refactor(state): consolidate wide rows, plugin index, workspace attestations, and shared auth singletons at schema v13 (#130466)

* refactor(state): make cron and subagent rows JSON-canonical

* refactor(state): make gateway origin device tokens canonical at v13

The lazy ensure predates the table joining the canonical schema; at the
v13 bump the schema owns creation, so the feature-local DDL, WeakSet
dedupe, and lazy-list entry retire. The legacy-file guard the ensure
carried stays at each call site.

* test: drop obsolete lazy-ensure coverage for origin device tokens

The table is canonical at v13; same-version lazy creation no longer
exists to protect. Origin CRUD, isolation, and rotation coverage remains
in the surviving cases.

* refactor(state): fold installed_plugin_index into config_machine_state

The singleton index row becomes one JSON value under
plugins.installedIndex with its rollback-fencing revision inside the
value; reads, CAS restore, and the lease-held write transactions use
direct Kysely on config_machine_state so the state_leases assertion
stays in-transaction. The v13 migration imports the row and drops the
table; the additive workspace_dir entry folds with it. Doctor guidance,
docker staging, and the e2e probes name the machine-state row.

* refactor(state): merge workspace_attestations into workspace_setup_state

One row per workspace now carries both setup milestones and the
attestation clock: nullable setup columns represent attestation-only
workspaces (replaceWorkspaceAttestation can precede any setup write) and
setupExists derives from a non-null version. The bootstrap-hash FK
repoints to the merged table; migration receipts keep the historical
workspace_attestations discriminator string. The v13 migration grows and
rebuilds the table, merges attestation rows (orphans without a path
alias drop — their hashes re-derive at the next bootstrap attestation),
and the consolidation kind is renamed state-consolidation-v13 to cover
the batch.

* test(state): cover the workspace merge and consolidation fallout

The v12-to-v13 regression seeds merged, attestation-only, and orphan
attestation workspaces; the 13-to-12 downgrade fixture recreates
workspace_attestations and installed_plugin_index from the folded data;
the fold-in migration gates the additive workspace_dir column for
pre-additive rows; the workspace merge now triggers on the setup table's
own shape so stable-era databases without an attestations table still
reshape; the consolidation applied-message covers the batch.

* refactor(state): fold shared auth profile singletons into config_machine_state

The shared-state auth_profile_stores/auth_profile_state rows (fixed key
'shared') become authProfiles.store/authProfiles.state machine-state
values; the agent-DB tables of the same names are untouched. Git-backup
redaction moves from table-drop to the authProfiles. secret prefix with
seeded-secret absence proof; migration receipts keep the historical
table-name discriminators; the shared-auth relocation and receipt
verification project the KV cells back to the receipt-era row shapes so
persisted digests stay byte-compatible. mcp_oauth_stores stays a table —
its multi-key fold is a named follow-up.

* test(state): finish shared-auth fold coverage and annotate boundary casts

Auth seeders and assertions across the e2e/scripts/secrets suites target
the authProfiles machine-state cells; the v12-to-v13 regression proves
payload-byte fidelity, non-shared-row drop, and insert-if-absent
precedence; the downgrade fixture recreates and repopulates both v12
tables. Boundary type assertions in the plugin-index store carry SAFETY
invariants per the ratchet.

* chore: shrink assertion-safety baseline for plugin-index store

* refactor(doctor): delete the dead onboarding-recommendations migration

Its input — the unscoped 'primary' onboarding row — existed only between
9a93a52a8a and 473962b7de, a two-day beta window; no shipped stable
can produce it and the runtime table folded away at v12. The audit
backup list keeps recognizing system-agent.jsonl artifacts because beta
installs that ran that import may still carry its backups.

* docs: sync the 13-to-12 downgrade example with the executable fixture

* style: format the synced downgrade example

* style: drop unused import and duplicate union constituent

* fix(state): keep orphan attestations across the v13 workspace merge

The merged workspace_setup_state required a workspace path, but legacy
orphan hashed-key attestations never recorded one. workspace_path is now
nullable (setup rows still enforce it via CHECK), the v13 migration and
the doctor file import keep orphans with a NULL path that heals on the
next live access, and the 13-to-12 downgrade keeps attestation-owned
hashes. Doctor test seeds move to the folded KV row.

* perf(state): retire unused cron indexes

* fix(state): preserve v13 migration recovery

* fix(state): preserve v12 lazy-table upgrade

* docs(state): document v13 auth relocation

---------

Co-authored-by: Vincent Koc <vincentkoc@ieee.org>

test/scripts/plugin-index-sqlite.test.ts

@@ -32,44 +32,30 @@ function writeSqliteIndex(root: string, installRecordsJson: string) {
   const db = new DatabaseSync(dbPath);
   try {
     db.exec(`
-      CREATE TABLE installed_plugin_index (
-        index_key TEXT NOT NULL PRIMARY KEY,
-        version INTEGER NOT NULL,
-        host_contract_version TEXT NOT NULL,
-        compat_registry_version TEXT NOT NULL,
-        migration_version INTEGER NOT NULL,
-        policy_hash TEXT NOT NULL,
-        generated_at_ms INTEGER NOT NULL,
-        refresh_reason TEXT,
-        install_records_json TEXT NOT NULL,
-        plugins_json TEXT NOT NULL,
-        diagnostics_json TEXT NOT NULL,
-        warning TEXT,
+      CREATE TABLE config_machine_state (
+        state_key TEXT NOT NULL PRIMARY KEY,
+        value_json TEXT NOT NULL,
         updated_at_ms INTEGER NOT NULL
       );
     `);
     db.prepare(
-      `
-        INSERT INTO installed_plugin_index (
-          index_key, version, host_contract_version, compat_registry_version,
-          migration_version, policy_hash, generated_at_ms, refresh_reason,
-          install_records_json, plugins_json, diagnostics_json, warning, updated_at_ms
-        )
-        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-      `,
+      "INSERT INTO config_machine_state (state_key, value_json, updated_at_ms) VALUES (?, ?, ?)",
     ).run(
-      "installed-plugin-index",
-      1,
-      "1",
-      "1",
-      1,
-      "hash",
-      Date.now(),
-      null,
-      installRecordsJson,
-      "{}",
-      "{}",
-      null,
+      "plugins.installedIndex",
+      JSON.stringify({
+        revision: Date.now(),
+        index: {
+          version: 1,
+          hostContractVersion: "1",
+          compatRegistryVersion: "1",
+          migrationVersion: 1,
+          policyHash: "hash",
+          generatedAtMs: Date.now(),
+          installRecords: JSON.parse(installRecordsJson) as unknown,
+          plugins: [],
+          diagnostics: [],
+        },
+      }),
       Date.now(),
     );
   } finally {
@@ -139,7 +125,7 @@ describe("plugin index SQLite E2E helpers", () => {
 
       expect(() =>
         readPluginInstallIndex({ stateDir: root, configPath: configPath(root) }),
-      ).toThrow("plugin index install_records_json exceeded 64 bytes");
+      ).toThrow("plugin index value_json exceeded 64 bytes");
     } finally {
       rmSync(root, { force: true, recursive: true });
     }