BUG: Migrations, seeding, config cache, tool storage growth, deps

[echel0nn]

Labels: bug, migrations, config, dependencies
Severity: S2. (The knowledge Vector(384) vs (1024) ORM drift is already tracked in #37.)

Finding (path:line)	Issue
alembic/versions/051_vr_target_ingestion.py:82-95	Upgrade strips JSON keys (audit_mcp_index_id, binary_id, kernel_image_id) via UPDATE; the downgrade drops the new columns but does NOT restore the stripped keys -> permanent data loss on rollback
alembic/versions/060_vr_target_analysis_stages.py:54-79	Backfill selects ALL vr_targets into memory and updates row-by-row -> holds the migration txn open for minutes and risks OOM; no batching
alembic/versions/010_team_isolation.py:132-144	Downgrade REVOKEs from aila_app unconditionally; if the role was dropped independently the REVOKE is fatal and the downgrade half-tears RLS
runtime/builder.py:184-185	Seed loop iterates modules in one session with no per-module try/except -> one module's seed_data() failure aborts all later modules and leaves earlier partial commits
modules/malware/module.py:156-157	seed_data() returns without stamping a SeedVersionRecord despite declaring SEED_VERSION='1.0' -> future re-seed logic can never detect the need
storage/registry.py:67,206-207	ConfigRegistry cache is process-local; a set() on one worker invalidates only that worker -> other workers serve stale config for up to cache_ttl=60s with no cross-process invalidation
platform/tools/{registry,cache,artifacts}.py + storage/memory.py	Memory/decision-cache/artifact tools persist with no eviction/TTL/row-cap/size-limit -> unbounded table growth; expired cache entries never pruned
pyproject.toml:38 + pnpm-workspace.yaml	slowapi==0.1.9 abandoned (blocks Starlette upgrades); html2canvas@1.4.1 and ogl@0.0.116 unmaintained with no security policy; openpyxl exact-pinned (no future security patches without manual bump)

Acceptance: destructive migrations archive removed data + restore on downgrade; large backfills batched; conditional REVOKE; per-module seed isolation + version stamping; cross-process config invalidation (or shorter TTL + pub/sub); eviction/TTL/size caps on tool storage; dependency review with a supported rate limiter and maintained frontend libs.

[echel0nn]

Implementation-ready design (2026-07-19). Wave 1b. Full design on disk: .run/designs/DESIGN_storage_contracts.md (8-heading template: grounded problem, design with signatures+DDL+Alembic, reworked concerns, test plan, rollout).

Key moves:

• Reversible/guarded destructive migrations (051/060/010); per-module seed isolation + SeedVersionRecord stamping.
• Cross-process config cache invalidation; tool-storage eviction/TTL/size caps; dependency review.