")
+
+IDS = {
+    "tenant_a": TENANT_A,
+    "tenant_b": TENANT_B,
+    "file_a": FILE_A,
+    "file_b": FILE_B,
+    "file_c": FILE_C,
+}
+
+
+async def _seeded(
+    qdrant_client: AsyncQdrantClient, qdrant_settings: QdrantSettings
+) -> QdrantPointRepository:
+    await ensure_chunks_collection(qdrant_client, collection=qdrant_settings.collection)
+    storage = QdrantPointStorage(qdrant_client, collection=qdrant_settings.collection)
+    await storage.upsert_points(
+        [chunk_point_for(spec) for spec in seed_specs(TENANT_A, TENANT_B, FILE_A, FILE_B, FILE_C)]
+    )
+    # Payload indexes are built asynchronously; without waiting, a full-text or
+    # ordered query can run against a half-built index and return short.
+    await _await_indexing(qdrant_client, qdrant_settings.collection)
+    return QdrantPointRepository(qdrant_client, collection=qdrant_settings.collection)
+
+
+async def _await_indexing(client: AsyncQdrantClient, collection: str) -> None:
+    for _ in range(100):
+        info = await client.get_collection(collection)
+        if info.status == models.CollectionStatus.GREEN and info.indexed_vectors_count is not None:
+            return
+    raise AssertionError(f"collection {collection!r} did not finish indexing")
+
+
+def _arguments(scenario: Scenario) -> dict[str, uuid.UUID]:
+    return {name: value for name, value in IDS.items() if name in scenario.__annotations__}
+
+
+@pytest.mark.parametrize(
+    "scenario",
+    [*point_contract.READ_SCENARIOS, *point_contract.WRITE_SCENARIOS],
+    ids=lambda scenario: scenario.__name__.removeprefix("scenario_"),
+)
+async def test_qdrant_point_repository_satisfies_the_contract(
+    scenario: Scenario, qdrant_client: AsyncQdrantClient, qdrant_settings: QdrantSettings
+) -> None:
+    repository = await _seeded(qdrant_client, qdrant_settings)
+    await scenario(repository, **_arguments(scenario))

tests/integration/qdrant/test_points_api.py

@@ -0,0 +1,395 @@
+"""`/v1/points` read paths over HTTP (ADR-0002, ADR-0008).
+
+Needs both containers: Postgres authenticates the key and derives the tenant,
+Qdrant holds the points. Testing them together is the point — the invariant this
+file exists for is that the tenant Postgres derived is the only one Qdrant is
+ever queried with.
+
+Everything below goes through the real app: real routing, real `require_scope`,
+real error envelope. Only the session factory is overridden, so a route that
+forgot its scope or read a tenant from the query string fails here.
+"""
+
+import uuid
+from collections.abc import AsyncIterator
+
+import pytest
+import pytest_asyncio
+from asgi_lifespan import LifespanManager
+from httpx import ASGITransport, AsyncClient
+from qdrant_client import AsyncQdrantClient
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from src.bootstrap.dependencies import get_sessionmaker
+from src.config import QdrantSettings, Settings
+from src.infrastructure.qdrant.collection import ensure_chunks_collection
+from src.infrastructure.qdrant.points import QdrantPointStorage
+from src.main import create_app
+from tests.support.factories import create_api_key, create_tenant
+from tests.support.point_contract import SeedSpec, chunk_point_for, point_id_for
+
+pytestmark = [
+    pytest.mark.integration,
+    pytest.mark.qdrant,
+    pytest.mark.postgres,
+    pytest.mark.asyncio(loop_scope="session"),
+]
+
+FILE_ID = uuid.UUID("aaaaaaaa-aaaa-4aaa-8aaa-aaaaaaaaaaaa")
+OTHER_FILE_ID = uuid.UUID("bbbbbbbb-bbbb-4bbb-8bbb-bbbbbbbbbbbb")
+
+
+@pytest.fixture
+def api_settings(settings: Settings, qdrant_settings: QdrantSettings) -> Settings:
+    """The unit-test settings with Qdrant pointed at the real container.
+
+    Everything else keeps its closed-port default, so this exercises the point
+    paths without the lifespan reaching a colleague's Ollama box or OpenAI.
+    """
+    return settings.model_copy(update={"qdrant": qdrant_settings})
+
+
+@pytest_asyncio.fixture(loop_scope="session")
+async def api_client(
+    api_settings: Settings, db_sessionmaker: async_sessionmaker[AsyncSession]
+) -> AsyncIterator[AsyncClient]:
+    app = create_app(api_settings)
+    app.dependency_overrides[get_sessionmaker] = lambda: db_sessionmaker
+    async with (
+        LifespanManager(app) as manager,
+        AsyncClient(transport=ASGITransport(app=manager.app), base_url="http://test") as client,
+    ):
+        yield client
+
+
+def _auth(token: str) -> dict[str, str]:
+    return {"Authorization": f"Bearer {token}"}
+
+
+async def _seed(
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+    specs: tuple[SeedSpec, ...],
+) -> None:
+    await ensure_chunks_collection(qdrant_client, collection=qdrant_settings.collection)
+    storage = QdrantPointStorage(qdrant_client, collection=qdrant_settings.collection)
+    await storage.upsert_points([chunk_point_for(spec) for spec in specs])
+
+
+async def _tenant_with_key(
+    db_session: AsyncSession, *, scopes: list[str] | None = None
+) -> tuple[uuid.UUID, str]:
+    tenant = await create_tenant(db_session)
+    _, token = await create_api_key(
+        db_session, tenant=tenant, scopes=scopes if scopes is not None else ["points:read"]
+    )
+    await db_session.commit()
+    return tenant.id, token
+
+
+async def test_list_points_returns_a_files_points_in_order_id_order(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "first", 1.0),
+            SeedSpec(tenant_id, FILE_ID, 2, "third", 3.0),
+            SeedSpec(tenant_id, FILE_ID, 1, "second", 2.0),
+        ),
+    )
+
+    response = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+
+    assert response.status_code == 200
+    assert [point["content"] for point in response.json()["points"]] == [
+        "first",
+        "second",
+        "third",
+    ]
+
+
+async def test_list_points_omits_the_tenant_id_from_the_response(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """Echoing `tenant_id` back invites clients to start sending it."""
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(qdrant_client, qdrant_settings, (SeedSpec(tenant_id, FILE_ID, 0, "only", 1.0),))
+
+    response = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+
+    assert "tenant_id" not in response.json()["points"][0]
+
+
+async def test_get_point_returns_404_for_another_tenants_point(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """`404`, not `403`: the API must not confirm the id exists (ADR-0016)."""
+    owner_id, _ = await _tenant_with_key(db_session)
+    _, intruder_token = await _tenant_with_key(db_session)
+    await _seed(qdrant_client, qdrant_settings, (SeedSpec(owner_id, FILE_ID, 0, "secret", 1.0),))
+
+    response = await api_client.get(
+        f"/v1/points/{point_id_for(FILE_ID, 0)}", headers=_auth(intruder_token)
+    )
+
+    assert response.status_code == 404
+    assert response.json()["error"]["code"] == "not_found"
+
+
+async def test_list_points_returns_nothing_for_another_tenants_file(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    owner_id, _ = await _tenant_with_key(db_session)
+    _, intruder_token = await _tenant_with_key(db_session)
+    await _seed(qdrant_client, qdrant_settings, (SeedSpec(owner_id, FILE_ID, 0, "secret", 1.0),))
+
+    response = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(intruder_token)
+    )
+
+    assert response.status_code == 200
+    assert response.json()["points"] == []
+
+
+async def test_list_points_excludes_inactive_points_unless_asked(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "live", 1.0),
+            SeedSpec(tenant_id, FILE_ID, 1, "deleted", 2.0, is_active=False),
+        ),
+    )
+
+    default = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+    opted_in = await api_client.get(
+        "/v1/points",
+        params={"file_id": str(FILE_ID), "include_inactive": True},
+        headers=_auth(token),
+    )
+
+    assert [point["content"] for point in default.json()["points"]] == ["live"]
+    assert [point["content"] for point in opted_in.json()["points"]] == ["live", "deleted"]
+
+
+async def test_list_points_pagination_does_not_skip_or_repeat_under_a_concurrent_insert(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """The defect an offset cursor would have.
+
+    Between page one and page two, a point is inserted *behind* the cursor
+    (`order_id` 0.5, ahead of everything already returned). An offset-based
+    cursor would shift every later row down by one and hand back `b` a second
+    time. A value-based cursor is unaffected: the reader has passed 2.0 and the
+    new row is behind it.
+    """
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "a", 1.0),
+            SeedSpec(tenant_id, FILE_ID, 1, "b", 2.0),
+            SeedSpec(tenant_id, FILE_ID, 2, "c", 3.0),
+            SeedSpec(tenant_id, FILE_ID, 3, "d", 4.0),
+        ),
+    )
+
+    first = await api_client.get(
+        "/v1/points",
+        params={"file_id": str(FILE_ID), "limit": 2},
+        headers=_auth(token),
+    )
+    await _seed(qdrant_client, qdrant_settings, (SeedSpec(tenant_id, FILE_ID, 9, "inserted", 0.5),))
+    second = await api_client.get(
+        "/v1/points",
+        params={
+            "file_id": str(FILE_ID),
+            "limit": 2,
+            "cursor": first.json()["next_cursor"],
+        },
+        headers=_auth(token),
+    )
+
+    assert [point["content"] for point in first.json()["points"]] == ["a", "b"]
+    assert [point["content"] for point in second.json()["points"]] == ["c", "d"]
+
+
+async def test_count_points_respects_tenant_and_domain_filters(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    other_id, _ = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "one", 1.0),
+            SeedSpec(tenant_id, OTHER_FILE_ID, 0, "two", 1.0, domain="ops"),
+            SeedSpec(other_id, FILE_ID, 5, "theirs", 1.0),
+        ),
+    )
+
+    everything = await api_client.get("/v1/points/count", headers=_auth(token))
+    scoped = await api_client.get(
+        "/v1/points/count", params={"domain": "ops"}, headers=_auth(token)
+    )
+
+    assert everything.json()["count"] == 2
+    assert scoped.json()["count"] == 1
+
+
+async def test_search_points_matches_content_within_the_tenant_only(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    other_id, _ = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "annual leave policy", 1.0),
+            SeedSpec(tenant_id, FILE_ID, 1, "expense policy", 2.0),
+            SeedSpec(tenant_id, FILE_ID, 2, "office address", 3.0),
+            SeedSpec(other_id, OTHER_FILE_ID, 0, "their leave policy", 1.0),
+        ),
+    )
+
+    response = await api_client.get(
+        "/v1/points/search", params={"q": "policy"}, headers=_auth(token)
+    )
+
+    body = response.json()
+    assert body["query"] == "policy"
+    assert {point["content"] for point in body["points"]} == {
+        "annual leave policy",
+        "expense policy",
+    }
+
+
+async def test_search_points_folds_arabic_letterforms_in_the_query(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """A query typed on an Arabic keyboard must match Persian-folded content.
+
+    Ingestion folds U+064A/U+0643 to U+06CC/U+06A9 before storing, so an
+    unfolded query would match nothing — an empty result rather than an error,
+    which is exactly the kind of silent failure nobody reports as a bug.
+    Codepoints, not literals: the two forms are visually identical here.
+    """
+    persian = "مدیریت"  # stored, Persian yeh
+    arabic = "مديريت"  # queried, Arabic yeh
+    assert persian != arabic
+
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(qdrant_client, qdrant_settings, (SeedSpec(tenant_id, FILE_ID, 0, persian, 1.0),))
+
+    response = await api_client.get("/v1/points/search", params={"q": arabic}, headers=_auth(token))
+
+    assert [point["content"] for point in response.json()["points"]] == [persian]
+
+
+async def test_point_read_routes_require_the_points_read_scope(
+    api_client: AsyncClient, db_session: AsyncSession
+) -> None:
+    """An upload key must not double as a way to read every chunk."""
+    _, token = await _tenant_with_key(db_session, scopes=["files:write"])
+
+    response = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+
+    assert response.status_code == 403
+    assert response.json()["error"]["code"] == "missing_scope"
+
+
+async def test_count_and_search_paths_are_not_parsed_as_point_ids(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """Route order regression guard.
+
+    `/{point_id}` declared before `/count` would make this `422` — Pydantic
+    failing to read "count" as a UUID — rather than a count. The bug is one
+    tidy-up reorder away, and nothing else in the suite would catch it.
+
+    Seeds nothing but still bootstraps the collection: querying a collection
+    that does not exist is a `500`, which `/readyz` is responsible for
+    preventing, and which would mask the `422` this test is watching for.
+    """
+    _, token = await _tenant_with_key(db_session)
+    await _seed(qdrant_client, qdrant_settings, ())
+
+    count = await api_client.get("/v1/points/count", headers=_auth(token))
+    search = await api_client.get(
+        "/v1/points/search", params={"q": "anything"}, headers=_auth(token)
+    )
+
+    assert count.status_code == 200
+    assert search.status_code == 200
+
+
+async def test_file_points_route_lists_the_same_points_as_the_query_form(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    await _seed(
+        qdrant_client,
+        qdrant_settings,
+        (
+            SeedSpec(tenant_id, FILE_ID, 0, "first", 1.0),
+            SeedSpec(tenant_id, FILE_ID, 1, "second", 2.0),
+        ),
+    )
+
+    by_query = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+    by_path = await api_client.get(f"/v1/files/{FILE_ID}/points", headers=_auth(token))
+
+    assert by_path.status_code == 200
+    assert by_path.json() == by_query.json()

tests/integration/qdrant/test_points_deletion_api.py

@@ -0,0 +1,276 @@
+"""Soft delete over HTTP, against real Postgres and real Qdrant (ADR-0002).
+
+The unit tests in `tests/unit/application/points/test_deletion.py` decide
+whether the relink logic is right. This file decides whether it is right
+*through the stack*: real routing and scope checks, a tenant derived from a real
+API key, and a real filtered `set_payload` batch — the last of which is the part
+a fake can only approximate, since Qdrant reports success for a patch that
+matched nothing.
+
+`DELETE /v1/files/{file_id}` is here too rather than with the upload tests: it
+spans both stores, and the assertion that matters is the one about points.
+"""
+
+import uuid
+from collections.abc import AsyncIterator
+
+import pytest
+import pytest_asyncio
+from asgi_lifespan import LifespanManager
+from httpx import ASGITransport, AsyncClient
+from qdrant_client import AsyncQdrantClient
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from src.bootstrap.dependencies import get_sessionmaker
+from src.config import QdrantSettings, Settings
+from src.infrastructure.postgres.repositories import source_files as source_files_repo
+from src.infrastructure.qdrant.collection import ensure_chunks_collection
+from src.infrastructure.qdrant.points import QdrantPointStorage
+from src.main import create_app
+from tests.support.factories import create_api_key, create_source_file, create_tenant
+from tests.support.point_contract import SeedSpec, chunk_point_for, point_id_for
+
+pytestmark = [
+    pytest.mark.integration,
+    pytest.mark.qdrant,
+    pytest.mark.postgres,
+    pytest.mark.asyncio(loop_scope="session"),
+]
+
+FILE_ID = uuid.UUID("cccccccc-cccc-4ccc-8ccc-cccccccccccc")
+
+
+@pytest.fixture
+def api_settings(settings: Settings, qdrant_settings: QdrantSettings) -> Settings:
+    return settings.model_copy(update={"qdrant": qdrant_settings})
+
+
+@pytest_asyncio.fixture(loop_scope="session")
+async def api_client(
+    api_settings: Settings, db_sessionmaker: async_sessionmaker[AsyncSession]
+) -> AsyncIterator[AsyncClient]:
+    app = create_app(api_settings)
+    app.dependency_overrides[get_sessionmaker] = lambda: db_sessionmaker
+    async with (
+        LifespanManager(app) as manager,
+        AsyncClient(transport=ASGITransport(app=manager.app), base_url="http://test") as client,
+    ):
+        yield client
+
+
+def _auth(token: str) -> dict[str, str]:
+    return {"Authorization": f"Bearer {token}"}
+
+
+async def _tenant_with_key(
+    db_session: AsyncSession, *, scopes: list[str] | None = None
+) -> tuple[uuid.UUID, str]:
+    tenant = await create_tenant(db_session)
+    _, token = await create_api_key(
+        db_session,
+        tenant=tenant,
+        scopes=scopes if scopes is not None else ["points:read", "points:write"],
+    )
+    await db_session.commit()
+    return tenant.id, token
+
+
+async def _seed_chain(
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+    *,
+    tenant_id: uuid.UUID,
+    file_id: uuid.UUID = FILE_ID,
+    length: int = 3,
+) -> list[uuid.UUID]:
+    """A linked run of points, written the way ingestion writes them."""
+    await ensure_chunks_collection(qdrant_client, collection=qdrant_settings.collection)
+    ids = [point_id_for(file_id, index) for index in range(length)]
+    points = []
+    for index in range(length):
+        chunk_point = chunk_point_for(
+            SeedSpec(tenant_id, file_id, index, f"chunk {index}", float(index + 1))
+        )
+        chunk_point.payload["previous_chunk_id"] = str(ids[index - 1]) if index else None
+        chunk_point.payload["next_chunk_id"] = str(ids[index + 1]) if index + 1 < length else None
+        points.append(chunk_point)
+
+    storage = QdrantPointStorage(qdrant_client, collection=qdrant_settings.collection)
+    await storage.upsert_points(points)
+    return ids
+
+
+async def _read_point(
+    api_client: AsyncClient, token: str, point_id: uuid.UUID
+) -> dict[str, object]:
+    response = await api_client.get(f"/v1/points/{point_id}", headers=_auth(token))
+    assert response.status_code == 200
+    payload: dict[str, object] = response.json()
+    return payload
+
+
+async def test_delete_point_deactivates_it_and_relinks_its_neighbours(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    first, middle, last = await _seed_chain(qdrant_client, qdrant_settings, tenant_id=tenant_id)
+
+    response = await api_client.delete(f"/v1/points/{middle}", headers=_auth(token))
+
+    assert response.status_code == 200
+    assert response.json()["is_active"] is False
+    assert response.json()["deleted_at"] is not None
+    assert (await _read_point(api_client, token, first))["next_chunk_id"] == str(last)
+    assert (await _read_point(api_client, token, last))["previous_chunk_id"] == str(first)
+
+
+async def test_delete_point_keeps_the_point_in_qdrant(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """Soft delete means soft: the point is still there, just not listed."""
+    tenant_id, token = await _tenant_with_key(db_session)
+    _, middle, _ = await _seed_chain(qdrant_client, qdrant_settings, tenant_id=tenant_id)
+
+    await api_client.delete(f"/v1/points/{middle}", headers=_auth(token))
+
+    listed = await api_client.get(
+        "/v1/points", params={"file_id": str(FILE_ID)}, headers=_auth(token)
+    )
+    assert str(middle) not in [point["point_id"] for point in listed.json()["points"]]
+    assert (await _read_point(api_client, token, middle))["is_active"] is False
+
+
+async def test_delete_point_is_a_noop_success_the_second_time(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant_id, token = await _tenant_with_key(db_session)
+    first, middle, _ = await _seed_chain(qdrant_client, qdrant_settings, tenant_id=tenant_id)
+    await api_client.delete(f"/v1/points/{middle}", headers=_auth(token))
+    version_after_first = (await _read_point(api_client, token, first))["version"]
+
+    again = await api_client.delete(f"/v1/points/{middle}", headers=_auth(token))
+
+    assert again.status_code == 200
+    assert again.json()["is_active"] is False
+    assert (await _read_point(api_client, token, first))["version"] == version_after_first
+
+
+async def test_delete_point_returns_404_for_another_tenants_point(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """`404`, not `403`, and nothing is deactivated on the way to saying so."""
+    owner_id, owner_token = await _tenant_with_key(db_session)
+    _, intruder_token = await _tenant_with_key(db_session)
+    _, middle, _ = await _seed_chain(qdrant_client, qdrant_settings, tenant_id=owner_id)
+
+    response = await api_client.delete(f"/v1/points/{middle}", headers=_auth(intruder_token))
+
+    assert response.status_code == 404
+    assert response.json()["error"]["code"] == "not_found"
+    assert (await _read_point(api_client, owner_token, middle))["is_active"] is True
+
+
+async def test_delete_point_requires_the_points_write_scope(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """A read-only key can see a point but must not be able to remove it."""
+    tenant_id, token = await _tenant_with_key(db_session, scopes=["points:read"])
+    _, middle, _ = await _seed_chain(qdrant_client, qdrant_settings, tenant_id=tenant_id)
+
+    response = await api_client.delete(f"/v1/points/{middle}", headers=_auth(token))
+
+    assert response.status_code == 403
+    assert (await _read_point(api_client, token, middle))["is_active"] is True
+
+
+async def test_delete_file_deactivates_every_point_and_retires_the_row(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    db_sessionmaker: async_sessionmaker[AsyncSession],
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    tenant = await create_tenant(db_session)
+    _, token = await create_api_key(
+        db_session, tenant=tenant, scopes=["points:read", "points:write"]
+    )
+    file_id = uuid.uuid4()
+    await create_source_file(db_session, tenant=tenant, source_file_id=file_id)
+    await db_session.commit()
+    await _seed_chain(qdrant_client, qdrant_settings, tenant_id=tenant.id, file_id=file_id)
+
+    response = await api_client.delete(f"/v1/files/{file_id}", headers=_auth(token))
+
+    assert response.status_code == 200
+    assert response.json()["points_soft_deleted"] == 3
+    listed = await api_client.get(
+        "/v1/points", params={"file_id": str(file_id)}, headers=_auth(token)
+    )
+    assert listed.json()["points"] == []
+
+    async with db_sessionmaker() as session:
+        row = await source_files_repo.get_by_id(
+            session, tenant_id=tenant.id, source_file_id=file_id
+        )
+    assert row is not None
+    assert row.status == "soft_deleted"
+    assert row.deleted_at is not None
+
+
+async def test_delete_file_returns_404_for_another_tenants_file(
+    api_client: AsyncClient,
+    db_session: AsyncSession,
+    qdrant_client: AsyncQdrantClient,
+    qdrant_settings: QdrantSettings,
+) -> None:
+    """The authorization check runs before the sweep, so nothing is deactivated."""
+    owner = await create_tenant(db_session)
+    _, owner_token = await create_api_key(
+        db_session, tenant=owner, scopes=["points:read", "points:write"]
+    )
+    intruder = await create_tenant(db_session)
+    _, intruder_token = await create_api_key(
+        db_session, tenant=intruder, scopes=["points:read", "points:write"]
+    )
+    file_id = uuid.uuid4()
+    await create_source_file(db_session, tenant=owner, source_file_id=file_id)
+    await db_session.commit()
+    await _seed_chain(qdrant_client, qdrant_settings, tenant_id=owner.id, file_id=file_id)
+
+    response = await api_client.delete(f"/v1/files/{file_id}", headers=_auth(intruder_token))
+
+    assert response.status_code == 404
+    assert response.json()["error"]["code"] == "not_found"
+    listed = await api_client.get(
+        "/v1/points", params={"file_id": str(file_id)}, headers=_auth(owner_token)
+    )
+    assert len(listed.json()["points"]) == 3
+
+
+async def test_delete_file_requires_the_points_write_scope(
+    api_client: AsyncClient, db_session: AsyncSession
+) -> None:
+    tenant = await create_tenant(db_session)
+    _, token = await create_api_key(db_session, tenant=tenant, scopes=["files:write"])
+    file_id = uuid.uuid4()
+    await create_source_file(db_session, tenant=tenant, source_file_id=file_id)
+    await db_session.commit()
+
+    response = await api_client.delete(f"/v1/files/{file_id}", headers=_auth(token))
+
+    assert response.status_code == 403

tests/support/factories.py

@@ -11,6 +11,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.application.auth.keys import generate_api_key, hash_secret
 from src.infrastructure.postgres.models.api_key import ApiKey
+from src.infrastructure.postgres.models.source_file import SourceFile
 from src.infrastructure.postgres.models.tenant import Tenant
 from src.infrastructure.postgres.models.tenant_domain import TenantDomain
 
@@ -50,6 +51,36 @@ async def create_api_key(
     return api_key, full_key
 
 
+async def create_source_file(
+    session: AsyncSession,
+    *,
+    tenant: Tenant,
+    source_file_id: uuid.UUID | None = None,
+    domain: str = "general",
+    status: str = "active",
+) -> SourceFile:
+    """A `source_files` row for tests that address a file without uploading one.
+
+    `DELETE /v1/files/{file_id}` authorizes against this row before touching a
+    single point, so a delete test needs it even though the interesting state
+    lives in Qdrant.
+    """
+    source_file = SourceFile(
+        id=source_file_id or uuid.uuid4(),
+        tenant_id=tenant.id,
+        domain=domain,
+        source_filename="handbook.docx",
+        source_type="docx",
+        content_sha256="0" * 64,
+        byte_size=1024,
+        storage_uri="s3://bucket/key",
+        status=status,
+    )
+    session.add(source_file)
+    await session.flush()
+    return source_file
+
+
 async def create_tenant_domain(
     session: AsyncSession,
     *,

tests/support/point_contract.py

@@ -0,0 +1,399 @@
+"""One behavioural contract, run against both `PointRepository` implementations.
+
+Plan 002 Phase 1's exit criterion is that the Qdrant adapter and the in-memory
+fake agree on filtering, ordering, and pagination. Asserting that by writing two
+parallel test files invites them to drift — the usual outcome is a fake that
+quietly grows more forgiving than the real store, so unit tests keep passing
+while production does something else.
+
+So the scenarios live here once. `tests/unit/application/points/` runs them
+against `FakePointRepository`; `tests/integration/qdrant/` runs the identical
+functions against real Qdrant. A divergence fails one of the two runs rather
+than hiding.
+
+Each scenario takes an already-seeded repository plus the ids it was seeded
+with, so seeding (which genuinely differs — one writes a dict, the other upserts
+vectors) stays outside the shared code.
+"""
+
+import uuid
+from dataclasses import dataclass
+from datetime import UTC, datetime
+
+from src.application.ingestion.chunking import chunk_id_for
+from src.application.ingestion.models import SparseVector
+from src.application.points.models import ChunkPoint
+from src.application.points.point import Point
+from src.application.ports.point_repository import PayloadPatch, PointRepository
+from src.infrastructure.qdrant.collection import (
+    DENSE_NOMIC_DIMENSIONS,
+    DENSE_OPENAI_DIMENSIONS,
+)
+
+# Two tenants and two files, so every scenario can assert both that the right
+# rows come back and that the wrong ones do not.
+SEEDED_AT = datetime(2026, 1, 1, 12, 0, tzinfo=UTC)
+
+
+@dataclass(frozen=True)
+class SeedSpec:
+    """One point to seed. Deliberately flat — the fixture builds the model."""
+
+    tenant_id: uuid.UUID
+    file_id: uuid.UUID
+    chunk_index: int
+    content: str
+    order_id: float
+    is_active: bool = True
+    version: int = 1
+    domain: str = "support"
+
+
+def point_id_for(file_id: uuid.UUID, chunk_index: int) -> uuid.UUID:
+    """The deterministic point id (ADR-0001), re-exported for readability."""
+    return chunk_id_for(file_id, chunk_index)
+
+
+def build_point(spec: SeedSpec) -> Point:
+    point_id = point_id_for(spec.file_id, spec.chunk_index)
+    return Point(
+        point_id=point_id,
+        tenant_id=spec.tenant_id,
+        domain=spec.domain,
+        file_id=spec.file_id,
+        chunk_id=point_id,
+        content=spec.content,
+        content_type="paragraph",
+        source_filename="handbook.docx",
+        source_type="docx",
+        order_id=spec.order_id,
+        chunk_index=spec.chunk_index,
+        previous_chunk_id=None,
+        next_chunk_id=None,
+        is_active=spec.is_active,
+        deleted_at=None if spec.is_active else SEEDED_AT,
+        created_at=SEEDED_AT,
+        updated_at=SEEDED_AT,
+        created_by="ingestion",
+        updated_by="ingestion",
+        version=spec.version,
+        content_hash="0" * 64,
+        embedding_model_version="test-model",
+    )
+
+
+def chunk_point_for(spec: SeedSpec) -> ChunkPoint:
+    """A `SeedSpec` as something upsertable into real Qdrant.
+
+    The payload is taken straight off `build_point`'s read model rather than
+    hand-written, so the write shape and the read shape cannot drift apart. The
+    vectors are constant filler: nothing in plan 002's read paths scores by
+    similarity, so their values are irrelevant and their dimensions are not.
+    """
+    point = build_point(spec)
+    return ChunkPoint(
+        point_id=point.point_id,
+        dense={
+            "dense_nomic": [0.1] * DENSE_NOMIC_DIMENSIONS,
+            "dense_openai": [0.2] * DENSE_OPENAI_DIMENSIONS,
+        },
+        sparse=SparseVector(indices=[1, 2], values=[0.5, 0.25]),
+        payload=point.model_dump(mode="json", exclude={"point_id", "vectors"}),
+    )
+
+
+def seed_specs(
+    tenant_a: uuid.UUID,
+    tenant_b: uuid.UUID,
+    file_a: uuid.UUID,
+    file_b: uuid.UUID,
+    file_c: uuid.UUID,
+) -> tuple[SeedSpec, ...]:
+    """The fixed corpus every scenario below assumes.
+
+    Ordering is deliberately not insertion order: `order_id` 3.0 is seeded
+    before 2.0 so a repository that returns rows in write order fails
+    `scenario_list_orders_by_order_id` instead of passing by accident.
+
+    Tenant B owns its own file. Sharing a `file_id` across tenants would be a
+    fixture that cannot occur: point ids are derived from `file_id` plus
+    `chunk_index` alone, so two tenants in one file would collide on a single
+    id and the corpus would be testing an impossible state.
+    """
+    return (
+        SeedSpec(tenant_a, file_a, 0, "onboarding checklist for new staff", 1.0),
+        SeedSpec(tenant_a, file_a, 2, "payroll schedule and bank details", 3.0),
+        SeedSpec(tenant_a, file_a, 1, "expense policy and receipts", 2.0),
+        SeedSpec(tenant_a, file_a, 3, "retired parking policy", 4.0, is_active=False),
+        SeedSpec(tenant_a, file_b, 0, "supplier onboarding contacts", 1.0, domain="ops"),
+        SeedSpec(tenant_b, file_c, 0, "other tenant onboarding secrets", 1.0),
+    )
+
+
+async def scenario_get_returns_point_within_tenant(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    point = await repository.get(tenant_id=tenant_a, point_id=point_id_for(file_a, 0))
+    assert point is not None
+    assert point.content == "onboarding checklist for new staff"
+    assert point.chunk_index == 0
+    assert point.order_id == 1.0
+
+
+async def scenario_get_hides_other_tenants_point(
+    repository: PointRepository, *, tenant_b: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    """Tenant B probing a real point id that belongs to tenant A gets nothing.
+
+    The point exists, so this distinguishes a tenant filter from a plain
+    existence check — the difference between `404` and a leak.
+    """
+    assert await repository.get(tenant_id=tenant_b, point_id=point_id_for(file_a, 0)) is None
+
+
+async def scenario_get_reaches_inactive_points(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    """A direct `get` is not subject to the implied `is_active` read filter.
+
+    Soft delete and relinking both address points by id and must be able to see
+    a deactivated one; only listings hide them.
+    """
+    point = await repository.get(tenant_id=tenant_a, point_id=point_id_for(file_a, 3))
+    assert point is not None
+    assert point.is_active is False
+
+
+async def scenario_get_many_returns_only_this_tenants_points(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    found = await repository.get_many(
+        tenant_id=tenant_a,
+        point_ids=[point_id_for(file_a, 0), point_id_for(file_a, 1), uuid.uuid4()],
+    )
+    assert {point.chunk_index for point in found} == {0, 1}
+
+
+async def scenario_list_orders_by_order_id(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    page = await repository.list_by_file(tenant_id=tenant_a, file_id=file_a, limit=10)
+    assert [point.order_id for point in page.points] == [1.0, 2.0, 3.0]
+    assert page.next_cursor is None
+
+
+async def scenario_list_excludes_inactive_by_default(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    default = await repository.list_by_file(tenant_id=tenant_a, file_id=file_a, limit=10)
+    assert 4.0 not in [point.order_id for point in default.points]
+
+    opted_in = await repository.list_by_file(
+        tenant_id=tenant_a, file_id=file_a, limit=10, include_inactive=True
+    )
+    assert [point.order_id for point in opted_in.points] == [1.0, 2.0, 3.0, 4.0]
+
+
+async def scenario_list_paginates_without_skipping_or_repeating(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    first = await repository.list_by_file(tenant_id=tenant_a, file_id=file_a, limit=2)
+    assert [point.order_id for point in first.points] == [1.0, 2.0]
+    assert first.next_cursor is not None
+
+    second = await repository.list_by_file(
+        tenant_id=tenant_a, file_id=file_a, limit=2, cursor=first.next_cursor
+    )
+    assert [point.order_id for point in second.points] == [3.0]
+    assert second.next_cursor is None
+
+
+async def scenario_list_is_scoped_to_one_file(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_b: uuid.UUID
+) -> None:
+    page = await repository.list_by_file(tenant_id=tenant_a, file_id=file_b, limit=10)
+    assert [point.content for point in page.points] == ["supplier onboarding contacts"]
+
+
+async def scenario_count_respects_tenant_and_filters(
+    repository: PointRepository,
+    *,
+    tenant_a: uuid.UUID,
+    tenant_b: uuid.UUID,
+    file_a: uuid.UUID,
+) -> None:
+    assert await repository.count(tenant_id=tenant_a) == 4
+    assert await repository.count(tenant_id=tenant_a, include_inactive=True) == 5
+    assert await repository.count(tenant_id=tenant_a, file_id=file_a) == 3
+    assert await repository.count(tenant_id=tenant_a, domain="ops") == 1
+    assert await repository.count(tenant_id=tenant_b) == 1
+
+
+async def scenario_keyword_search_matches_content_within_tenant(
+    repository: PointRepository, *, tenant_a: uuid.UUID, tenant_b: uuid.UUID
+) -> None:
+    found = await repository.keyword_search(tenant_id=tenant_a, query="onboarding", limit=10)
+    assert {point.content for point in found.points} == {
+        "onboarding checklist for new staff",
+        "supplier onboarding contacts",
+    }
+
+    # The same term matches a different tenant's point, which must not leak.
+    other = await repository.keyword_search(tenant_id=tenant_b, query="onboarding", limit=10)
+    assert {point.content for point in other.points} == {"other tenant onboarding secrets"}
+
+
+async def scenario_keyword_search_excludes_inactive_by_default(
+    repository: PointRepository, *, tenant_a: uuid.UUID
+) -> None:
+    """ "retired parking policy" is seeded inactive, so only the opt-in sees it."""
+    default = await repository.keyword_search(tenant_id=tenant_a, query="parking", limit=10)
+    assert default.points == ()
+
+    opted_in = await repository.keyword_search(
+        tenant_id=tenant_a, query="parking", limit=10, include_inactive=True
+    )
+    assert {point.content for point in opted_in.points} == {"retired parking policy"}
+
+
+async def scenario_keyword_search_filters_by_domain(
+    repository: PointRepository, *, tenant_a: uuid.UUID
+) -> None:
+    found = await repository.keyword_search(
+        tenant_id=tenant_a, query="onboarding", limit=10, domain="ops"
+    )
+    assert {point.content for point in found.points} == {"supplier onboarding contacts"}
+
+
+async def scenario_patch_applies_when_version_matches(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    target = point_id_for(file_a, 0)
+    await repository.apply_patches(
+        tenant_id=tenant_a,
+        patches=[
+            PayloadPatch(
+                point_id=target,
+                payload={"content": "amended onboarding checklist", "version": 2},
+                expected_version=1,
+            )
+        ],
+    )
+    point = await repository.get(tenant_id=tenant_a, point_id=target)
+    assert point is not None
+    assert point.content == "amended onboarding checklist"
+    assert point.version == 2
+
+
+async def scenario_patch_is_a_noop_when_version_is_stale(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    """A stale guard must match nothing rather than raise or clobber.
+
+    This is the behaviour the service's post-apply check depends on: Qdrant
+    reports success for a filtered `set_payload` that matched zero points, so
+    "did my write land?" is only answerable by reading back.
+    """
+    target = point_id_for(file_a, 1)
+    await repository.apply_patches(
+        tenant_id=tenant_a,
+        patches=[
+            PayloadPatch(
+                point_id=target,
+                payload={"content": "should not land"},
+                expected_version=99,
+            )
+        ],
+    )
+    point = await repository.get(tenant_id=tenant_a, point_id=target)
+    assert point is not None
+    assert point.content == "expense policy and receipts"
+
+
+async def scenario_patch_cannot_cross_tenants(
+    repository: PointRepository, *, tenant_a: uuid.UUID, tenant_b: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    """Tenant B patching tenant A's point id must change nothing.
+
+    An unguarded patch (no `expected_version`) addressed by a known-good id is
+    the sharpest form of the probe: only the tenant condition can stop it, so a
+    repository that filtered on id alone would rewrite another tenant's row.
+    """
+    target = point_id_for(file_a, 0)
+    await repository.apply_patches(
+        tenant_id=tenant_b,
+        patches=[PayloadPatch(point_id=target, payload={"content": "hijacked"})],
+    )
+    victim = await repository.get(tenant_id=tenant_a, point_id=target)
+    assert victim is not None
+    assert victim.content == "onboarding checklist for new staff"
+
+
+async def scenario_patch_batch_applies_every_patch_in_one_call(
+    repository: PointRepository, *, tenant_a: uuid.UUID, file_a: uuid.UUID
+) -> None:
+    """One `apply_patches` call carrying several points applies all of them.
+
+    This is the primitive soft delete is built on: a deactivation plus its two
+    neighbour relinks go out together, and a batch that silently applied only
+    its first operation would leave the pointer chain broken — the exact defect
+    ADR-0002 rules out. Nulling a pointer is included because `None` and
+    "absent" are different payload values, and only one of them clears a link.
+    """
+    deleted, previous, following = (point_id_for(file_a, index) for index in (1, 0, 2))
+    await repository.apply_patches(
+        tenant_id=tenant_a,
+        patches=[
+            PayloadPatch(
+                point_id=deleted,
+                payload={"is_active": False, "version": 2},
+                expected_version=1,
+            ),
+            PayloadPatch(
+                point_id=previous,
+                payload={"next_chunk_id": str(following), "version": 2},
+                expected_version=1,
+            ),
+            PayloadPatch(
+                point_id=following,
+                payload={"previous_chunk_id": None, "version": 2},
+                expected_version=1,
+            ),
+        ],
+    )
+
+    applied = {
+        point.point_id: point
+        for point in await repository.get_many(
+            tenant_id=tenant_a, point_ids=[deleted, previous, following]
+        )
+    }
+    assert applied[deleted].is_active is False
+    assert applied[previous].next_chunk_id == following
+    assert applied[following].previous_chunk_id is None
+    assert [applied[point_id].version for point_id in (deleted, previous, following)] == [2, 2, 2]
+
+
+# Scenarios that only read, safe to run in any order against one seeded corpus.
+READ_SCENARIOS = (
+    scenario_get_returns_point_within_tenant,
+    scenario_get_hides_other_tenants_point,
+    scenario_get_reaches_inactive_points,
+    scenario_get_many_returns_only_this_tenants_points,
+    scenario_list_orders_by_order_id,
+    scenario_list_excludes_inactive_by_default,
+    scenario_list_paginates_without_skipping_or_repeating,
+    scenario_list_is_scoped_to_one_file,
+    scenario_count_respects_tenant_and_filters,
+    scenario_keyword_search_matches_content_within_tenant,
+    scenario_keyword_search_excludes_inactive_by_default,
+    scenario_keyword_search_filters_by_domain,
+)
+
+# Scenarios that mutate, and therefore need a freshly seeded corpus each.
+WRITE_SCENARIOS = (
+    scenario_patch_applies_when_version_matches,
+    scenario_patch_is_a_noop_when_version_is_stale,
+    scenario_patch_cannot_cross_tenants,
+    scenario_patch_batch_applies_every_patch_in_one_call,
+)

tests/unit/application/points/test_deletion.py

@@ -0,0 +1,379 @@
+"""Soft delete and neighbour relinking against the fake repository (ADR-0016).
+
+The point of these tests is the pointer chain, not the HTTP surface. ADR-0002
+treats a partial relink as a defect, and the ways to produce one are all here:
+deleting at either boundary, deleting the same point twice, losing a version
+race half way through a batch, and pointing at a neighbour that is gone.
+
+`tests/integration/qdrant/test_points_deletion.py` runs the two central cases
+against real Qdrant. What only this file can do cheaply is force the races.
+"""
+
+import uuid
+from collections.abc import Sequence
+from dataclasses import dataclass
+from typing import override
+
+import pytest
+import structlog.testing
+
+from src.application.points.deletion import soft_delete_file_points, soft_delete_point
+from src.application.points.errors import PointVersionConflictError
+from src.application.points.point import Point, PointNotFoundError
+from src.application.ports.point_repository import PayloadPatch
+from tests.fakes import FakePointRepository
+from tests.support.point_contract import SeedSpec, build_point
+
+pytestmark = [pytest.mark.unit, pytest.mark.asyncio]
+
+TENANT = uuid.UUID("11111111-1111-4111-8111-111111111111")
+OTHER_TENANT = uuid.UUID("22222222-2222-4222-8222-222222222222")
+FILE = uuid.UUID("33333333-3333-4333-8333-333333333333")
+OTHER_FILE = uuid.UUID("44444444-4444-4444-8444-444444444444")
+ACTOR = "api_key:test"
+
+
+def _chain(count: int, *, tenant: uuid.UUID = TENANT, file_id: uuid.UUID = FILE) -> list[Point]:
+    """`count` points of one file, linked head to tail in `order_id` order."""
+    points = [
+        build_point(SeedSpec(tenant, file_id, index, f"chunk {index}", float(index + 1)))
+        for index in range(count)
+    ]
+    return [
+        point.model_copy(
+            update={
+                "previous_chunk_id": points[index - 1].point_id if index else None,
+                "next_chunk_id": (points[index + 1].point_id if index + 1 < len(points) else None),
+            }
+        )
+        for index, point in enumerate(points)
+    ]
+
+
+def _seeded(*points: Point) -> FakePointRepository:
+    repository = FakePointRepository()
+    for point in points:
+        repository.add(point)
+    return repository
+
+
+def _stored(repository: FakePointRepository, point_id: uuid.UUID) -> Point:
+    return repository.points[str(point_id)]
+
+
+def _walk(repository: FakePointRepository, head: uuid.UUID) -> list[uuid.UUID]:
+    """Follow `next_chunk_id` from `head`, guarding against a cycle."""
+    visited: list[uuid.UUID] = []
+    current: uuid.UUID | None = head
+    while current is not None and len(visited) <= len(repository.points):
+        visited.append(current)
+        current = _stored(repository, current).next_chunk_id
+    return visited
+
+
+async def test_soft_delete_point_relinks_the_neighbours_of_a_middle_point() -> None:
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    deleted = await soft_delete_point(
+        repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR
+    )
+
+    assert deleted.is_active is False
+    assert deleted.deleted_at is not None
+    assert _stored(repository, first.point_id).next_chunk_id == last.point_id
+    assert _stored(repository, last.point_id).previous_chunk_id == first.point_id
+
+
+async def test_soft_delete_point_sends_the_deactivation_and_both_relinks_in_one_batch() -> None:
+    """A partial relink is a defect, so the three patches must not be split up."""
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+    assert len(repository.patch_batches) == 1
+    assert {patch.point_id for patch in repository.patch_batches[0]} == {
+        middle.point_id,
+        first.point_id,
+        last.point_id,
+    }
+
+
+async def test_soft_delete_point_bumps_the_version_of_every_point_it_touches() -> None:
+    """A relinked neighbour really changed, so a stale editor of it must `409`."""
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+    assert [_stored(repository, point.point_id).version for point in (first, middle, last)] == [
+        2,
+        2,
+        2,
+    ]
+    assert _stored(repository, first.point_id).updated_by == ACTOR
+
+
+async def test_soft_delete_point_leaves_the_new_head_without_a_previous_pointer() -> None:
+    first, second, third = _chain(3)
+    repository = _seeded(first, second, third)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=first.point_id, actor=ACTOR)
+
+    assert _stored(repository, second.point_id).previous_chunk_id is None
+
+
+async def test_soft_delete_point_leaves_the_new_tail_without_a_next_pointer() -> None:
+    first, second, third = _chain(3)
+    repository = _seeded(first, second, third)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=third.point_id, actor=ACTOR)
+
+    assert _stored(repository, second.point_id).next_chunk_id is None
+
+
+async def test_soft_delete_point_keeps_the_deleted_points_own_pointers() -> None:
+    """Nothing active points at it any more, so its pointers record where it sat.
+
+    That record is what the retry re-plans from, and what a later restore or an
+    audit reader would need to place the point back in the sequence.
+    """
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+    stored = _stored(repository, middle.point_id)
+    assert stored.previous_chunk_id == first.point_id
+    assert stored.next_chunk_id == last.point_id
+
+
+async def test_soft_delete_point_is_a_noop_for_an_already_inactive_point() -> None:
+    """Not a `404`, and not a second relink — no patch is issued at all."""
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+    versions_after_first = {
+        point.point_id: _stored(repository, point.point_id).version
+        for point in (first, middle, last)
+    }
+    repository.patch_batches.clear()
+
+    again = await soft_delete_point(
+        repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR
+    )
+
+    assert again.is_active is False
+    assert repository.patch_batches == []
+    assert {
+        point.point_id: _stored(repository, point.point_id).version
+        for point in (first, middle, last)
+    } == versions_after_first
+
+
+async def test_soft_delete_point_raises_not_found_for_another_tenants_point() -> None:
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    with pytest.raises(PointNotFoundError):
+        await soft_delete_point(
+            repository, tenant_id=OTHER_TENANT, point_id=middle.point_id, actor=ACTOR
+        )
+
+    assert repository.patch_batches == []
+    assert _stored(repository, middle.point_id).is_active is True
+
+
+async def test_soft_delete_point_raises_not_found_for_an_unknown_point() -> None:
+    repository = _seeded(*_chain(2))
+
+    with pytest.raises(PointNotFoundError):
+        await soft_delete_point(repository, tenant_id=TENANT, point_id=uuid.uuid4(), actor=ACTOR)
+
+
+async def test_soft_delete_point_skips_a_neighbour_that_is_not_there() -> None:
+    """A pointer naming an absent point means the chain was already broken.
+
+    The delete completes the half of the relink that exists rather than
+    refusing, which would leave the point unremovable through any endpoint.
+    """
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle)  # `last` is never stored
+
+    deleted = await soft_delete_point(
+        repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR
+    )
+
+    assert deleted.is_active is False
+    assert _stored(repository, first.point_id).next_chunk_id == last.point_id
+
+
+async def test_soft_delete_point_visits_every_active_point_exactly_once_after_several_deletes() -> (
+    None
+):
+    """The plan's traversal property, over a sequence of deletes.
+
+    Walking `next_chunk_id` from the head must reach every surviving point once
+    and never step into a deactivated one.
+    """
+    points = _chain(5)
+    repository = _seeded(*points)
+
+    for index in (1, 3):
+        await soft_delete_point(
+            repository, tenant_id=TENANT, point_id=points[index].point_id, actor=ACTOR
+        )
+
+    walked = _walk(repository, points[0].point_id)
+    assert walked == [points[0].point_id, points[2].point_id, points[4].point_id]
+    assert all(_stored(repository, point_id).is_active for point_id in walked)
+
+
+@dataclass
+class _ContendedRepository(FakePointRepository):
+    """Bumps one point's version just before an apply, as a rival writer would.
+
+    That makes the patch guarding on the old version match nothing while the
+    rest of the batch lands — Qdrant's real behaviour, and the partial apply the
+    service's retry exists to repair. `rounds` bounds how long the rival keeps
+    interfering.
+    """
+
+    rival: uuid.UUID | None = None
+    rounds: int = 0
+
+    @override
+    async def apply_patches(self, *, tenant_id: uuid.UUID, patches: Sequence[PayloadPatch]) -> None:
+        if self.rounds > 0 and self.rival is not None:
+            self.rounds -= 1
+            victim = self.points[str(self.rival)]
+            self.points[str(self.rival)] = victim.model_copy(update={"version": victim.version + 1})
+        await super().apply_patches(tenant_id=tenant_id, patches=patches)
+
+
+async def test_soft_delete_point_repairs_a_partially_applied_batch_on_retry() -> None:
+    first, middle, last = _chain(3)
+    repository = _ContendedRepository(rival=first.point_id, rounds=1)
+    for point in (first, middle, last):
+        repository.add(point)
+
+    await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+    # The first batch left `first` stale; the second re-planned only what was
+    # still missing, rather than re-deactivating the already-inactive point.
+    assert len(repository.patch_batches) == 2
+    assert [patch.point_id for patch in repository.patch_batches[1]] == [first.point_id]
+    assert _stored(repository, first.point_id).next_chunk_id == last.point_id
+    assert _stored(repository, middle.point_id).is_active is False
+
+
+async def test_soft_delete_point_conflicts_when_the_relink_never_settles() -> None:
+    first, middle, last = _chain(3)
+    repository = _ContendedRepository(rival=first.point_id, rounds=99)
+    for point in (first, middle, last):
+        repository.add(point)
+
+    with pytest.raises(PointVersionConflictError):
+        await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+
+async def test_soft_delete_file_points_deactivates_every_active_point_of_the_file() -> None:
+    points = _chain(3)
+    other_file = _chain(2, file_id=OTHER_FILE)
+    other_tenant = _chain(1, tenant=OTHER_TENANT, file_id=uuid.uuid4())
+    repository = _seeded(*points, *other_file, *other_tenant)
+
+    swept = await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+
+    assert swept == 3
+    assert all(not _stored(repository, point.point_id).is_active for point in points)
+    assert all(_stored(repository, point.point_id).is_active for point in other_file)
+    assert all(_stored(repository, point.point_id).is_active for point in other_tenant)
+
+
+async def test_soft_delete_file_points_leaves_the_chain_intact() -> None:
+    """No survivor can dangle, so the sweep rewrites no pointer at all."""
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+
+    assert _stored(repository, first.point_id).next_chunk_id == middle.point_id
+    assert _stored(repository, middle.point_id).previous_chunk_id == first.point_id
+    assert _stored(repository, last.point_id).previous_chunk_id == middle.point_id
+
+
+async def test_soft_delete_file_points_pages_past_one_batch() -> None:
+    """More points than one sweep page, so the re-listing loop has to run."""
+    points = _chain(230)
+    repository = _seeded(*points)
+
+    swept = await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+
+    assert swept == 230
+    assert all(not _stored(repository, point.point_id).is_active for point in points)
+
+
+async def test_soft_delete_file_points_is_a_noop_the_second_time() -> None:
+    repository = _seeded(*_chain(3))
+    await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+    repository.patch_batches.clear()
+
+    swept = await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+
+    assert swept == 0
+    assert repository.patch_batches == []
+
+
+async def test_soft_delete_file_points_returns_zero_for_an_unknown_file() -> None:
+    repository = _seeded(*_chain(2))
+
+    assert (
+        await soft_delete_file_points(
+            repository, tenant_id=TENANT, file_id=uuid.uuid4(), actor=ACTOR
+        )
+        == 0
+    )
+
+
+async def test_soft_delete_point_logs_its_duration_and_round_count() -> None:
+    """ADR-0011's `duration_ms`, plus the field that explains a slow one.
+
+    Relinking is O(1), so a delete's cost is Qdrant round trips; `rounds` above
+    1 means a concurrent writer forced a re-plan rather than the store being
+    slow, and the two fields are only useful together.
+    """
+    first, middle, last = _chain(3)
+    repository = _seeded(first, middle, last)
+
+    with structlog.testing.capture_logs() as logs:
+        await soft_delete_point(repository, tenant_id=TENANT, point_id=middle.point_id, actor=ACTOR)
+
+    event = next(entry for entry in logs if entry["event"] == "points.soft_deleted")
+    assert event["rounds"] == 1
+    assert isinstance(event["duration_ms"], float)
+
+
+async def test_soft_delete_file_points_logs_a_round_per_sweep_page() -> None:
+    """The sweep is the delete path whose cost tracks the size of the file."""
+    repository = _seeded(*_chain(230))
+
+    with structlog.testing.capture_logs() as logs:
+        await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)
+
+    event = next(entry for entry in logs if entry["event"] == "points.file_soft_deleted")
+    assert event["points_soft_deleted"] == 230
+    assert event["rounds"] == 3
+    assert isinstance(event["duration_ms"], float)
+
+
+async def test_soft_delete_file_points_conflicts_when_a_round_makes_no_progress() -> None:
+    """A sweep round that attempts the same ids as the one before is stuck."""
+    points = _chain(3)
+    repository = _ContendedRepository(rival=points[0].point_id, rounds=99)
+    for point in points:
+        repository.add(point)
+
+    with pytest.raises(PointVersionConflictError):
+        await soft_delete_file_points(repository, tenant_id=TENANT, file_id=FILE, actor=ACTOR)

tests/unit/application/points/test_point_repository_contract.py

@@ -0,0 +1,57 @@
+"""`FakePointRepository` against the shared `PointRepository` contract.
+
+The same scenarios run against real Qdrant in
+`tests/integration/qdrant/test_point_repository.py`. Keeping both runs green is
+what stops the fake from drifting into something more permissive than the store
+it stands in for — see `tests/support/point_contract.py`.
+"""
+
+import uuid
+from collections.abc import Awaitable, Callable
+
+import pytest
+
+from src.application.ports.point_repository import PointRepository
+from tests.fakes import FakePointRepository
+from tests.support import point_contract
+from tests.support.point_contract import build_point, seed_specs
+
+pytestmark = [pytest.mark.unit, pytest.mark.asyncio]
+
+type Scenario = Callable[..., Awaitable[None]]
+
+TENANT_A = uuid.UUID("11111111-1111-4111-8111-111111111111")
+TENANT_B = uuid.UUID("22222222-2222-4222-8222-222222222222")
+FILE_A = uuid.UUID("33333333-3333-4333-8333-333333333333")
+FILE_B = uuid.UUID("44444444-4444-4444-8444-444444444444")
+FILE_C = uuid.UUID("55555555-5555-4555-8555-555555555555")
+
+IDS = {
+    "tenant_a": TENANT_A,
+    "tenant_b": TENANT_B,
+    "file_a": FILE_A,
+    "file_b": FILE_B,
+    "file_c": FILE_C,
+}
+
+
+def _seeded() -> FakePointRepository:
+    repository = FakePointRepository()
+    for spec in seed_specs(TENANT_A, TENANT_B, FILE_A, FILE_B, FILE_C):
+        repository.add(build_point(spec))
+    return repository
+
+
+def _arguments(scenario: Scenario) -> dict[str, uuid.UUID]:
+    """Pass only the ids a scenario declares, so each one names its own inputs."""
+    return {name: value for name, value in IDS.items() if name in scenario.__annotations__}
+
+
+@pytest.mark.parametrize(
+    "scenario",
+    [*point_contract.READ_SCENARIOS, *point_contract.WRITE_SCENARIOS],
+    ids=lambda scenario: scenario.__name__.removeprefix("scenario_"),
+)
+async def test_fake_point_repository_satisfies_the_contract(scenario: Scenario) -> None:
+    repository: PointRepository = _seeded()
+    await scenario(repository, **_arguments(scenario))

tests/unit/application/points/test_queries.py

@@ -0,0 +1,103 @@
+"""`application/points/queries.py` against the fake repository (ADR-0016).
+
+The HTTP-level behaviour is covered in `tests/integration/qdrant/`. What is
+worth isolating here is the small amount of logic the service actually owns —
+raising instead of returning `None`, and folding a query's Arabic letterforms —
+because both are cheap to test directly and expensive to notice when broken.
+"""
+
+import uuid
+
+import pytest
+
+from src.application.points.point import PointNotFoundError
+from src.application.points.queries import (
+    count_points,
+    get_point,
+    list_file_points,
+    search_points,
+)
+from tests.fakes import FakePointRepository
+from tests.support.point_contract import SeedSpec, build_point, point_id_for
+
+pytestmark = [pytest.mark.unit, pytest.mark.asyncio]
+
+TENANT = uuid.UUID("11111111-1111-4111-8111-111111111111")
+OTHER_TENANT = uuid.UUID("22222222-2222-4222-8222-222222222222")
+FILE = uuid.UUID("33333333-3333-4333-8333-333333333333")
+
+
+def _repository(*specs: SeedSpec) -> FakePointRepository:
+    repository = FakePointRepository()
+    for spec in specs:
+        repository.add(build_point(spec))
+    return repository
+
+
+async def test_get_point_returns_the_point_for_its_owner() -> None:
+    repository = _repository(SeedSpec(TENANT, FILE, 0, "hello", 1.0))
+
+    point = await get_point(repository, tenant_id=TENANT, point_id=point_id_for(FILE, 0))
+
+    assert point.content == "hello"
+
+
+async def test_get_point_raises_for_another_tenants_point() -> None:
+    """Raising, not returning `None`, so a route cannot serve `200 null`."""
+    repository = _repository(SeedSpec(TENANT, FILE, 0, "hello", 1.0))
+
+    with pytest.raises(PointNotFoundError):
+        await get_point(repository, tenant_id=OTHER_TENANT, point_id=point_id_for(FILE, 0))
+
+
+async def test_get_point_raises_for_an_unknown_point() -> None:
+    repository = _repository()
+
+    with pytest.raises(PointNotFoundError):
+        await get_point(repository, tenant_id=TENANT, point_id=uuid.uuid4())
+
+
+async def test_search_points_folds_arabic_letterforms_before_matching() -> None:
+    """The query is normalized the same way ingestion normalized the content.
+
+    Stored content carries Persian yeh (U+06CC) because `normalize_persian_text`
+    folded it at ingest. A query typed with Arabic yeh (U+064A) is a different
+    codepoint and would match nothing — silently, with no error to notice.
+    """
+    persian = "مدیریت"
+    arabic = "مديريت"
+    assert persian != arabic
+
+    repository = _repository(SeedSpec(TENANT, FILE, 0, persian, 1.0))
+
+    found = await search_points(repository, tenant_id=TENANT, query=arabic, limit=10)
+
+    assert [point.content for point in found.points] == [persian]
+
+
+async def test_search_points_does_not_reach_another_tenant() -> None:
+    repository = _repository(SeedSpec(OTHER_TENANT, FILE, 0, "secret", 1.0))
+
+    found = await search_points(repository, tenant_id=TENANT, query="secret", limit=10)
+
+    assert found.points == ()
+
+
+async def test_list_file_points_returns_an_empty_page_for_a_foreign_file() -> None:
+    """Indistinguishable from an unknown file — the same non-disclosure rule."""
+    repository = _repository(SeedSpec(OTHER_TENANT, FILE, 0, "secret", 1.0))
+
+    page = await list_file_points(repository, tenant_id=TENANT, file_id=FILE, limit=10)
+
+    assert page.points == ()
+    assert page.next_cursor is None
+
+
+async def test_count_points_excludes_inactive_unless_asked() -> None:
+    repository = _repository(
+        SeedSpec(TENANT, FILE, 0, "live", 1.0),
+        SeedSpec(TENANT, FILE, 1, "gone", 2.0, is_active=False),
+    )
+
+    assert await count_points(repository, tenant_id=TENANT) == 1
+    assert await count_points(repository, tenant_id=TENANT, include_inactive=True) == 2