[WIP] Plan TraceDecay V2 brain rewrite

[ScriptedAlchemy]

WIP: plan only

This PR contains only the TraceDecay V2 total-rewrite design: one master plan, one plan-set index, and 28 linked subsystem/crate/product plans (30 documentation files). It deliberately contains no implementation.

Unified product and architecture

• Rebuild TraceDecay as one coherent profile-wide brain across projects, repositories, worktrees, branches, threads, turns, agents, workflows, tools, artifacts, code, Git, facts, memories, tasks, plans, delivery, and time.
• Make an immutable sanitized observation/event stream the write authority; derive versioned projections, graph/read models, search indexes, analytics, hints, and UI views through fenced replayable projectors with checkpoints, dead letters, repair, and provenance.
• Replace ambiguous project-only identity and split stores with canonical profile/project/repository/worktree/session/message/agent/task/artifact/code identities, explicit source bindings, temporal validity, variant safety, and protected consolidation/quarantine workflows.
• Define crate ownership, dependency/release DAGs, anti-corruption boundaries, migration/deletion gates, negative-code budgets, and shared kernels so the rewrite converges instead of recreating fragmented subsystems.

Multi-machine shared Brain

• Adds plan 28 for local-only, remote-authority, cached-client, read-replica, standby, and hybrid-placement operation under one BrainId.
• Keeps every SQLite/WAL family host-local. Remote nodes exchange sanitized observations, signed snapshots/tails, immutable packs, and typed commands through the authenticated application/API contract; no network-mounted database or database URL is exposed.
• Correlates equivalent clones across machines through credential-free Git remote evidence plus verified object/commit/tree/ancestry evidence. Paths and worktrees stay node-scoped; forks, shallow/rewritten histories, and contradictions remain explicit candidates.
• Uses exactly one writable authority per mutable shard, signed/expiring node and cache grants, bounded causal frontiers, authority/placement epochs, offline idempotent capture, visible lag/pending/conflict state, and positive external fencing before standby promotion.
• Makes Tailscale an optional connectivity profile only. Ordinary authenticated HTTPS/mTLS, LAN/VPN, reverse proxy, or tunnel deployments use the same TraceDecay identity, authorization, privacy, revocation, and fencing rules.
• Adds wrapped-key disaster recovery after total authority-node/keyring loss, explicit remote schemas/retention, node/store/repository topology UI, Sync Observatory, Brain Settings, CLI/API/SDK bindings, compact default MCP status, operator-only MCP administration, and multi-machine fault/RPO/RTO gates.

Product surfaces and task execution

• Replace the project-only dashboard with an All / Brain workspace plus scoped lenses; interactive Git, code, thread, turn, agent, task, plan, memory, impact, and timeline graphs; reasoning/code/artifact lineage; synchronized explorers; and accessible table/outline parity.
• Add hermetic replay/debug labs for search, LCM, facts/memory, hooks, hints, context scouting, redaction, curation, automation, scheduling, configuration, and experiments with current-versus-historical policy comparisons and reproducible receipts.
• Port and redesign the Hermes Kanban concept as a native TraceDecay task/plan graph—not an adapter—with federated initiatives/boards, DAG dependencies, multi-project work bundles, model/effort routing, executor/provider capabilities, offers/admission, leases, grants, work packets, nearby-agent awareness, and duplicate/conflict prevention.
• Add validated sharded frontmatter/CommonMark task-graph edit workspaces for large agent edits, authoritative validate/diff/rebase/submit flows, safe temporary cleanup, exact candidate refs, and atomic owner-shard publication.

Search, hints, automation, APIs, CLI, and MCP

• Redesign hybrid lexical/vector/graph/temporal retrieval, supersession-aware ranking, contextual retrieval IDs, cross-project scope, explainability, qrels/judgments, real-session replay evaluation, and precision/recall promotion gates.
• Make adaptive hint arbitration and optional incremental model-backed context scouting compact, material, deduplicated, privacy-safe, nearby-work aware, and measurable against useful-silence baselines.
• Make autonomous memory/skill curation and self-improvement event-driven and frontier-fenced: unchanged/no-activity inputs create no repeated runs or model/tool work.
• Publish one typed application contract through an official HTTP API, Rust/TypeScript/Python SDKs, CLI, optional MCP, dashboard, hooks, and executors; centralize typed views, Markdown/JSON rendering, errors, pagination, and capability discovery.
• Split MCP into independently installable context/work/operator trust-boundary registrations backed by one binary/daemon/catalog. Skills plus CLI remain the complete MCP-free baseline; eager clients must pass the same security/context budgets as deferred clients.

Claude Code, Codex, and Cursor bundles

• Adds plan 27 with primary-source research for official Claude Code, Codex, and Cursor plugin, skill, command, agent/subagent, hook, MCP, configuration, marketplace, permission, and progressive-disclosure behavior.
• Keeps one canonical HostIntegrationManifestV1; PR 22A owns its catalog/source IR, PR 22I deterministically emits unsigned HostBundlePayloadV1 trees, PR 36R independently rebuilds/scans/conformance-tests/attests/signs HostBundleManifestV1, and application alone binds a signed release to current host capability state.
• Uses host capability evidence and stock-host conformance instead of assuming cross-host parity. Unsupported/version-gated behavior gets an explicit omission and skill/CLI/API fallback.
• Ships a small skills-first core plus optional least-privilege MCP companions; commands remain thin compatibility/explicit-user affordances, hooks remain bounded, and specialist roles receive exact task/scope/worktree/retrieval-anchor handoffs.

Privacy and control plane

• Add ingest/retrieval/export/presentation secret detection and redaction with policy versions, sensitivity labels, grants, audit receipts, protected quarantine, leak-regression tests, and UI/CLI controls.
• Put configuration—including redaction, retention, providers/models, hints, hooks, search, automation, executors, task routing, host integrations, shared-Brain placement/sync/cache/failover, and sharing—in one versioned control plane available through UI, CLI, API, and optional MCP.
• Preserve fully autonomous curation semantics; there is no generic preview/apply/rollback proposal queue.

Accepted-base reconciliation and evidence

• Current with master at 273f50c0372f063b97f4755563a3ded65ef324d5 (chore: release v0.0.53 (#437)); branch is not behind.
• Incorporates accepted changes through fix(doctor): isolate registry diff conflicts #440, including fix(storage): add explicit split-store consolidation #425 split-store consolidation and fix(doctor): derive orphan stores from registry reconstruction #439/fix(doctor): isolate registry diff conflicts #440 registry-reconstruction truth/conflict isolation. At publication, this draft [WIP] Plan TraceDecay V2 brain rewrite #421 is the only open PR.
• Planning used TraceDecay LCM/session/message/fact/code/Git/analytics/diagnostic/automation surfaces, supported CLI/provider-local fallbacks when context tools failed, several independent subagent audits, Hermes source analysis, and primary-source/web/arXiv research.
• Private chronological exports remain outside Git under /fast/tracedecay-redesign-research (0700; files 0600): 34,352 secret-scanned role-user records and a 9,988-record best-effort human subset through 2026-07-11T01:04:10.875Z.
• Retained sanitized-content SHA-256: broad 0c56ebd9c54edfc76cda10b62de05e0a9443004c3ddce960daf300208bbdf340; human 942f6662c77f820c4d8a2b7063889c4521cecee68bc0258c7c7c12ddc6309dc2.
• No transcript, database, generated fixture, or private research artifact is committed or indexed by this PR.

Validation

• 30/30 intended documentation files and no other changed paths.
• Internal relative links valid; Markdown fences balanced; git diff --check clean.
• Failure modes FM-001 through FM-137 contiguous and unique.
• Cross-plan type owners, signed sync/cache contracts, positive failover fencing, recovery keys, physical schemas, PR sequencing, closed Brain operation bindings, host compiler/signing/runtime boundaries, task-edit ceilings, configuration targets, and integration operations reconciled by independent final audits.
• Corpus ordering, deduplication, timestamps, content hashes, permissions, and redacted-copy equality validated.
• Direct plan scan, private-corpus scans, and staged-diff scan pass with gitleaks and zero findings.

Draft/WIP remains intentional until the plan is reviewed as one flowing architecture.

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