fix(environment): count no write for a collection once a read shows its entity gone

A whole list's read checks the collection, so it exercised every write
that changed it since the last check. A create whose entity an
unmodelled delete removed, and a 404 then showed gone, was still among
them, so a whole list taken afterwards confirmed a create it cannot
show. The absent entity now leaves every write's claim on its
collection, as a modelled delete's replacement does.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

docs/specs/agent-environments/list-lines/plan.md

@@ -6,5 +6,7 @@
 2. **Counters.** Count `number`-of-items members as item totals.
 3. **Consumers.** One helper says whether a view lists all on a line; serving, the write gate's list checks and the
    insert retry use it, and an argument-less call may answer on any such line.
-4. **Tests and docs.** Domain and serving tests as the acceptance lists; the membership row of the environment-state
+4. **Absences.** When a read shows an entity absent, drop it from every write's claim on its collection, so a write
+   left with none no longer counts there.
+5. **Tests and docs.** Domain and serving tests as the acceptance lists; the membership row of the environment-state
    docs and the list answer row of the agent-environment docs.

docs/specs/agent-environments/list-lines/spec.md

@@ -18,13 +18,19 @@ against the whole collection, and a create's insert rule may be retried on it, a
 their recorded members. Without such a line, or when every line is one, the view is unchanged and the member is absent,
 so existing states keep their values.
 
+A whole line's read checks the collection, so it exercises every write that changed the collection since it was last
+read. A write whose entity a read has since shown absent, for example a create an unmodelled delete removed and a 404
+then showed gone, no longer counts there, as when a modelled delete replaces it. Otherwise a whole list taken after the
+entity was gone would confirm a create it cannot show.
+
 `numberOfElements` and similar number-of-items members (`number` with `elements`, `entries`, `items` or `results`)
 count the listed entities, so a whole line's counter follows the state as `totalElements` does.
 
 ## Acceptance
 
 - Domain: a tool with a whole line and a filtered line names the whole one; a create the whole line later lists is
-  confirmed; a tool whose lines are all whole, or none, names none.
+  confirmed; a tool whose lines are all whole, or none, names none; a whole list taken after a read showed the created
+  entity gone confirms no create.
 - Serving: after a served create, the whole line lists the created entity with its counters, and the filtered line
   keeps its recorded members.
 - Measured: the six published environments compared with the application before and after, on the probes of the

docs/specs/agent-environments/list-lines/tasks.md

@@ -3,6 +3,7 @@
 - [x] Judge whole-collection membership per checked line.
 - [x] Count number-of-items members.
 - [x] Serve, check and place creates per line.
+- [x] Drop a write from its collection once a read shows its entity absent.
 - [x] Add domain and serving tests.
 - [x] Document per-line membership.
 - [x] Measure the six published environments before and after.

docs/specs/agent-environments/list-lines/verification.md

@@ -1,14 +1,15 @@
 # Verification
 
-Verified commit: 87e94d12 (this branch before this file). Executed on macOS with Node v22.23.1 (the repository pins 24.18.0 in `.nvmrc`, which was
-not installed); the probes were recorded earlier against the live applications on six disposable Linux VMs.
+Verified commit: 8a374b6b (this branch with the write-plan branch's head `dc5e2aad` merged in). Executed on macOS with
+Node v22.23.1 (the repository pins 24.18.0 in `.nvmrc`, which was not installed); the probes were recorded earlier
+against the live applications on six disposable Linux VMs.
 
 ## Gates
 
 - `npm run build:cached`, `npm run check:fast` (typecheck and lint), `npm run format:check`, `npx knip`,
   `npm run scan:todos`, `npm run docs:check`, `npm run verify:test-discovery` and `npm run mcp-catalog:check`: passed.
-- `npm run jscpd`: 3.46% duplicated lines over 3601 files, under the 3.5% gate.
-- `npx vitest run --project domain --project services`: 7479 passed, 5 pre-existing skips.
+- `npm run jscpd`: 3.45% duplicated lines over 3646 files, under the 3.5% gate.
+- `npx vitest run --project domain --project services`: 7615 passed, 5 pre-existing skips.
 - `npm run test:prepare`, then `npm run test:focused --` the environment serve and export CLI boundaries, the serve
   and served-writes MCP boundaries, the analysis-view CLI and MCP boundaries, the compact input schema boundary and
   tool schema validity: 8 files, 78 passed.
@@ -18,37 +19,39 @@ one, with `numberOfElements` and `totalElements` as counters, and a create the w
 whose lines are all whole, or none, names none) and one serving test in `environmentStateWriteAnswer` (after a served
 create, the whole line lists the created book with its counters, and the filtered line keeps its recorded member).
 
-## Six published environments before and after
+## Fifty published captures
 
-The six published environments of the fidelity comparison (NetBox, Komga, Mealie, n8n, Shlink, self-hosted Sentry),
-each built from its original capture, were compared with `environment-compare` before and after this change. The
-probes were recorded against each application restored from one snapshot: the fidelity comparison's capture re-run,
-create/read/update/delete scenario and read of every seeded entity, and held-out sessions recorded later with values
-no capture sent (two creates, updates and deletes of created and seeded entities, and the reads and lists after them).
-Both builds merged the environment-compare and prefix-variance branches, which the comparison and the manifests need.
+The environment-state view ran over the 50 published captures with each manifest's template rules, on builds with and
+without this change. Both merged the prefix-variance branch, which some manifests need.
+
+- 47 list views in 20 environments gain a whole line, among them Komga's books, series, collections and read lists,
+  BookStack's books, chapters and pages, Mealie's cookbooks, shopping lists, categories and tags, WordPress's posts and
+  comments, Vikunja's labels and Paperless's groups. On that line a call now lists the state's entities, including
+  those a task loads with `data/add` and those served writes create or delete, where it listed only the recorded
+  members.
+- Served write tools go from 31 to 33: Komga's collection create, which a whole list after the create confirms, and
+  Airbyte's tag delete. Four of the gained lists belong to a type with a served write (Airbyte tags, BookStack books,
+  Komga collections, Linkding tags).
+- Komga's list views also count `numberOfElements`. No other view or write plan changed.
+
+## Six environments against their applications
+
+The six environments of the fidelity comparison (NetBox, Komga, Mealie, n8n, Shlink, self-hosted Sentry) were compared
+with their applications by `environment-compare` with and without this change. The probes were the comparison's capture
+re-run, create/read/update/delete scenario and read of every seeded entity, and held-out sessions recorded later with
+values no capture sent. Both builds merged the environment-compare and prefix-variance branches.
 
 | Environment | Steps | Before | After | Ignoring order, before | After |
 | ----------- | ----: | -----: | ----: | ---------------------: | ----: |
 | NetBox      |   479 |  98.5% | 98.5% |                  98.5% | 98.5% |
-| Komga       |   600 |  94.7% | 95.2% |                  94.7% | 95.5% |
+| Komga       |   600 |  91.5% | 91.5% |                  91.5% | 91.5% |
 | Mealie      |   449 |  94.0% | 94.0% |                  94.9% | 94.9% |
 | n8n         |   278 |  71.6% | 71.6% |                  84.2% | 84.2% |
 | Shlink      |   202 |  87.1% | 87.1% |                  90.1% | 90.1% |
 | Sentry      |   372 |  24.5% | 24.5% |                  47.6% | 47.6% |
 
-Komga is the one environment whose list tools have both kinds of line: `/api/v1/collections` lists every collection,
-`?library_id=…` filters them. After the change the whole line lists created collections with `totalElements` and
-`numberOfElements` following, which three list reads after creates now agree on; in two more the created collection
-is listed but placed where the insert rule puts it, not where Komga sorts it (`order`). No step of any environment
-agreed before and differs after.
-
-The other environments' lists did not meet the per-line conditions or did not need them:
-
-- NetBox's sites list was already `all`.
-- Mealie's recipe lines all carry ordering or search parameters.
-- Shlink's short-URL list replays (`query-varies`).
-- n8n's workflow list is `list-differs`.
-
-Their remaining differences are elsewhere: sets the application returns in varying order, writes the capture never
-confirmed, preconditions such as n8n's archive-before-delete, and, for Sentry, values the capture's preparation
-replaced before inspection.
+No step changed. This Komga environment's capture creates, updates and deletes a collection before any whole list, so
+with the write-plan branch's head its create and update are unconfirmed and serve nothing a list could show. Before
+that head (at `f2b95351`), when a list taken after the delete still confirmed them, the same comparison moved Komga
+from 94.7% to 95.2%: three list reads after creates agreed and two more differed only in where the created collection
+was placed. None of the other five environments has a list tool with both kinds of line and a served write on its type.

docs/web-network-captures.md

@@ -634,8 +634,9 @@ with its recording as the read plans are, as the whole response it would serve:
 the entity or list rendered into the envelope of the item view's or the line's
 base recording, with the members the state still holds. A 400, 404 or 410 (or a
 `null` body) agrees with an entity the copy does not hold. A match confirms
-the writes that changed its entity or collection since it was last read; a
-mismatch contradicts them, or, when an unmodelled write came after them, is
+the writes that changed its entity or collection since it was last read, less
+those whose entity a read since showed absent, which no longer count for the
+collection; a mismatch contradicts them, or, when an unmodelled write came after them, is
 checked only on the members they sent; a mismatch no write explains marks the related writes since as
 `side-effect`. A plan is `served` when a read confirmed it and none
 contradicted it; otherwise its `reason` is the first of its build reason

src/domain/analysisView/EnvironmentStateWriteSimulation.ts

@@ -271,6 +271,11 @@ export class EnvironmentStateWriteSimulation {
     this.#touched.delete(target);
     if (isAbsence(record.status)) {
       this.#state.remove(entity);
+      this.#effects.removed(
+        this.#touched,
+        target,
+        collectionTarget(entity.type, entity.collection),
+      );
       return;
     }
     const object = this.#input.io.withBody(record.ordinal, (body) =>

src/domain/analysisView/environmentStateWriteChecks.ts

@@ -177,6 +177,18 @@ export class WriteEffects {
     this.#members.delete(key);
   }
 
+  /** A read showed the entity absent: no write's effect on it remains, so a write left with no entity drops from the collection. */
+  removed(touched: TouchedTargets, entity: string, collection: string): void {
+    this.#changed.delete(entity);
+    const byTool = this.#members.get(collection);
+    if (byTool === undefined) return;
+    for (const [tool, entities] of byTool) {
+      if (!entities.delete(entity) || entities.size > 0) continue;
+      byTool.delete(tool);
+      touched.get(collection)?.delete(tool);
+    }
+  }
+
   supersede(
     touched: TouchedTargets,
     writer: string,

src/domain/analysisView/environmentStateWrites.test.ts

@@ -513,6 +513,21 @@ describe("list lines", () => {
     });
   });
 
+  it("confirms no create by a whole list taken after a read showed its entity gone", () => {
+    const rows: TimedCaptureRow[] = [
+      ...BOOK_INIT_ROWS,
+      ["POST", "/api/books", THIRD_BOOK, 201, { name: "Third Book" }],
+      // A redirected delete is not modelled; the read after it shows the book gone.
+      ["DELETE", "/api/books/3", "", 302],
+      ["GET", "/api/books/3", BOOK_NOT_FOUND, 404],
+      ["GET", "/api/books", [FIRST_BOOK, SECOND_BOOK]],
+    ];
+    expect(planOf(stateOf(rows), "post_books")).toMatchObject({
+      served: false,
+      reason: "unconfirmed",
+    });
+  });
+
   it("names no line when every line lists its whole collection, or none does", () => {
     const listOf = (rows: readonly TimedCaptureRow[]) =>
       stateOf(rows).views.find((view) => view.tool === "get_books");