refactor(storage): migrate exact managed mutations

[Jurij89]

Summary

• Migrate the remaining exact managed-state writes for requester join state, graph-scoped KA materialization, and subgraph registration into bounded structured storage operations.
• Include the merged refactor(storage): add bounded managed mutation capabilities #2186 expansion: one closed TripleStore.structuredMutation() union, bounded validation and serialization, first-party adapter/decorator forwarding, and migrations for catalog, retention, curator refresh, RS repair, and KA metadata callers.
• Reuse the canonical store-chain traversal for capability discovery, so transparent wrappers participate through their existing chain link instead of maintaining a parallel forwarding protocol.
• Guard every RS-heal materialization write boundary with the current subscription/on-chain binding so a stale repair pass cannot clear a valid completion marker.
• Remove the subgraph deregistration fallback that sent a SPARQL mutation through query(), while preserving rolling-upgrade behavior through explicit capability checks.
• Keep raw-channel contraction separate in stacked PR security(storage): close leased raw SPARQL mutation routes #2187 so the ownership-lease security boundary can be reviewed independently.

Related

• Related to security(storage): close the raw update() route to reserved system-record state before activation #2162
• Part of Reconnect-triggered background sync amplification can starve foreground catch-up #2052
• Includes merged refactor(storage): add bounded managed mutation capabilities #2186
• Stacked PR: security(storage): close leased raw SPARQL mutation routes #2187
• Follow-up: refactor(storage): keep structured mutation effects behind storage ownership #2188

Diagrams

Managed-state mutation path

flowchart LR
    A[Domain caller] --> B[Structured mutation descriptor]
    B --> C{Validate scope and bounds}
    C -->|invalid| D[Typed refusal]
    C -->|valid| E[Decorators account for touched graphs]
    E --> F[Adapter-authored bounded SPARQL]
    F --> G[Storage backend]

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Stack boundary

flowchart TB
    P2186[PR 2186: bounded capability layer]
    P2185[PR 2185: migrate exact callers]
    P2187[PR 2187: close leased raw mutation channels]
    P2186 --> P2185
    P2185 --> P2187

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Files changed

Area	What
packages/storage/src/**	Defines, validates, forwards, and implements the closed structured mutation capability across first-party stores and decorators.
packages/agent/src/**	Migrates join state, registration cleanup, retention, curator refresh, and RS repair away from caller-authored mutations; guards RS-heal writes against stale ownership.
packages/publisher/src/**	Migrates graph-scoped KA materialization, catalog cleanup, agents retention, and Merkle-root metadata.
packages/{storage,agent,publisher}/test/**	Covers bounds, atomicity, reserved scopes, decorator accounting, worker parity, retries, retention, rolling-upgrade behavior, and stale RS-heal cancellation.

Test plan

• Post-rebase builds: core, storage, publisher, and agent
• Canonical capability-chain regression: 30 focused storage tests, including link-only capable and incapable wrappers
• Post-rebase Agent selected suites: 32 passed
• Decorated RS-repair suite after the final review fix: 16 passed
• Companion RS-repair suite after the final review fix: 15 passed
• Post-rebase Publisher selected suites: 22 passed
• Agent type and package-root checks
• Merged refactor(storage): add bounded managed mutation capabilities #2186 storage suite evidence: 948 passed, 26 skipped integration tests
• Merged refactor(storage): add bounded managed mutation capabilities #2186 changed Agent suite: 76 passed
• Merged refactor(storage): add bounded managed mutation capabilities #2186 focused Publisher suite: 65 passed
• Real worker-RPC coverage for all six structured mutation variants
• Multi-root and over-budget RS repair coverage, including ordered chunks below the 4 MiB serialized-update cap
• Stale-before-first-write and stale-after-data-copy RS-heal regressions proving later metadata/completion writes are not dispatched
• Over-cap retention integration across multiple bounded mutations
• Raw mutation inventory at the merged capability head: no Agent/Publisher store.update() or mutating store.query() caller remains
• git diff --check; worktree clean after rebasing onto current integration/2052-system-record-sync

[otReviewAgent]

Review Agent completed this review and found no issues.