agentera 3.0.0-dev.26 → 3.0.0-dev.27

package/LICENSE

@@ -0,0 +1,201 @@
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package/README.md

@@ -74,14 +74,24 @@ details.
 
 Requires Node.js 22+ and pnpm 10.30.3.
 
+### Generated-output ownership and recovery
+
+The canonical producer, reader, packing, retention, and recovery contract is
+[v3 npm packaging and verification](../../docs/packaging/v3-packaging.md).
+Generated generations are disposable; source files and the package registry
+remain authoritative. Use its recovery matrix rather than deleting uncertain
+state.
+
 ```bash
 pnpm -C packages/cli test
 pnpm -C packages/cli run verify:package
 pnpm -C packages/cli run typecheck
 pnpm -C packages/cli build
+pnpm -C packages/cli run verify:generated-overlap
+pnpm -C packages/cli run generated:cleanup -- --dry-run --json
 pnpm -C packages/cli run lint
 ```
 
-Use `npm pack --dry-run --json --ignore-scripts` after `build` and
-`bundle:data` to inspect the exact publication surface. Do not publish from a
-normal development or capability cycle.
+Use `pnpm -C packages/cli run pack:dry-run` to inspect the exact isolated
+publication surface. Do not publish from a normal development or capability
+cycle.

package/bundle/CHANGELOG.md

@@ -38,7 +38,7 @@
 - Retained runtime lifecycle contracts only as migration evidence and for explicit `agentera upgrade --legacy-cleanup claude --dry-run|--yes`, which can remove only the ownership-proven legacy Agentera skill link and excludes user data.
 - Added typed artifact writes under `agentera state`: progress/decision/audit appends, decision satisfaction updates, plan create/task/status/archive lifecycle operations, schema-derived `explain`, server-assigned identifiers, exact retry replay, dry-run diffs, project locking, strict mapped-path safety, staged 10/40/50 compaction, final-byte validation, and atomic publication.
 - Added `install_track` to `prime --format json` (`app_home.install_track`) and `doctor --format json`. Values are `v2`, `v3`, `source`, and `unknown`.
-- Added the TypeScript CLI on the npm development channel (`npx -y agentera@next`), bundling app data at pack time via `prepack` (`tsc` + `scripts/copy-bundle.mjs`) and the `.agentera-npx-bundle.json` sentinel checked by `packages/cli/test/packaging/prepack.test.ts`.
+- Added the TypeScript CLI on the npm development channel (`npx -y agentera@next`) as a self-contained package whose governed isolated construction stages compiled commands, registry-owned app data, and the `.agentera-npx-bundle.json` sentinel before packing with lifecycle scripts disabled.
 - Added `packages/cli/src/migrate/v2HandoffManifest.ts` to read `v3-handoff.json` during v2→v3 cleanup preflight per `references/cli/v3-handoff-manifest.schema.yaml`.
 - Added v3 `agentera doctor` coexistence detection in `packages/cli/src/upgrade/coexistenceProbe.ts` with regression coverage in `packages/cli/test/cli/coexistenceProbe.test.ts`.
 - Added maintainer gates under `agentera check` (`validate`, `verify`, `lint`, `compact`) with JSON parity oracles for validate families, verify eval targets, invalid-input envelopes, and `source_contract` emissions on `prime`, `prime --context`, `state plan`, and `state query --list-artifacts`.
@@ -74,6 +74,9 @@
 
 ### Fixed
 
+- Fixed overlapping source, build, and package verification to use isolated construction and one atomically selected `dist` + `bundle` generation; clean source no longer requires checkout output, package proof still runs from an extracted tarball, and `pnpm -C packages/cli run pack:dry-run` replaces direct checkout `npm pack`.
+- Fixed `agentera prime --context status` to report severity totals across every open TODO while keeping attention and routing detail bounded with explicit omission recovery.
+- Fixed `agentera prime --context status` to exclude resolved entity TODOs before bounded pagination, so severity counts, attention, and next-action routing reflect only open work.
 - Fixed overlapping `upgrade --yes` runs to hold separate exclusive project and shared-runtime locks, reject stale or malformed lock state with bounded manual recovery, and release only a matching ownership token.
 - Fixed migration-required recovery commands to shell-quote project paths so shell substitutions remain literal and the intended project receives the v2-to-v3 cutover.
 - Fixed marker-absent v2 projects to select the entity cutover from project state under npm or source v3 execution, so the recovery command emitted by `prime` can complete the forward migration instead of reporting an unrelated no-op.

package/bundle/references/adapters/package-surface-characterization.md

@@ -25,15 +25,20 @@ implementing this check are excluded, avoiding a circular source reference.
 
 ## npm bundle
 
+Contributor construction, checkout-generation, and recovery behavior is owned
+by [`docs/packaging/v3-packaging.md`](../../docs/packaging/v3-packaging.md).
+
 The self-contained npm package ships `dist/` plus `bundle/`. Bundle data
 includes the canonical `skills/` tree, required `references/`, `registry.json`,
 and package guidance. Compiled commands ship in `dist/`. The shared-skill tree
 includes its capability schemas, artifact schemas, and canonical
 `skills/agentera/agents/*.toml` descriptors.
 
-Packaging tests inspect `npm pack --dry-run --json --ignore-scripts` and fail if
-the CLI or required bundle data disappears, or if a current host-native
-descriptor/runtime path enters the package.
+The package lane's isolated package fixture invokes `npm pack --json
+--ignore-scripts` after governed construction and fails if the CLI or required
+bundle data disappears, or if a current host-native descriptor/runtime path
+enters the package. Contributors use `pnpm -C packages/cli run pack:dry-run`;
+direct checkout packing remains rejected by the canonical packaging authority.
 
 ## Native package boundary
 

package/bundle/references/analysis/analytics-boundary-proportional-2026-07-20.yaml

@@ -0,0 +1,74 @@
+schemaVersion: agentera.verificationMeasurement.v1
+status: pass
+captured: 2026-07-20
+
+comparison:
+  metric: assertion_duration_ms
+  direction: lower
+  before:
+    authority: references/analysis/verification-baseline-2026-07-20.yaml
+    production_shard_byte_cap: 67108864
+    assertions:
+      - test: reports oversized with the artifact path when a shard exceeds the cap
+        samples_ms: [13089, 10497, 10245]
+        median_ms: 10497
+        disposition: consolidated_into_retention_assertion
+      - test: retains an oversized record in its own shard and reports oversized state
+        samples_ms: [9350, 8554, 8589]
+        median_ms: 8589
+    cumulative_median_ms: 19086
+  after:
+    proportional_shard_byte_cap: 8192
+    test: retains an oversized record in its own shard and reports oversized state
+    samples_ms: [25.284901, 25.359614, 24.883412]
+    median_ms: 25.284901
+    raw_report_compression: gzip_lossless_mtime_zero
+    raw_reports:
+      - references/analysis/evidence/analytics-boundary-proportional-2026-07-20/source-focused-1.json.gz
+      - references/analysis/evidence/analytics-boundary-proportional-2026-07-20/source-focused-2.json.gz
+      - references/analysis/evidence/analytics-boundary-proportional-2026-07-20/source-focused-3.json.gz
+  retained_assertion_reduction_ms: 8563.715099
+  retained_assertion_reduction_percent: 99.705613
+  cumulative_dense_assertion_reduction_ms: 19060.715099
+  cumulative_dense_assertion_reduction_percent: 99.867521
+
+protocol:
+  inherited_from: references/analysis/verification-baseline-2026-07-20.yaml#protocol.source
+  environment:
+    VITEST_MAX_WORKERS: "4"
+  warmup_runs: 1
+  retained_runs: 3
+  command: >-
+    pnpm -C packages/cli exec vp test run --config vite.config.ts
+    test/analytics/tierReader.test.ts -t "retains an oversized record"
+    --reporter=json
+  note: >-
+    Before samples are Task 1's exact full-source assertion durations. After
+    samples isolate the retained assertion; the duplicate artifact-path case
+    was consolidated into it rather than assigned a synthetic zero duration.
+
+coverage:
+  proportional_shard_boundary:
+    owner: source
+    path: packages/cli/test/analytics/tierReader.test.ts
+    byte_cap: 8192
+    pass: reports current when tiers are published and complete
+    fail: retains an oversized record in its own shard and reports oversized state
+    guarantees: [retention, recovery, state, artifact_path]
+  production_constants:
+    owner: source
+    path: packages/cli/test/analytics/oversizedRegression.test.ts
+    shard_byte_cap: 67108864
+    signal_byte_cap: 67108864
+    reader_byte_cap: 67108864
+  production_wiring:
+    owner: performance
+    path: packages/cli/test/performance/analyticsEvidenceTierCap.test.ts
+    shard_byte_cap: 67108864
+    owner_command: pnpm -C packages/cli test:performance
+    policies: [scheduled, release]
+
+caveats:
+  - The decisions query remained degraded; omitted decision detail was not reconstructed.
+  - Build startup omitted decisions, vision, and profile state; no refresh or inferred approval was performed.
+  - Decision satisfaction remained unavailable for llavvlpcmb and djmjbmruyk.

package/bundle/references/analysis/benchmark.md

@@ -23,6 +23,17 @@ contract validators, and runtime smoke checks.
 | --- | --- | --- | --- |
 | Startup state benchmark | `mage bench:startupState` | Measures how often Agentera CLI state reads are followed by raw artifact access during startup/state gathering. | Manual only; forbidden in normal CI. |
 
+Verification optimization uses a separate retained baseline rather than this
+runtime-history benchmark. The 2026-07-20 source and pre-commit samples,
+production-scale ownership map, and unresolved worker/lane criteria live in
+[`verification-baseline-2026-07-20.yaml`](./verification-baseline-2026-07-20.yaml).
+That baseline remains measurement authority. Current test ownership, independent
+owner commands, mixed-file separation markers, conservative routing, and named
+execution-policy compositions live in
+[`verification-policy.yaml`](./verification-policy.yaml).
+Losslessly compressed raw reports live beside a dependency-free recomputation
+command under `references/analysis/evidence/verification-baseline-2026-07-20/`.
+
 The startup benchmark is an optimization signal for Decision 51 and Decision 52.
 It does not implement a startup state envelope or change runtime behavior.
 

package/bundle/references/analysis/evidence/verification-baseline-2026-07-20/recompute.mjs

@@ -0,0 +1,98 @@
+#!/usr/bin/env node
+import fs from "node:fs";
+import path from "node:path";
+import zlib from "node:zlib";
+
+const root = import.meta.dirname;
+const median = (values) => [...values].sort((a, b) => a - b)[Math.floor(values.length / 2)];
+const round = (value) => Math.round(value * 1000) / 1000;
+const sources = [];
+const assertionsByIdentity = new Map();
+
+for (let sample = 1; sample <= 3; sample += 1) {
+  const report = JSON.parse(
+    zlib.gunzipSync(fs.readFileSync(path.join(root, `source-${sample}.json.gz`))),
+  );
+  const assertions = report.testResults.flatMap((file) =>
+    file.assertionResults.map((assertion) => ({
+      file: file.name.split("/packages/cli/").at(-1),
+      name: assertion.fullName,
+      duration_ms: assertion.duration ?? 0,
+    })),
+  );
+  const jsonElapsedMs =
+    Math.max(...report.testResults.map((file) => file.endTime)) - report.startTime;
+  sources.push({
+    sample,
+    files: report.testResults.length,
+    tests: report.numTotalTests,
+    cumulative_assertion_ms: round(
+      assertions.reduce((total, assertion) => total + assertion.duration_ms, 0),
+    ),
+    json_elapsed_ms: round(jsonElapsedMs),
+  });
+  for (const assertion of assertions) {
+    const identity = `${assertion.file}\n${assertion.name}`;
+    const entry = assertionsByIdentity.get(identity) ?? {
+      file: assertion.file,
+      test: assertion.name,
+      samples_ms: [],
+    };
+    entry.samples_ms.push(assertion.duration_ms);
+    assertionsByIdentity.set(identity, entry);
+  }
+}
+
+const slowest = [...assertionsByIdentity.values()]
+  .map((entry) => ({
+    ...entry,
+    samples_ms: entry.samples_ms.map(round),
+    median_ms: round(median(entry.samples_ms)),
+  }))
+  .sort((a, b) => b.median_ms - a.median_ms)
+  .slice(0, 10);
+
+function hook(name) {
+  const text = zlib.gunzipSync(fs.readFileSync(path.join(root, name))).toString("utf8");
+  const wrapper = JSON.parse(text.trim().split("\n").at(-1));
+  const lefthook = Number(/done in ([0-9.]+) seconds/.exec(text)?.[1]) * 1000;
+  const policies = [...text.matchAll(/✔️ ([^\n]+?) \(([0-9.]+) seconds\)/g)].map((match) => ({
+    name: match[1],
+    duration_ms: Number(match[2]) * 1000,
+  }));
+  return {
+    wall_ms: wrapper.wall_ms,
+    lefthook_ms: lefthook,
+    exit_status: wrapper.exit_status,
+    policies,
+  };
+}
+
+const route = zlib
+  .gunzipSync(fs.readFileSync(path.join(root, "precommit-cli-route.log.gz")))
+  .toString("utf8")
+  .trim()
+  .split("\n");
+
+console.log(
+  JSON.stringify(
+    {
+      source_samples: sources,
+      source_medians: {
+        cumulative_assertion_ms: round(
+          median(sources.map((sample) => sample.cumulative_assertion_ms)),
+        ),
+        json_elapsed_ms: round(median(sources.map((sample) => sample.json_elapsed_ms))),
+        files: median(sources.map((sample) => sample.files)),
+        tests: median(sources.map((sample) => sample.tests)),
+      },
+      slowest_tests_by_median: slowest,
+      pre_commit: {
+        representative_cli: { ...hook("precommit-cli.log.gz"), route },
+        representative_documentation: hook("precommit-documentation.log.gz"),
+      },
+    },
+    null,
+    2,
+  ),
+);

package/bundle/references/analysis/migration-pagination-proportional-2026-07-20.yaml

@@ -0,0 +1,64 @@
+schemaVersion: agentera.verificationMeasurement.v1
+status: pass
+captured: 2026-07-20
+
+comparison:
+  test: uses snapshot-bound whole-entry pagination to recover every entry without gaps or duplicates
+  metric: assertion_duration_ms
+  direction: lower
+  before:
+    authority: references/analysis/verification-baseline-2026-07-20.yaml
+    fixture_entries: 400
+    samples_ms: [18325, 16575, 16680]
+    median_ms: 16680
+  after:
+    fixture_entries: 40
+    samples_ms: [179.449348, 164.137058, 178.642103]
+    median_ms: 178.642103
+    raw_report_compression: gzip_lossless_mtime_zero
+    raw_reports:
+      - references/analysis/evidence/migration-pagination-proportional-2026-07-20/source-focused-1.json.gz
+      - references/analysis/evidence/migration-pagination-proportional-2026-07-20/source-focused-2.json.gz
+      - references/analysis/evidence/migration-pagination-proportional-2026-07-20/source-focused-3.json.gz
+  reduction_ms: 16501.357897
+  reduction_percent: 98.929004
+  speedup: 93.371046
+
+protocol:
+  inherited_from: references/analysis/verification-baseline-2026-07-20.yaml#protocol.source
+  environment:
+    VITEST_MAX_WORKERS: "4"
+  warmup_runs: 1
+  retained_runs: 3
+  command: >-
+    pnpm -C packages/cli exec vp test run --config vite.config.ts
+    test/state/entityMigrationPreview.test.ts
+    -t "uses snapshot-bound whole-entry pagination" --reporter=json
+  note: >-
+    The before samples are the exact assertion durations retained by Task 1's
+    full-source protocol. The after samples isolate the same assertion so the
+    proportional fixture cost is directly reproducible without rerunning
+    unrelated source tests.
+
+coverage:
+  proportional_source:
+    owner: source
+    path: packages/cli/test/state/entityMigrationPreview.test.ts
+    fixture_entries: 40
+    guarantees: [multi_page, whole_entry, byte_bound, no_gaps, no_duplicates, continuation_command]
+  cursor_mutations:
+    owner: source
+    mutations: [source, authority, filter, order, project]
+    guarantees: [continuation_rejected, restart_without_cursor, zero_write]
+  production_cap:
+    owner: performance
+    path: packages/cli/test/performance/entityMigrationPreviewCap.test.ts
+    fixture_entries: 400
+    response_cap_bytes: 32768
+    owner_command: pnpm -C packages/cli test:performance
+    policies: [scheduled, release]
+
+caveats:
+  - The decisions query remained degraded; missing decision detail was not reconstructed.
+  - Build startup omitted decisions, vision, and profile state; no refresh or inferred approval was performed.
+  - Decision satisfaction remained unavailable for llavvlpcmb and djmjbmruyk.